diff --git a/BrainstemSS/Makefile.am b/BrainstemSS/Makefile.am deleted file mode 100644 index 3bcf40e88c0..00000000000 --- a/BrainstemSS/Makefile.am +++ /dev/null @@ -1,31 +0,0 @@ -# -# Makefile.am for BrainstemSS (brainstem substructure segmentation tools) -# - -foodir=$(prefix)/average/BrainstemSS/atlas -foo_datafiles=AtlasDump.mgz AtlasMesh.gz compressionLookupTable.txt - -if HAVE_MAC_OSX - -SUBDIRS=mac_osx - -else - -SUBDIRS=linux_x86_64 - -endif - -# platform-independent data and scripts: -dist_bin_SCRIPTS = \ -segmentBS.sh \ -quantifyBrainstemStructures.sh - -install-data-local: - test -z $(DESTDIR)$(foodir) || $(mkdir_p) $(DESTDIR)$(foodir) - $(INSTALL_DATA) $(foo_datafiles) $(DESTDIR)$(foodir) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/BrainstemSS/linux_x86_64/Makefile.am b/BrainstemSS/linux_x86_64/Makefile.am deleted file mode 100644 index 747d8674be1..00000000000 --- a/BrainstemSS/linux_x86_64/Makefile.am +++ /dev/null @@ -1,28 +0,0 @@ -# -# Makefile.am for BrainstemSS/linux_x86_64 -# - -dist_bin_SCRIPTS = \ - run_SegmentSubject.sh - -# -# We handle the binary files differently because binary -# files are treated as a separate compenent to the -# repository, and thus may not be present at compile time. -# - -foodir=$(prefix)/bin - -foo_binaryfiles = \ - segmentSubject - -install-data-local: - test -z $(DESTDIR)$(foodir) || $(mkdir_p) $(DESTDIR)$(foodir) - $(INSTALL) -m 755 $(foo_binaryfiles) $(DESTDIR)$(foodir) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - diff --git a/BrainstemSS/mac_osx/Makefile.am b/BrainstemSS/mac_osx/Makefile.am deleted file mode 100644 index 1b8f9855073..00000000000 --- a/BrainstemSS/mac_osx/Makefile.am +++ /dev/null @@ -1,25 +0,0 @@ - -# -# Makefile.am for BrainstemSS/mac_osx -# - -dist_bin_SCRIPTS = \ - run_SegmentSubject.sh - -# -# We handle the binary files differently because binary -# files are treated as a separate compenent to the -# repository, and thus may not be present at compile time. -# - -foodir=$(prefix)/bin - -install-data-local: - cp -RL segmentSubject.app $(foodir) - chmod -R 755 $(foodir)/segmentSubject.app - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/CMakeLists.txt b/CMakeLists.txt index d5dc309cdd3..fde861bf91a 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -9,13 +9,9 @@ enable_language(C CXX Fortran) # a few build options option(MINIMAL "Only build core components" OFF) -option(BUILD_QDEC "Build QDEC" OFF) option(BUILD_GUIS "Build GUIs" ON) option(USE_OPENCL "Build OpenCL algorithms" OFF) option(INFANT_MODULE "Include infant recon-all" OFF) -if(APPLE) - option(BUILD_OSX_TK_GUIS "Compile OSX Tk GUIs" OFF) -endif() # enable ctest enable_testing() @@ -175,12 +171,6 @@ if(BUILD_GUIS) # -------- tcltktixblt -------- find_package(TCLTKTIXBLT) - # -------- kwwidgets -------- - # once qdec is deprecated, KWWidgets can be removed - if(BUILD_QDEC) - find_package(KWWidgets) - endif() - # -------- wxwidgets -------- # only used by mris_decimate_gui find_package(WXWidgets) @@ -275,7 +265,7 @@ endif() # setup python # -------------------------------------------------- -# Unfortunately, the python version used to run wrapped c-libraries must be equal to +# Unfortunately, the python version used to run wrapped c-libraries must be equivalent to # the version used to build the libraries. The easiest and least intrusive way of making freesurfer # python scripts run out-of-the-box (and to help guarantee reproducibility) requires # distributing a minimal, custom python installation called fspython. This fspython package @@ -358,7 +348,7 @@ add_subdirectories( opencl_algorithms ) -# the following utility libraries are required for freeview and qdec +# the following utility libraries are required for freeview add_subdirectories(vtkfsio vtkutils lineprof) # the fem elastic subdir also builds a library, so it should be added first @@ -712,7 +702,6 @@ if(NOT MINIMAL) oct_train optseq2 qdecproject - qdec qdec_glmfit rbftest regdat2xfm @@ -726,8 +715,6 @@ if(NOT MINIMAL) template test_makevol ThalamicNuclei - tkmedit - # tksurfer trc tridec ) diff --git a/HippoSF/Makefile.am b/HippoSF/Makefile.am deleted file mode 100644 index 39db9bb74ef..00000000000 --- a/HippoSF/Makefile.am +++ /dev/null @@ -1,34 +0,0 @@ -# -# Makefile.am for HippoSF (hippocampal subfield segmentation tools) -# - -foodir=$(prefix)/average/HippoSF/atlas -foo_datafiles=AtlasDump.mgz AtlasMesh.gz compressionLookupTable.txt - -if HAVE_MAC_OSX - -SUBDIRS=mac_osx - -else - -SUBDIRS=linux_x86_64 - -endif - -# platform-independent data and scripts: -dist_bin_SCRIPTS = \ -segmentHA_T1_long.sh \ -segmentHA_T1.sh \ -segmentHA_T2.sh \ -quantifyHAsubregions.sh - - -install-data-local: - test -z $(DESTDIR)$(foodir) || $(mkdir_p) $(DESTDIR)$(foodir) - $(INSTALL_DATA) $(foo_datafiles) $(DESTDIR)$(foodir) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/HippoSF/linux_x86_64/Makefile.am b/HippoSF/linux_x86_64/Makefile.am deleted file mode 100644 index 24cf394f188..00000000000 --- a/HippoSF/linux_x86_64/Makefile.am +++ /dev/null @@ -1,34 +0,0 @@ -# -# Makefile.am for HippoSF/linux_x86_64 -# - -dist_bin_SCRIPTS = \ - run_SegmentSubfieldsT1Longitudinal.sh \ - run_segmentSubjectT1_autoEstimateAlveusML.sh \ - run_segmentSubjectT1T2_autoEstimateAlveusML.sh \ - run_segmentSubjectT2_autoEstimateAlveusML.sh - -# -# We handle the binary files differently because binary -# files are treated as a separate compenent to the -# repository, and thus may not be present at compile time. -# - -foodir=$(prefix)/bin - -foo_binaryfiles = \ - SegmentSubfieldsT1Longitudinal \ - segmentSubjectT1_autoEstimateAlveusML \ - segmentSubjectT1T2_autoEstimateAlveusML \ - segmentSubjectT2_autoEstimateAlveusML - -install-data-local: - test -z $(DESTDIR)$(foodir) || $(mkdir_p) $(DESTDIR)$(foodir) - $(INSTALL) -m 755 $(foo_binaryfiles) $(DESTDIR)$(foodir) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - diff --git a/HippoSF/mac_osx/Makefile.am b/HippoSF/mac_osx/Makefile.am deleted file mode 100644 index 079bdb43927..00000000000 --- a/HippoSF/mac_osx/Makefile.am +++ /dev/null @@ -1,35 +0,0 @@ - -# -# Makefile.am for HippoSF/mac_osx -# - -dist_bin_SCRIPTS = \ - run_segmentSubjectT1_autoEstimateAlveusML.sh \ - run_segmentSubjectT1T2_autoEstimateAlveusML.sh \ - run_segmentSubjectT2_autoEstimateAlveusML.sh \ - run_SegmentSubfieldsT1Longitudinal.sh - -# -# We handle the binary files differently because binary -# files are treated as a separate compenent to the -# repository, and thus may not be present at compile time. -# - -foodir=$(prefix)/bin - -install-data-local: - test -z $(DESTDIR)$(foodir) || $(mkdir_p) $(DESTDIR)$(foodir) - cp -RL segmentSubjectT1_autoEstimateAlveusML.app $(foodir) - chmod -R 755 $(foodir)/segmentSubjectT1_autoEstimateAlveusML.app - cp -RL segmentSubjectT1T2_autoEstimateAlveusML.app $(foodir) - chmod -R 755 $(foodir)/segmentSubjectT1T2_autoEstimateAlveusML.app - cp -RL segmentSubjectT2_autoEstimateAlveusML.app $(foodir) - chmod -R 755 $(foodir)/segmentSubjectT2_autoEstimateAlveusML.app - cp -RL SegmentSubfieldsT1Longitudinal.app $(foodir) - chmod -R 755 $(foodir)/SegmentSubfieldsT1Longitudinal.app - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/LICENSE b/LICENSE.txt similarity index 100% rename from LICENSE rename to LICENSE.txt diff --git a/Makefile.am b/Makefile.am deleted file mode 100644 index 5cf4698b231..00000000000 --- a/Makefile.am +++ /dev/null @@ -1,561 +0,0 @@ -## -## Makefile.am -## - -ACLOCAL_AMFLAGS=-I m4 - -foodir=$(prefix) -foo_DATA=LICENSE NOTICE README AUTHORS INSTALL COPYING - -OCTSUBDIRS=\ - oct_train \ - oct_register_mosaic - -DMRISUBDIRS=\ - dmri_tensoreig - -GLSUBDIRS=\ - glut \ - stim_polar \ - tkmedit \ - tkregister2 \ - tksurfer \ - mri_probedicom \ - qdec \ - mris2rgb - -MRISUBDIRS=\ - check_siemens_dir \ - repair_siemens_file \ - mkxsubjreg \ - rbftest \ - lta_convert \ - mri_interpolate \ - mri_elastic_energy \ - mri_jacobian \ - mri_update_gca \ - mri_coreg \ - mri_compile_edits \ - mri_compute_volume_fractions \ - mri_label_accuracy \ - mri_add_xform_to_header \ - mri_bias \ - mri_annotation2label \ - mri_aparc2aseg \ - mri_aparc2wmseg \ - mri_auto_fill \ - mri_average \ - mri_dct_align \ - mri_binarize \ - mri_build_priors \ - mri_ca_label \ - mri_correct_segmentations \ - mri_cal_renormalize_gca \ - mri_divide_segmentation \ - mri_gtmpvc \ - mri_rf_label \ - mri_rf_train \ - mri_rf_long_label \ - mri_rf_long_train \ - mri_aseg_edit_train \ - mri_aseg_edit_reclassify \ - mri_ca_normalize \ - mri_ca_tissue_parms \ - mri_ca_register \ - mri_ca_train \ - mri_cvs_register \ - mri_gcab_train \ - mri_gtmseg \ - mri_gcut \ - mri_cc mri_cht2p \ - mri_cnr \ - mri_compute_overlap \ - mri_concat \ - mri_concatenate_gcam \ - mri_convert \ - mri_mosaic \ - mri_mi \ - mri_convert_mdh \ - mri_copy_values \ - mri_cor2label \ - mri_deface \ - mri_diff \ - mri_hires_register \ - mri_edit_segmentation \ - mri_edit_segmentation_with_surfaces \ - mri_em_register \ - mri_estimate_tissue_parms \ - mri_evaluate_morph \ - mri_extract \ - mri_extract_conditions \ - mri_extract_label \ - mri_extract_fcd_features \ - mri_fcili \ - mri_fdr \ - mri_fieldsign \ - mri_fill \ - mri_fit_bias \ - mri_fwhm \ - mri_gca_ambiguous \ - mri_head \ - histo_segment \ - histo_synthesize \ - histo_fix_topology \ - mri_histo_eq \ - mri_compute_structure_transforms \ - mri_ibmc \ - mri_iic \ - mri_info \ - mri_and \ - mri_hausdorff_dist \ - mri_histo_normalize \ - mri_fuse_segmentations \ - mri_fuse_intensity_images \ - mri_sbbr \ - mri_simulate_atrophy \ - mri_joint_density \ - mri_label_histo \ - mri_label_vals \ - mri_label_volume \ - mri_label2label \ - mri_label2vol \ - mri_linear_register \ - mri_make_bem_surfaces \ - mri_make_labels \ - mri_make_register \ - mri_make_template \ - mri_map_cpdat \ - mri_mark_temporal_lobe \ - mri_mask mri_ms_fitparms \ - mri_mcsim \ - mri_mc \ - mri_matrix_multiply \ - mri_modify \ - mri_multispectral_segment \ - mri_multiscale_segment \ - mri_nlfilter \ - mri_normalize \ - mri_otl \ - mri_partial_ribbon \ - mri_paint \ - mri_parselabel \ - mri_parse_sdcmdir \ - mri_polv \ - mri_probe_ima \ - mri_reduce \ - mri_register \ - mri_relabel_hypointensities \ - mri_relabel_nonwm_hypos \ - mri_remove_neck \ - mri_ribbon \ - mri_rigid_register \ - mri_robust_register \ - mri_seg_diff \ - mri_segcentroids \ - mri_segment \ - mri_segment_tumor \ - mri_seghead \ - mri_surfacemask \ - mri_strip_subject_info \ - mri_strip_nonwhite \ - mri_surf2surf \ - mri_surf2vol \ - mri_surfcluster \ - mri_synthesize \ - mri_tessellate \ - mri_distance_transform \ - mri_transform \ - mri_train \ - mri_train_autoencoder \ - mri_classify \ - mri_twoclass \ - mri_volcluster \ - mri_voldiff \ - mri_volsynth \ - mri_vol2roi \ - mri_vol2vol \ - mri_segreg \ - mri_segstats \ - mri_stats2seg \ - mri_vol2surf \ - mri_warp_concat \ - mri_warp_convert \ - mri_watershed \ - mri_wbc \ - mri_wmfilter \ - mri_xcorr \ - mri_xvolavg \ - mri_z2p \ - mri_threshold \ - mri_edit_wm_with_aseg \ - mri_bc_sc_bias_correct \ - mri_morphology \ - mri_topologycorrection \ - mri_segment_wm_damage \ - mri_make_density_map \ - mri_path2label \ - mri_fslmat_to_lta \ - mri_ms_EM \ - mri_ms_EM_with_atlas \ - mri_extract_largest_CC \ - mri_compute_seg_overlap \ - mri_concatenate_lta \ - mri_normalize_tp2 \ - mri_ms_LDA \ - mri_transform_to_COR \ - mri_log_likelihood \ - mri_compute_change_map \ - mri_apply_inu_correction \ - talairach_afd \ - talairach_avi \ - template - -MRISSUBDIRS=\ - label_area \ - label_border \ - label2patch \ - label2flat \ - spherical_stats \ - tridec \ - mris_copy_header \ - mris_segmentation_stats \ - mris_simulate_atrophy \ - mris_register_to_volume \ - mris_init_global_tractography \ - mris_interpolate_warp \ - mris_parcellate_connectivity \ - mris_map_cuts \ - mris_hausdorff_dist \ - mris_merge_parcellations \ - mris_distance_transform \ - mris_svm_classify \ - mris_svm_train \ - mris_calc \ - mris_shrinkwrap \ - mris_density \ - mris_rf_label \ - mris_rf_train \ - mris_fbirn_annot \ - mris_fill \ - mris_add_template \ - mris_anatomical_stats \ - mris_transmantle_dysplasia_paths \ - mris_annot_to_segmentation \ - mris_apply_reg \ - mris_aseg_distance \ - mris_average_curvature \ - mris_ca_label \ - mris_divide_parcellation \ - mris_ca_train \ - mris_classify_thickness \ - mris_compute_acorr \ - mris_compute_lgi \ - mris_compute_overlap \ - mris_compute_parc_overlap \ - mris_convert \ - mris_decimate \ - mris_decimate_gui \ - mris_distance_map \ - mris_curvature \ - mris_curvature_stats \ - mris_entropy \ - mris_errors \ - mris_euler_number \ - mris_expand \ - mris_extract_patches \ - mris_find_flat_regions \ - mris_fix_topology \ - mris_topo_fixer \ - mris_flatten \ - mris_fwhm \ - mris_inflate \ - mris_info \ - mris_jacobian \ - mris_label_area \ - mris_label_calc \ - mris_label_mode \ - mris_label2annot \ - mris_make_average_surface \ - mris_make_surfaces \ - mris_make_map_surfaces \ - mris_longitudinal_surfaces \ - mris_make_template \ - mris_morph_stats \ - mris_deform \ - mris_multiscale_stats \ - mris_niters2fwhm \ - mris_pmake \ - mris_remove_variance \ - mris_rescale \ - mris_reverse \ - mris_rotate \ - mris_ms_refine \ - mris_diff \ - mris_distance_to_label \ - mris_register_label_map \ - mris_register \ - mris_left_right_register \ - mris_congeal \ - mris_resample \ - mris_sample_label \ - mris_sample_parc \ - mris_segment_vals \ - mris_segment \ - mris_seg2annot \ - mris_smooth \ - mris_make_face_parcellation \ - mris_sphere \ - mris_spherical_average \ - mris_average_parcellation \ - mris_surface_to_vol_distances \ - mrisp_paint \ - mrisp_write \ - mris_talairach \ - mris_surface_change \ - mris_thickness \ - mris_BA_segment \ - mris_compute_optimal_kernel \ - mris_thickness_comparison \ - mris_transform \ - mris_translate_annotation \ - mris_twoclass \ - mris_watershed \ - mris_w_to_curv \ - mris_volmask \ - mris_volume \ - mris_warp \ - mris_thickness_diff \ - mris_ms_surface_CNR \ - mris_mesh_subdivide \ - mris_surface_stats \ - mris_compute_volume_fractions - -FSGDF=\ - fsgdf \ - mri_gdfglm \ - mri_glmfit \ - mris_glm - -FSLUTILS=fslutils - -STATSDIRS=\ - optseq2 \ - stat_normalize - -MISCDIRS=\ - histo_compute_joint_density \ - histo_register_block \ - regdat2xfm \ - test_makevol \ - images \ - dummy \ - fem_elastic \ - hiam_make_surfaces\ - hiam_make_template\ - hiam_register \ - histo_register \ - spline3 \ - swi_processing \ - HippoSF \ - BrainstemSS \ - ThalamicNuclei - -# ordering is important here for proper 'make check' and 'make distcheck' function -COREDIRS=\ - include \ - unix \ - dicom \ - hipsstubs \ - expat \ - jpeg \ - tiff \ - xml2 \ - rgb \ - log \ - gpu_utils \ - opencl_algorithms \ - minc_1_5_1 \ - netcdf_3_6_0_p1 \ - utils \ - utilscpp \ - vtkfsio \ - vtkutils \ - itkio \ - itkutils \ - tetgen \ - lineprof \ - $(FSGDF) \ - connectgraph \ - qdecproject \ - svm-lib \ - scripts \ - distribution \ - $(FSLUTILS) \ - $(STATSDIRS) \ - $(GLSUBDIRS) - -# dependent on COREDIRS -OTHERDIRS=\ - $(MRISUBDIRS) \ - $(MRISSUBDIRS) \ - $(MISCDIRS) \ - $(DMRISUBDIRS) \ - $(OCTSUBDIRS) \ - fsfast \ - matlab \ - qdec_glmfit \ - cudatest - -# these have lots of files, each will maximize the multi-threaded make option (-j) -BIGDIRS=\ - freeview \ - trc - -# SUBDIRS is the automake definition of the 'all' for make -SUBDIRS=\ - $(COREDIRS) \ - $(OTHERDIRS) \ - $(BIGDIRS) - -# this target is an ad-hoc way to run the build a lot faster -# by launching makes in parallel, after the dependencies are -# built. also make is run multi-threaded, which speeds the -# build within a directory. -# the default is to use no more than 8 threads. -# if FS_FASTBUILD_THREADS is defined in the enviro to some -# other number, it will use that thread count. -fastbuild: - if test "x$(FS_FASTBUILD_THREADS)" = "x" ; then \ - export FS_FASTBUILD_THREADS=8 ; \ - fi; - @list='$(COREDIRS)'; \ - for d in $$list; do \ - cd "$$d"; make -j --max-load $(FS_FASTBUILD_THREADS) ; cd - ; \ - done - @list='$(OTHERDIRS)'; \ - for d in $$list; do \ - cd "$$d"; (make -j --max-load $(FS_FASTBUILD_THREADS) &) ; sleep 0.2; cd - ; \ - done - @list='$(BIGDIRS)'; \ - for d in $$list; do \ - cd "$$d"; (make -j --max-load $(FS_FASTBUILD_THREADS) ); cd - ; \ - done - sleep 30 - make - -# build stamp and symlinks to necessary 3rd-party packages. -# in the case of FSL, just copy the 'flirt' utility to our bin -install-data-hook: - echo "$(PACKAGE)-$(target_triplet)-$(VERSION)-`date +%Y%m%d`" \ - > $(DESTDIR)$(prefix)/build-stamp.txt ; - cp -f $(DESTDIR)$(prefix)/build-stamp.txt \ - $(DESTDIR)$(prefix)/VERSION - if test ! "x$(MNI_DIR)" = "x" ; then \ - if test ! "$(MNI_DIR)" = "$(DESTDIR)$(prefix)/mni" ; then \ - if test -e $(MNI_DIR) ; then \ - rm -Rf $(DESTDIR)$(prefix)/mni ; \ - ln -s $(MNI_DIR) $(DESTDIR)$(prefix)/mni ; \ - fi; \ - fi; \ - fi; - if test ! "x$(FSLDIR)" = "x" ; then \ - if test -e $(FSLDIR) ; then \ - cp -f $(FSLDIR)/bin/flirt $(DESTDIR)$(bindir)/flirt.fsl ; \ - cp -f $(FSLDIR)/bin/fslmaths $(DESTDIR)$(bindir)/fslmaths.fsl ; \ - cp -f $(FSLDIR)/bin/slicetimer $(DESTDIR)$(bindir)/slicetimer.fsl ; \ - cp -f $(FSLDIR)/bin/bet $(DESTDIR)$(bindir)/bet.fsl ; \ - cp -f $(FSLDIR)/bin/fslswapdim $(DESTDIR)$(bindir)/fslswapdim.fsl ; \ - cp -f $(FSLDIR)/bin/fslorient $(DESTDIR)$(bindir)/fslorient.fsl ; \ - fi; \ - fi; - if test ! "x$(DCMTKDIR)" = "x" ; then \ - if test -e $(DCMTKDIR) ; then \ - cp -f $(DCMTKDIR)/bin/dcmdjpeg $(DESTDIR)$(bindir)/dcmdjpeg.fs ; \ - cp -f $(DCMTKDIR)/bin/dcmdrle $(DESTDIR)$(bindir)/dcmdrle.fs ; \ - fi; \ - fi; - if test ! "x$(GDCMDIR)" = "x" ; then \ - if test -e $(GDCMDIR) ; then \ - cp -f $(GDCMDIR)/bin/gdcmconv $(DESTDIR)$(bindir)/gdcmconv.fs ; \ - fi; \ - fi; - if test ! "x$(AFNIDIR)" = "x" ; then \ - if test -e $(AFNIDIR)/bin/3dvolreg ; then \ - cp -f $(AFNIDIR)/bin/3dvolreg $(DESTDIR)$(bindir)/3dvolreg.afni ; \ - fi; \ - if test -e $(AFNIDIR)/3dvolreg ; then \ - cp -f $(AFNIDIR)/3dvolreg $(DESTDIR)$(bindir)/3dvolreg.afni ; \ - fi; \ - fi; - if test ! "x$(TCL_DIR)" = "x" ; then \ - if test ! "$(TCL_DIR)" = "$(DESTDIR)$(prefix)/lib/tcltktixblt" ; then \ - if test -e $(TCL_DIR) ; then \ - rm -Rf $(DESTDIR)$(prefix)/lib/tcltktixblt ; \ - ln -s $(TCL_DIR) $(DESTDIR)$(prefix)/lib/tcltktixblt ; \ - fi; \ - fi; \ - fi; - if test ! "x$(VTK_DIR)" = "x" ; then \ - if test ! "$(VTK_DIR)" = "$(DESTDIR)$(prefix)/lib/vtk" ; then \ - if test -e $(VTK_DIR) ; then \ - rm -Rf $(DESTDIR)$(prefix)/lib/vtk ; \ - ln -s $(VTK_DIR) $(DESTDIR)$(prefix)/lib/vtk ; \ - fi; \ - fi; \ - fi; - if test ! "x$(QT_DIR)" = "x" ; then \ - if test ! "$(QT_DIR)" = "$(DESTDIR)$(prefix)/lib/qt" ; then \ - if test -e $(QT_DIR) ; then \ - rm -Rf $(DESTDIR)$(prefix)/lib/qt ; \ - ln -s $(QT_DIR) $(DESTDIR)$(prefix)/lib/qt ; \ - fi; \ - fi; \ - fi; - if test ! "x$(KWWIDGETS_DIR)" = "x" ; then \ - if test ! "$(KWWIDGETS_DIR)" = "$(DESTDIR)$(prefix)/lib/KWWidgets" ; then \ - if test -e $(KWWIDGETS_DIR) ; then \ - rm -Rf $(DESTDIR)$(prefix)/lib/KWWidgets ; \ - ln -s $(KWWIDGETS_DIR) $(DESTDIR)$(prefix)/lib/KWWidgets ; \ - fi; \ - fi; \ - fi; - if test ! "x$(PETSC_DIR)" = "x" ; then \ - if test ! "$(PETSC_DIR)" = "$(DESTDIR)$(prefix)/lib/petsc" ; then \ - if test -e $(PETSC_DIR) ; then \ - rm -Rf $(DESTDIR)$(prefix)/lib/petsc ; \ - ln -s $(PETSC_DIR) $(DESTDIR)$(prefix)/lib/petsc ; \ - fi; \ - fi; \ - fi; - if test ! "x$(CUDA_DIR)" = "x" ; then \ - if test ! "$(CUDA_DIR)" = "$(DESTDIR)$(prefix)/lib/cuda" ; then \ - if test -e $(CUDA_DIR) ; then \ - rm -Rf $(DESTDIR)$(prefix)/lib/cuda ; \ - ln -s $(CUDA_DIR) $(DESTDIR)$(prefix)/lib/cuda ; \ - fi; \ - fi; \ - fi; - -uninstall-hook: - rm -f $(DESTDIR)$(prefix)/build-stamp.txt - rm -f $(DESTDIR)$(prefix)/VERSION - rm -f $(DESTDIR)$(bindir)/3dvolreg.afni - rm -f $(DESTDIR)$(bindir)/flirt.fsl - rm -f $(DESTDIR)$(bindir)/slicetimer.fsl - rm -f $(DESTDIR)$(bindir)/bet.fsl - -EXTRA_DIST=setup_configure Makefile.extra x86cpucaps \ - doxy-file-header Doxyfile $(foo_DATA) - -DISTCLEANFILES=cpuflags.mak - -# we have files in our dist that dont and shouldnt get cleaned, like testdata. -# this target override allows make distcheck to pass -distcleancheck: - echo "Skipping target distcleancheck" - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES=CVS core -include $(top_srcdir)/Makefile.extra diff --git a/Makefile.extra b/Makefile.extra deleted file mode 100644 index a4cf06aebdc..00000000000 --- a/Makefile.extra +++ /dev/null @@ -1,34 +0,0 @@ - -.PHONY: release - -# A rule for making the release. -# It just creates a list of files for later removal from files in an exclude list. -release: install - list=( $(EXCLUDE_FILES) ); for p in $${list[@]}; do \ - echo "rm -fv $(prefix)/$(subdir)/$$p" >> $(prefix)/EXCLUDE_FILES_rm_cmds \;; \ - done; \ - list=( $(SUBDIRS) ); for subdir in $${list[@]}; do \ - echo "Making release in $$subdir"; \ - (cd $$subdir && $(MAKE) $(AM_MAKEFLAGS) release) \ - || exit 1; \ - done; - -# A rule for making the source tarball. It removes files declared in a -# Makefile.am's EXCLUDE_FILES list (stuff that should not go outside the -# NMR Center). -dist-hook: - list=( $(EXCLUDE_FILES) ); for p in $${list[@]}; do \ - find $(distdir) -follow -name $$p -exec rm -Rf {} \;; \ - done; \ - extra_dist=( $(EXTRA_DIST) ); - -if HAVE_XXD -# A rule to create a header from an xml file in order to -# include the file as a string at compilation time (see ProjectHelp wiki page) -%.xml.h : %.xml - xxd -i $< $@ -endif - -# A rule to create an html file from an xml file (see ProjectHelp wiki page) -%.xml.html : %.xml - $(top_builddir)/utils/xmlToHtml $< $@ diff --git a/Makefile.smalldist.am b/Makefile.smalldist.am deleted file mode 100644 index 270986d1947..00000000000 --- a/Makefile.smalldist.am +++ /dev/null @@ -1,205 +0,0 @@ -## -## Makefile.smalldist.am -## -## This makes only the binaries needed to run recon-all -all , ie. a minimal install. -## To use, just include the flag --enable-small-build-dist with configure. That will -## disable the build of the GUI apps, and enable the 'small dist' data install, and -## replace Makefile with this Makefile.smalldist. One could also include --disable-g -## with configure to compile without debug symbols. -## For a working installation, the MNI tools (namely nu_correct) will need to be -## installed, so one with need to do this after their make install: -## cd $FREESURFER_HOME -## ln -s /some/path/to/mni/build mni -## - -ACLOCAL_AMFLAGS=-I m4 - -foodir=$(prefix) -foo_DATA=LICENSE NOTICE README AUTHORS INSTALL COPYING - -# as executed by recon-all -all -# these are the scripts, found in /scripts dir: -# mri_nu_correct.mni -# tal_QC_AZS -# vertexvol -# apas2aseg -# and: -# mri_pretess is in mri_mc -# mris_extract_main_component is in mri_mc -# tkregister2_cmdl is in tkregister2/cmdl -RECONALLDIRS=\ - lta_convert \ - mri_add_xform_to_header \ - mri_annotation2label \ - mri_aparc2aseg \ - mri_aparc2wmseg \ - mri_binarize \ - mri_ca_label \ - mri_ca_normalize \ - mri_ca_register \ - mri_cc \ - mri_compute_overlap \ - mri_compute_seg_overlap \ - mri_concat \ - mri_concatenate_lta \ - mri_convert \ - mri_coreg \ - mri_deface \ - mri_diff \ - mri_edit_segmentation \ - mri_edit_segmentation_with_surfaces \ - mri_edit_wm_with_aseg \ - mri_em_register \ - mri_extract_largest_CC \ - mri_fill \ - mri_fuse_segmentations \ - mri_fwhm \ - mri_gcut \ - mri_info \ - mri_label2label \ - mri_label2vol \ - mri_log_likelihood \ - mri_mask \ - mri_matrix_multiply \ - mri_mc \ - mri_normalize \ - mri_normalize_tp2 \ - mri_relabel_hypointensities \ - mri_relabel_nonwm_hypos \ - mri_remove_neck \ - mri_robust_register \ - mris_anatomical_stats \ - mris_ca_label \ - mris_calc \ - mris_convert \ - mris_curvature \ - mris_curvature_stats \ - mris_diff \ - mris_divide_parcellation \ - mri_segment \ - mri_segreg \ - mri_segstats \ - mris_euler_number \ - mris_fix_topology \ - mris_inflate \ - mris_info \ - mris_jacobian \ - mris_label2annot \ - mris_left_right_register \ - mris_make_surfaces \ - mrisp_paint \ - mris_register \ - mris_smooth \ - mris_sphere \ - mris_surface_stats \ - mri_stats2seg \ - mris_thickness \ - mris_thickness_diff \ - mris_topo_fixer \ - mri_surf2surf \ - mri_surf2vol \ - mri_surfcluster \ - mris_volmask \ - mri_tessellate \ - mri_vol2surf \ - mri_vol2vol \ - mri_voldiff \ - mri_watershed \ - talairach_afd \ - talairach_avi \ - tkregister2 -# tkregister2 is included to build tkregister2_cmdl only! - -EXTRADIRS=\ - mri_probedicom - -# ordering is important here for proper 'make check' and 'make distcheck' function -COREDIRS=\ - include \ - unix \ - dicom \ - expat \ - jpeg \ - tiff \ - xml2 \ - rgb \ - log \ - minc_1_5_1 \ - netcdf_3_6_0_p1 \ - utils \ - utilscpp \ - scripts \ - distribution \ - fsgdf \ - hipsstubs \ - tetgen - -# dependent on COREDIRS -OTHERDIRS=\ - $(RECONALLDIRS) \ - $(EXTRADIRS) - -# SUBDIRS is the automake definition of the 'all' for make -SUBDIRS=\ - $(COREDIRS) \ - $(OTHERDIRS) - -# this target is an ad-hoc way to run the build a lot faster -# by launching makes in parallel, after the dependencies are -# built. also make is run multi-threaded, which speeds the -# build within a directory. -# the default is to use no more than 8 threads. -# if FS_FASTBUILD_THREADS is defined in the enviro to some -# other number, it will use that thread count. -fastbuild: - if test "x$(FS_FASTBUILD_THREADS)" = "x" ; then \ - export FS_FASTBUILD_THREADS=8 ; \ - fi; - @list='$(COREDIRS)'; \ - for d in $$list; do \ - cd "$$d"; make -j --max-load $(FS_FASTBUILD_THREADS) ; cd - ; \ - done - @list='$(OTHERDIRS)'; \ - for d in $$list; do \ - cd "$$d"; (make -j --max-load $(FS_FASTBUILD_THREADS) &) ; sleep 0.2; cd - ; \ - done - sleep 30 - make - -# build stamp and symlinks to necessary 3rd-party packages. -install-data-hook: - echo "$(PACKAGE)-$(target_triplet)-$(VERSION)-small-dist-`date +%Y%m%d`" \ - > $(DESTDIR)$(prefix)/build-stamp.txt ; - cp -f $(DESTDIR)$(prefix)/build-stamp.txt \ - $(DESTDIR)$(prefix)/VERSION - if test ! "x$(MNI_DIR)" = "x" ; then \ - if test ! "$(MNI_DIR)" = "$(DESTDIR)$(prefix)/mni" ; then \ - if test -e $(MNI_DIR) ; then \ - rm -Rf $(DESTDIR)$(prefix)/mni ; \ - ln -s $(MNI_DIR) $(DESTDIR)$(prefix)/mni ; \ - fi; \ - fi; \ - fi; - -uninstall-hook: - rm -f $(DESTDIR)$(prefix)/build-stamp.txt - rm -f $(DESTDIR)$(prefix)/VERSION - -EXTRA_DIST=setup_configure Makefile.extra x86cpucaps \ - doxy-file-header Doxyfile $(foo_DATA) - -DISTCLEANFILES=cpuflags.mak - -distclean-hook: - rm -f Makefile - -# we have files in our dist that dont and shouldnt get cleaned, like testdata. -# this target override allows make distcheck to pass -distcleancheck: - echo "Skipping target distcleancheck" - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES=CVS core -include $(top_srcdir)/Makefile.extra diff --git a/NOTICE b/NOTICE deleted file mode 100644 index 5e7fbe25e33..00000000000 --- a/NOTICE +++ /dev/null @@ -1,124 +0,0 @@ -FreeSurfer. -Copyright © 2011-2016 The General Hospital Corporation (Boston, MA) "MGH" - -This product includes software developed at the -Athinoula A. Martinos Center for Biomedical Imaging -149 Thirteenth Street, Suite 2301 -Charlestown, Massachusetts 02129 - -FreeSurfer is based on other software packages, where the corresponding -license is found in either the docs/ directory of the binary distribution, -or in the /dev/distribution/docs directory of the source distribution: - -Tck/Tk. -Parts of this software are based on the Tcl/Tk software copyrighted by the -Regents of the University of California, Sun Microsystems, Inc., and other -parties. The original license terms of the Tcl/Tk software distribution is -included in the file docs/license.tcltk.txt - -Tix. -Parts of this software are based on the Tix software copyrighted by the Ioi Kim -Lam, and Expert Interface Technologies. The original license terms of the Tix -software distribution is included in the file -docs/license.tix.txt - -BLT. -Parts of this software are based on the BLT software copyrighted by Lucent -Technologies. The original license terms of the BLT software distribution is -included in the file docs/license.blt.txt - -Tiff. -Parts of this software are based on the Tiff software. The original license -terms of the Tiff software distribution is included in the file -docs/license.tiff.txt - -JPEG. -Parts of this software are based on the JPEG software. The original license -terms of the JPEG software distribution is included in the file -docs/license.jpeg.txt - -GLUT. -Parts of this software are based on the GLUT software. The original license -terms of the GLUT software distribution is included in the file -docs/license.glut.txt - -VXL. -Parts of this software are based on the VXL software. The original license -terms of the VXL software distribution is included in the file -docs/license.vxl.txt - -LAPACK/BLAS. -Parts of this software are based on the LAPACK software. The original license -terms of the LAPACK software distribution is included in the file -docs/license.lapack.txt - -MINC. -Parts of this software are based on the MINC software. The original license -terms of the MINC software distribution is included in the file -docs/license.minc.txt - -VTK/KWWidgets. -Parts of this software are based on the VTK/KWWidgets software. The original -license terms of the VTK/KWWidgets software distribution is included in the -file docs/license.vtk.txt - -ITK. -Parts of this software are based on the ITK software. The original license -terms of the ITK software distribution is included in the file -docs/license.itk.txt - -Qt. -Parts of this software are based on the Qt software. The original license -terms of the Qt software distribution is included in the file -docs/license.qt.html. - -Expat. -Parts of this software are based on the Expat software. The original license -terms of the Expat software distribution is included in the file -docs/license.expat.txt - -XML2. -Parts of this software are based on the XML2 software. The original license -terms of the XML2 software distribution is included in the file -docs/license.xml2.txt - -Boost. -Parts of this software are based on the Boost software. The original license -terms of the Boost software distribution is included in the file -docs/license.boost.txt - -Thrust. -Parts of this software are based on the Thrust software. The original license -terms of the Thrust software distribution is included in the file -docs/license.thrust.txt - -PETSc. -Parts of this software are based on the PETSc software. The original license -terms of the PETSc software distribution is included in the file -docs/license.petsc.txt - -NrrdIO. -Parts of this software are based on the NrrdIO software. The original license -terms of the NrrdIO software distribution is included in the file -docs/license.nrrdio.txt - -NIfTI. -Parts of this software are based on the NIfTI software. The original license -terms of the NIfTI software distribution is included in the file -docs/license.nifti.txt - -GIfTI. -Parts of this software are based on the GIfTI software. The original license -terms of the GIfTI software distribution is included in the file -docs/license.gifti.txt - -CUDA. -Parts of this software are based on the CUDA software from NVIDIA. -The original license terms of the CUDA DSK software distribution is included -in the file docs/license.cuda.txt - -FSL. -Parts of this software make use of the FSL software package, eg. 'flirt' is -redistributed as 'flirt.fsl'. The original license terms of the FSL software -distribution is included in the file docs/license.fsl.txt - diff --git a/README b/README deleted file mode 100644 index d6f6a87d6fd..00000000000 --- a/README +++ /dev/null @@ -1,20 +0,0 @@ -FreeSurfer © 2011-2018 The General Hospital Corporation (Boston, MA) "MGH" - -Terms and conditions for use, reproduction, distribution and contribution -are found in the 'FreeSurfer Software License Agreement' contained -in the file 'LICENSE' found in the FreeSurfer distribution, and here: - -https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense - -For instructions on how to obtain and build the source code, see: - -https://surfer.nmr.mgh.harvard.edu/fswiki/DevelopersGuide - -FreeSurfer documentation is found online at: - -http://surfer.nmr.mgh.harvard.edu/fswiki - -For questions and support, email: - -freesurfer@nmr.mgh.harvard.edu - diff --git a/README.md b/README.md index c6f7464baa3..dc6f485a044 100644 --- a/README.md +++ b/README.md @@ -1,28 +1,19 @@ # FreeSurfer [![Build Status](https://travis-ci.org/freesurfer/freesurfer.svg?branch=dev)](https://travis-ci.org/freesurfer/freesurfer) ->*The official FreeSurfer repository maintained by LCN* +>*The official FreeSurfer repository maintained by the Laboratory for Computational Neuroimaging* ### Documentation and Support -FreeSurfer documentation is found online at: http://surfer.nmr.mgh.harvard.edu/fswiki +FreeSurfer documentation is found online at https://surfer.nmr.mgh.harvard.edu/fswiki -For questions and support, email: freesurfer@nmr.mgh.harvard.edu +For questions and support, email freesurfer@nmr.mgh.harvard.edu ### Building -See the following webpage for information on how to build the FreeSurfer source code: -https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page - -### Contributing - -See the following webpage if you are interested in contributing to the project: -https://surfer.nmr.mgh.harvard.edu/fswiki/Freesurfer_github +Please visit our [build guide](https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page) for information on how to build the source code. ### License -Terms and conditions for use, reproduction, distribution and contribution -are found in the FreeSurfer Software License Agreement contained -in the LICENSE file, and here: -https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense +Terms and conditions for use, reproduction, distribution and contribution are found in the FreeSurfer software license agreement contained in the **LICENSE.txt** file and [on our wiki](https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense). -*FreeSurfer © 2011-2017 The General Hospital Corporation (Boston, MA) "MGH"* +*FreeSurfer © 2011-2019 The General Hospital Corporation (Boston, MA) "MGH"* diff --git a/ThalamicNuclei/Makefile.am b/ThalamicNuclei/Makefile.am deleted file mode 100644 index d6afe58110a..00000000000 --- a/ThalamicNuclei/Makefile.am +++ /dev/null @@ -1,31 +0,0 @@ -# -# Makefile.am for ThalamicNuclei (segmentation tools for thalamic nuclei) -# - -foodir=$(prefix)/average/ThalamicNuclei/atlas -foo_datafiles=AtlasDump.mgz AtlasMesh.gz compressionLookupTable.txt - -if HAVE_MAC_OSX - -SUBDIRS=mac_osx - -else - -SUBDIRS=linux_x86_64 - -endif - -# platform-independent data and scripts: -dist_bin_SCRIPTS = \ -segmentThalamicNuclei.sh \ -quantifyThalamicNuclei.sh - -install-data-local: - test -z $(DESTDIR)$(foodir) || $(mkdir_p) $(DESTDIR)$(foodir) - $(INSTALL_DATA) $(foo_datafiles) $(DESTDIR)$(foodir) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/ThalamicNuclei/linux_x86_64/Makefile.am b/ThalamicNuclei/linux_x86_64/Makefile.am deleted file mode 100644 index 684df5fc1b6..00000000000 --- a/ThalamicNuclei/linux_x86_64/Makefile.am +++ /dev/null @@ -1,28 +0,0 @@ -# -# Makefile.am for ThalamicNuclei/linux_x86_64 -# - -dist_bin_SCRIPTS = \ - run_SegmentThalamicNuclei.sh - -# -# We handle the binary files differently because binary -# files are treated as a separate compenent to the -# repository, and thus may not be present at compile time. -# - -foodir=$(prefix)/bin - -foo_binaryfiles = \ - SegmentThalamicNuclei - -install-data-local: - test -z $(DESTDIR)$(foodir) || $(mkdir_p) $(DESTDIR)$(foodir) - $(INSTALL) -m 755 $(foo_binaryfiles) $(DESTDIR)$(foodir) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - diff --git a/ThalamicNuclei/mac_osx/Makefile.am b/ThalamicNuclei/mac_osx/Makefile.am deleted file mode 100644 index 41304d3313c..00000000000 --- a/ThalamicNuclei/mac_osx/Makefile.am +++ /dev/null @@ -1,25 +0,0 @@ - -# -# Makefile.am for ThalamicNuclei/mac_osx -# - -dist_bin_SCRIPTS = \ - run_SegmentThalamicNuclei.sh - -# -# We handle the binary files differently because binary -# files are treated as a separate compenent to the -# repository, and thus may not be present at compile time. -# - -foodir=$(prefix)/bin - -install-data-local: - cp -RL SegmentThalamicNuclei.app $(foodir) - chmod -R 755 $(foodir)/SegmentThalamicNuclei.app - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/acinclude.m4 b/acinclude.m4 deleted file mode 100644 index 5a2a59b4c19..00000000000 --- a/acinclude.m4 +++ /dev/null @@ -1,6488 +0,0 @@ -# -# acinclude.m4 -# -# contains the following macro taken from -# 1. autoconf m4 archive: http://www.gnu.org/software/ac-archive/ -# -# m4 archive -# sets -# ACX_PTHREAD --> PTHREAD_CFLAGS, PTHREAD_CC, PTHREAD_LIBS -# AX_CHECK_GL --> GL_CFLAGS GL_LIBS -# AX_CHECK_GLU --> GLU_CFLAGS GLU_LIBS -# AX_CHECK_GLUT --> GLUT_CFLAGS GLUT_LIBS -# AC_C_BIGENDIAN_CROSS -> - -# serial 47 AC_PROG_LIBTOOL - -dnl Available from the GNU Autoconf Macro Archive at: -dnl http://www.gnu.org/software/ac-archive/htmldoc/acx_pthread.html -dnl -AC_DEFUN([ACX_PTHREAD], [ -AC_REQUIRE([AC_CANONICAL_HOST]) -AC_LANG_SAVE -AC_LANG_C -acx_pthread_ok=no - -# We used to check for pthread.h first, but this fails if pthread.h -# requires special compiler flags (e.g. on True64 or Sequent). -# It gets checked for in the link test anyway. - -# First of all, check if the user has set any of the PTHREAD_LIBS, -# etcetera environment variables, and if threads linking works using -# them: -if test x"$PTHREAD_LIBS$PTHREAD_CFLAGS" != x; then - save_CFLAGS="$CFLAGS" - CFLAGS="$CFLAGS $PTHREAD_CFLAGS" - save_LIBS="$LIBS" - LIBS="$PTHREAD_LIBS $LIBS" - AC_MSG_CHECKING([for pthread_join in LIBS=$PTHREAD_LIBS with CFLAGS=$PTHREAD_CFLAGS]) - AC_TRY_LINK_FUNC(pthread_join, acx_pthread_ok=yes) - AC_MSG_RESULT($acx_pthread_ok) - if test x"$acx_pthread_ok" = xno; then - PTHREAD_LIBS="" - PTHREAD_CFLAGS="" - fi - LIBS="$save_LIBS" - CFLAGS="$save_CFLAGS" -fi - -# We must check for the threads library under a number of different -# names; the ordering is very important because some systems -# (e.g. DEC) have both -lpthread and -lpthreads, where one of the -# libraries is broken (non-POSIX). - -# Create a list of thread flags to try. Items starting with a "-" are -# C compiler flags, and other items are library names, except for "none" -# which indicates that we try without any flags at all, and "pthread-config" -# which is a program returning the flags for the Pth emulation library. - -acx_pthread_flags="pthreads none -Kthread -kthread lthread -pthread -pthreads -mthreads pthread --thread-safe -mt pthread-config" - -# The ordering *is* (sometimes) important. Some notes on the -# individual items follow: - -# pthreads: AIX (must check this before -lpthread) -# none: in case threads are in libc; should be tried before -Kthread and -# other compiler flags to prevent continual compiler warnings -# -Kthread: Sequent (threads in libc, but -Kthread needed for pthread.h) -# -kthread: FreeBSD kernel threads (preferred to -pthread since SMP-able) -# lthread: LinuxThreads port on FreeBSD (also preferred to -pthread) -# -pthread: Linux/gcc (kernel threads), BSD/gcc (userland threads) -# -pthreads: Solaris/gcc -# -mthreads: Mingw32/gcc, Lynx/gcc -# -mt: Sun Workshop C (may only link SunOS threads [-lthread], but it -# doesn't hurt to check since this sometimes defines pthreads too; -# also defines -D_REENTRANT) -# pthread: Linux, etcetera -# --thread-safe: KAI C++ -# pthread-config: use pthread-config program (for GNU Pth library) - -case "${host_cpu}-${host_os}" in - *solaris*) - - # On Solaris (at least, for some versions), libc contains stubbed - # (non-functional) versions of the pthreads routines, so link-based - # tests will erroneously succeed. (We need to link with -pthread or - # -lpthread.) (The stubs are missing pthread_cleanup_push, or rather - # a function called by this macro, so we could check for that, but - # who knows whether they'll stub that too in a future libc.) 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See the -# GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program; if not, write to the Free Software -# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, -# USA. -# -# In addition, as a special exception, the copyright holders of AutoTroll -# give you unlimited permission to copy, distribute and modify the configure -# scripts that are the output of Autoconf when processing the macros of -# AutoTroll. You need not follow the terms of the GNU General Public License -# when using or distributing such scripts, even though portions of the text of -# AutoTroll appear in them. The GNU General Public License (GPL) does govern -# all other use of the material that constitutes AutoTroll. -# -# This special exception to the GPL applies to versions of AutoTroll -# released by the copyright holders of AutoTroll. Note that people who make -# modified versions of AutoTroll are not obligated to grant this special -# exception for their modified versions; it is their choice whether to do so. -# The GNU General Public License gives permission to release a modified version -# without this exception; this exception also makes it possible to release a -# modified version which carries forward this exception. - - # ------------- # - # DOCUMENTATION # - # ------------- # - -# See autotroll.m4 :) - - -SUFFIXES = .moc.cpp .moc.cc .moc.cxx .moc.C .h .hh .hpp \ - .ui .ui.h .ui.hh .ui.hpp \ - .qrc .qrc.cpp .qrc.cc .qrc.cxx .qrc.C - -# --- # -# MOC # -# --- # - -.hpp.moc.cpp: - $(MOC) $(QT_CPPFLAGS) $(EXTRA_CPPFLAGS) $< -o $@ -.hh.moc.cpp: - $(MOC) $(QT_CPPFLAGS) $(EXTRA_CPPFLAGS) $< -o $@ -.h.moc.cpp: - $(MOC) $(QT_CPPFLAGS) $(EXTRA_CPPFLAGS) $< -o $@ - -.hpp.moc.cc: - $(MOC) $(QT_CPPFLAGS) $(EXTRA_CPPFLAGS) $< -o $@ -.hh.moc.cc: - $(MOC) $(QT_CPPFLAGS) $(EXTRA_CPPFLAGS) $< -o $@ -.h.moc.cc: - $(MOC) $(QT_CPPFLAGS) $(EXTRA_CPPFLAGS) $< -o $@ - -.hpp.moc.cxx: - $(MOC) $(QT_CPPFLAGS) $(EXTRA_CPPFLAGS) $< -o $@ -.hh.moc.cxx: - $(MOC) $(QT_CPPFLAGS) $(EXTRA_CPPFLAGS) $< -o $@ -.h.moc.cxx: - $(MOC) $(QT_CPPFLAGS) $(EXTRA_CPPFLAGS) $< -o $@ - -.hpp.moc.C: - $(MOC) $(QT_CPPFLAGS) $(EXTRA_CPPFLAGS) $< -o $@ -.hh.moc.C: - $(MOC) $(QT_CPPFLAGS) $(EXTRA_CPPFLAGS) $< -o $@ -.h.moc.C: - $(MOC) $(QT_CPPFLAGS) $(EXTRA_CPPFLAGS) $< -o $@ - -%.moc: %.cpp - $(MOC) $(QT_CPPFLAGS) $(EXTRA_CPPFLAGS) $< -o $@ - -moc_%.cpp: %.h - $(MOC) $(QT_CPPFLAGS) $(EXTRA_CPPFLAGS) $< -o $@ - - -# --- # -# UIC # -# --- # - -.ui.ui.hpp: - $(UIC) $< -o $@ - -.ui.ui.hh: - $(UIC) $< -o $@ - -.ui.ui.h: - $(UIC) $< -o $@ - -ui_%.h: %.ui - $(UIC) $< -p -o $@ - - -# --- # -# RCC # -# --- # - -.qrc.qrc.cpp: - $(RCC) -name `echo "$<" | sed 's|^.*/\(.*\)\.qrc$$|\1|'` $< -o $@ - -.qrc.qrc.cc: - $(RCC) -name `echo "$<" | sed 's|^.*/\(.*\)\.qrc$$|\1|'` $< -o $@ - -.qrc.qrc.cxx: - $(RCC) -name `echo "$<" | sed 's|^.*/\(.*\)\.qrc$$|\1|'` $< -o $@ - -.qrc.qrc.C: - $(RCC) -name `echo "$<" | sed 's|^.*/\(.*\)\.qrc$$|\1|'` $< -o $@ - -qrc_%.cpp: %.qrc - $(RCC) $< -o $@ - -DISTCLEANFILES = $(BUILT_SOURCES) diff --git a/check.mk b/check.mk deleted file mode 100755 index c5882b4494d..00000000000 --- a/check.mk +++ /dev/null @@ -1,501 +0,0 @@ -# This makefile fragment runs the "check-TESTS" target from the generated -# Makefiles. 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Tests have been empirically grouped -# according to time needed to run into short, medium and long sets. -# -# To see the subdirectories with check-TESTS to run, and the test sets do, -# $ make -f check.mk -# or -# $ make -f check.mk list -# -# To run the check-TEST target for an indivudual directory, use the subdirectory name(s) -# as the target(s) to make, -# $ make -f check.mk mri_ca_register -# $ make -j8 -f check.mk mri_ca_register mrisp_write -# -# To run thre predefined groups/lists of tests from below do, -# $ make -f check.mk short <--- runs short length tests serially, ~10-15 mins* -# $ make -f check.mk medium <--- runs medium length tests in parallel with -j8, ~1 hour* -# $ make -f check.mk long <--- runs long length tests in parallel with -j8, more than 1 hour* -# -# A good place to start is with, -# -# $ make -f check.mk short -# -# * machine configuration: -# I7 chip with 4 physcial 3.0 GHz cores (hyperthreading turned on -# to yield 8 virtual cores) with 16GB RAM using an SSD disk for I/O. - -SHELL:=/bin/sh -MAKE:=/usr/bin/make - -ifeq (,$(FREESURFER_HOME)) -$(error Please set FREESURFER_HOME in the environment) -else -$(warning FREESURFER_HOME = $(FREESURFER_HOME)) -endif - -ifeq (,$(SUBJECTS_DIR)) -$(error Please set SUBJECTS_DIR in the environment) -else -$(warning SUBJECTS_DIR = $(SUBJECTS_DIR)) -endif - -ifeq (,$(FS_LICENSE)) -$(error Please set FS_LICENSE in the environment) -else -$(warning FS_LICENSE = $(FS_LICENSE)) -endif - -linux_default_subjects_dir:= -darwin_default_subjects_dir:=/Applications/freesurfer/subjects - -os:=$(shell uname -s | tr -s '[A-Z]' '[a-z]') -ifeq ($(os),linux) - ifeq (,$(SUBJECTS_DIR)) - SUBJECTS_DIR:=$(linux_default_subjects_dir) - endif - platform:=x86_64-$(os) - platform_short:=linux -else ifeq ($(os),darwin) - ifeq (,$(SUBJECTS_DIR)) - SUBJECTS_DIR:=$(darwin_default_subjects_dir) - endif - platform:=i386-mac - platform_short:=mac -else - $(error Cannot build for unknown os = $(os)) -endif - -ifeq (,$(SUBJECTS_DIR)) - $(error Please set SUBJECTS_DIR for $(platform_short) in environment prior to running tests) -endif -ifeq (,$(wildcard $(SUBJECTS_DIR))) - $(error Cannot stat SUBJECTS_DIR=$(SUBJECTS_DIR) for $(platform_short)) -endif -$(warning Using SUBJECTS_DIR=$(SUBJECTS_DIR)) -export SUBJECTS_DIR - -this_makefile:=$(lastword $(MAKEFILE_LIST)) -this_makefile_path:=$(dir $(abspath $(this_makefile))) -# absolute path -# src_base:=$(this_makefile_path) -# relative path (know we are at the top of the tree) -src_base:=. -# $(warning src_base=$(src_base)) - -# get all Makefiles with generated check-TESTS targets -check_tests_dirs:=$(shell find $(src_base) -maxdepth 2 -name Makefile -exec grep "check-TESTS:" {} \; -print | grep Makefile | sed 's;^\.\/;;' | sed 's;\/\/;\/;' | sed 's;\/Makefile;;') -# $(warning check_tests_dirs=$(check_tests_dirs)) - -no_tests:=mris_extract_patches - -# remove anything in no_tests -check_tests_filt1:=$(filter-out $(no_tests),$(check_tests_dirs)) -# $(warning check_test_filt1=$(check_tests_filt1)) - -# manually ran tests to find those that take relatively longer -medium_tests:=mri_aparc2aseg mri_ca_normalize mri_ca_register mri_convert \ - mri_coreg mri_em_register mri_normalize mri_robust_register mris_anatomical_stats \ - mris_ca_label mris_convert mris_curvature mris_expand mris_fix_topology mris_inflate \ - mris_register mris_sphere mris_transform mris_volmask talairach_avi xml2 -# $(warning medium=$(medium_tests)) - -long_tests = mri_ca_label mris_make_surfaces -# $(warning long=$(long_tests)) - -short_tests_filt1:=$(filter-out $(long_tests),$(check_tests_filt1)) -short_tests:=$(filter-out $(medium_tests),$(short_tests_filt1)) - - -.PHONY: list all_dirs -list: - @echo "NO TESTS:" - @echo $(no_tests) | tr -s ' ' '\n' - @echo - @echo "LONG TESTS:" - @echo $(long_tests) | tr -s ' ' '\n' - @echo - @echo "MEDIUM TESTS:" - @echo $(medium_tests) | tr -s ' ' '\n' - @echo - @echo "SHORT TESTS:" - @echo $(short_tests) | tr -s ' ' '\n' -all_dirs: - @echo "ALL check-TEST SUBDIRS:" - @echo $(check_tests_dirs) | tr -s ' ' '\n' - @echo - -# Setup as a target here each subdir with (generated) Makefile contaning check-TEST target. -# For cmake generated check targets, the list of subdirs $(check_tests_dirs) will only contain -# an entry for subdirs with a Makefile contaning that target. So if setup_configure and configure -# are not run to create Makefiles, then the empty list will cause make to exit w/o error (nothing to do). - -.PHONY: $(check_tests_dirs) -$(check_tests_dirs): - @echo "Making \"check-TESTS\" target under $@" - (cd $@ && make && $(MAKE) check-TESTS) - -# do not use := here as {short,medium,long}_tests may be appended to below -make_long_j8=$(MAKE) -k -j8 -f $(this_makefile) $(long_tests) -make_medium_j8=$(MAKE) -k -j8 -f $(this_makefile) $(medium_tests) -make_short_j1=$(MAKE) -k -j1 -f $(this_makefile) $(short_tests) - -.PHONY: long medium short -.PHONY: long_tests medium_tests short_tests -long: - @date - $(make_long_j8) - @date -medium: - @date - $(make_medium_j8) - @date -short: - @date - $(make_short_j1) - @date - -# ========================================================== -# programmed tests for dirs w/o generated check-TESTS target - -# FORCE: - -define test_rule -.PHONY: $(1) -$(1): - @echo - @echo "############ Starting $(1) test ############" - which $(2) && rm -rf $(3) && mkdir -p $(3) -ifeq ("False","$(5)") - (cd $(1) && $(4)) -else ifeq ("True","$(5)") - @echo " >>>>> Test set to force exit status 0 <<<<< " - (cd $(1) && $(4); exit 0) -endif -endef - -define test_rule_no_cd -.PHONY: $(1) -$(1): - @echo - @echo "############ Starting $(1) test ############" - which $(2) && rm -rf $(3) && mkdir -p $(3) -ifeq ("False","$(5)") - $(4) -else ifeq ("True","$(5)") - @echo " >>>>> Test set to force exit status 0 <<<<< " - $(4); exit 0 -endif -endef -# use $SUBJECTS_DIR data already in tree - -local_test_base:=/tmp/test - -# mri_binarize -# -# mri_binarize.bin --i ../mri_ca_label/testdata/mri/aseg.mgz --o /tmp/test/mri_binarize/mri_binarize.mgz --match 17 -define test_mri_binarize -binarize_name := $1 -binarize_prog := $$(binarize_name).bin -binarize_input := ../mri_ca_label/testdata/mri/aseg.mgz --match 17 -binarize_output_dir := $(local_test_base)/$$(binarize_name) -binarize_output_file := $$(binarize_output_dir)/$$(binarize_name).mgz -binarize_cmd := $$(binarize_prog) --i $$(binarize_input) --o $$(binarize_output_dir)/$$(binarize_output_file) -binarize_force_exit_zero := False -$(call test_rule,$$(binarize_name),$$(binarize_prog),$$(binarize_output_dir),$$(binarize_cmd),$$(binarize_force_exit_zero)) -endef -short_tests += mri_binarize - -# mri_annotation2label -# -# mri_annotation2label --subject bert --hemi rh --labelbase /tmp/test/mri_annotation2label/labels/aparc-rh - -define test_mri_annotation2label -anntl_name := $1 -anntl_prog := $$(anntl_name) -anntl_input := --subject bert --hemi rh --labelbase -anntl_output_dir := $(local_test_base)/$$(anntl_name)/labels -anntl_output_file := -anntl_cmd := $$(anntl_prog) $$(anntl_input) $$(anntl_output_dir)/aparc-rh -anntl_force_exit_zero := False -$(call test_rule,$$(anntl_name),$$(anntl_prog),$$(anntl_output_dir),$$(anntl_cmd),$$(anntl_force_exit_zero)) -endef -short_tests += mri_annotation2label - -# mri_concat -# -# mri_concat $SUBJECTS_DIR/fsaverage_sym/std.rh.*.mgh --o /tmp/rhout.mgh - -define test_mri_concat -concat_name := $1 -concat_prog := $$(concat_name) -concat_input := $(SUBJECTS_DIR)/fsaverage_sym/surf/std.rh.*.mgh -concat_output_dir := $(local_test_base)/$$(concat_name) -concat_output_file := rhout.mgh -concat_cmd := $$(concat_prog) $$(concat_input) --o $$(concat_output_dir)/$$(concat_output_file) -concat_force_exit_zero := False -$(call test_rule,$$(concat_name),$$(concat_prog),$$(concat_output_dir),$$(concat_cmd),$$(concat_force_exit_zero)) -endef -short_tests += mri_concat - -# mri_diff -# -# mri_diff ./fsaverage_sym/mri/lh.ribbon.mgz ./fsaverage_sym/mri/rh.ribbon.mgz --log /tmp/diff1 - -define test_mri_diff -diff_name := $1 -diff_prog := $$(diff_name) -diff_input := $(SUBJECTS_DIR)/fsaverage_sym/mri/lh.ribbon.mgz $(SUBJECTS_DIR)/fsaverage_sym/mri/rh.ribbon.mgz -diff_output_dir := $(local_test_base)/$$(diff_name) -diff_output_file := diff_lh_and_rh_ribbon -diff_cmd := $$(diff_prog) $$(diff_input) --log $$(diff_output_dir)/$$(diff_output_file) -diff_force_exit_zero := True -$(call test_rule,$$(diff_name),$$(diff_prog),$$(diff_output_dir),$$(diff_cmd),$$(diff_force_exit_zero)) -endef -short_tests += mri_diff - -# mri_fuse_segmentations - -# mri_info -# -# find $SUBJECTS_DIR -name "*.mgz" -exec mri_info {} \; - -define test_mri_info -info_name := $1 -info_prog := $$(info_name) -info_input := $(SUBJECTS_DIR) -name "*.mgz" -exec $$(info_name) {} \; -info_output_dir := $(local_test_base)/$$(info_name) -info_output_file := mri_info_output -info_cmd := find $$(info_input) -info_force_exit_zero := False -$(call test_rule,$$(info_name),$$(info_prog),$$(info_output_dir),$$(info_cmd),$$(info_force_exit_zero)) -endef -short_tests += mri_info - -# mri_label2label -# -# mri_label2label --srclabel $SUBJECTS_DIR/bert/label/lh.BA1_exvivo.label --srcsubject bert --trglabel $SUBJECTS_DIR /cvs_avg35/label/lh.BA1.label --trgsubject cvs_avg35 --regmethod surface --hemi lh - -define test_mri_label2label -l2l_name := $1 -l2l_prog := $$(l2l_name) -l2l_input := --srclabel $(SUBJECTS_DIR)/bert/label/lh.BA1_exvivo.label --srcsubject bert --trglabel $(SUBJECTS_DIR)/cvs_avg35/label/lh.BA1.label --trgsubject cvs_avg35 --regmethod surface --hemi lh -l2l_output_dir := $(local_test_base)/$$(l2l_name) -l2l_output_file := l2l_lh_and_rh_ribbon -l2l_cmd := $$(l2l_prog) $$(l2l_input) -l2l_force_exit_zero := False -$(call test_rule,$$(l2l_name),$$(l2l_prog),$$(l2l_output_dir),$$(l2l_cmd),$$(l2l_force_exit_zero)) -endef -short_tests += mri_label2label - -# mri label2vol -# -# mri_label2vol --label $SUBJECTS_DIR/bert/label/lh.cortex.label --regheader $SUBJECTS_DIR/bert/mri/rawavg.mgz --temp $SUBJECTS_DIR/bert/mri/aparc+aseg.mgz --o /tmp/l2v.nii - -define test_mri_label2vol -l2v_name := $1 -l2v_prog := $$(l2v_name) -l2v_input := --label $(SUBJECTS_DIR)/bert/label/lh.cortex.label --regheader $(SUBJECTS_DIR)/bert/mri/rawavg.mgz --temp $(SUBJECTS_DIR)/bert/mri/aparc+aseg.mgz -l2v_output_dir := $(local_test_base)/$$(l2v_name) -l2v_output_file := l2v.nii -l2v_cmd := $$(l2v_prog) $$(l2v_input) --o $$(l2v_output_dir)/$$(l2v_output_file) -l2v_force_exit_zero := False -$(call test_rule,$$(l2v_name),$$(l2v_prog),$$(l2v_output_dir),$$(l2v_cmd),$$(l2v_force_exit_zero)) -endef -short_tests += mri_label2vol - -# mri_log_likelihood - -# mri_matrix_multiply -# -# mri_matrix_multiply -im $SUBJECTS_DIR/bert/mri/transforms/talairach.xfm -im $SUBJECTS_DIR/cvs_avg35/mri/transforms/talairach.xfm -v -om /tmp/mmult.xfm - -define test_mri_matrix_multiply -mmult_name := $1 -mmult_prog := $$(mmult_name) -mmult_input_1 := $(SUBJECTS_DIR)/bert/mri/transforms/talairach.xfm -mmult_input_2 := $(SUBJECTS_DIR)/cvs_avg35/mri/transforms/talairach.xfm -mmult_input := -v -im $$(mmult_input_1) -im $$(mmult_input_2) -mmult_output_dir := $(local_test_base)/$$(mmult_name) -mmult_output_file := mmult.xfm -mmult_result := $$(mmult_output_dir)/$$(mmult_output_file) -# output switch is -om ! -mmult_cmd := cat $$(mmult_input_1) && cat $$(mmult_input_2) && $$(mmult_prog) $$(mmult_input) -om $$(mmult_result) && cat $$(mmult_result) -mmult_force_exit_zero := False -$(call test_rule,$$(mmult_name),$$(mmult_prog),$$(mmult_output_dir),$$(mmult_cmd),$$(mmult_force_exit_zero)) -endef -short_tests += mri_matrix_multiply - -# mri_normalize_tp2 - -# mri_nu_correct.mni -# -# mri_nu_correct.mni --no-rescale --i $SUBJECTS_DIR/bert/mri/orig.mgz --proto-iters 1000 --distance 50 --o /tmp/orig_nu.mgz - -define test_mri_nu_correct.mni -mncm_name := $1 -mncm_prog := $$(mncm_name) -mncm_input := --no-rescale --i $(SUBJECTS_DIR)/bert/mri/orig.mgz --proto-iters 1000 --distance 50 -mncm_output_dir := $(local_test_base)/$$(mncm_name) -mncm_output_file := orig_nu.mgz -mncm_result := $$(mncm_output_dir)/$$(mncm_output_file) -mncm_cmd := $$(mncm_prog) $$(mncm_input) --o $$(mncm_result) -mncm_force_exit_zero := False -# no such subdir as mri_nu_correct.mni -$(call test_rule_no_cd,$$(mncm_name),$$(mncm_prog),$$(mncm_output_dir),$$(mncm_cmd),$$(mncm_force_exit_zero)) -endef -short_tests += mri_nu_correct.mni - -# mri_pretess -# -# mri_pretess -test -w $SUBJECTS_DIR/bert/mri/wm.mgz wm $SUBJECTS_DIR/bert/mri/norm.mgz /tmp/wm_new.mgz - -define test_mri_pretess -mrip_name := $1 -mrip_prog := $$(mrip_name) -mrip_input := -test -w $(SUBJECTS_DIR)/bert/mri/wm.mgz wm $(SUBJECTS_DIR)/bert/mri/norm.mgz -mrip_output_dir := $(local_test_base)/$$(mrip_name) -mrip_output_file := wm_new.mgz -mrip_result := $$(mrip_output_dir)/$$(mrip_output_file) -mrip_cmd := $$(mrip_prog) $$(mrip_input) --o $$(mrip_result) -mrip_force_exit_zero := False -$(call test_rule_no_cd,$$(mrip_name),$$(mrip_prog),$$(mrip_output_dir),$$(mrip_cmd),$$(mrip_force_exit_zero)) -endef -short_tests += mri_pretess - -# mri_relabel_hypointensities -# -# mri_relabel_hypointensities $SUBJECTS_DIR/bert/mri/aseg.presurf.mgz $SUBJECTS_DIR/bert/surf /tmp/aseg_hypoint_out.mgz - -define test_mri_relabel_hypointensities -mrrhypo_name := $1 -mrrhypo_prog := $$(mrrhypo_name) -mrrhypo_input := $(SUBJECTS_DIR)/bert/mri/aseg.presurf.mgz $(SUBJECTS_DIR)/bert/surf -mrrhypo_output_dir := $(local_test_base)/$$(mrrhypo_name) -mrrhypo_output_file := aseg_hypoint_out.mgz -mrrhypo_result := $$(mrrhypo_output_dir)/$$(mrrhypo_output_file) -# no --o switch for output -mrrhypo_cmd := $$(mrrhypo_prog) $$(mrrhypo_input) $$(mrrhypo_result) -mrrhypo_force_exit_zero := False -$(call test_rule_no_cd,$$(mrrhypo_name),$$(mrrhypo_prog),$$(mrrhypo_output_dir),$$(mrrhypo_cmd),$$(mrrhypo_force_exit_zero)) -endef -short_tests += mri_relabel_hypointensities - -# mri_relabel_nonwm_hypos - -# mri_robust_template -# -# Note addition of --debug generates output saying no permission to write (but not where), and exist status still zero -# Has exxample output for registration of TP1 to TP2 -# -# mri_robust_template --debug -mov $SUBJECTS_DIR/bert/mri/orig/001.mgz $SUBJECTS_DIR/bert/mri/orig/002.mgz --average 1 --template /tmp/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --subsample 200 - -define test_mri_robust_template -mrt_name := $1 -mrt_prog := $$(mrt_name) -mrt_input := --debug -mov $(SUBJECTS_DIR)/bert/mri/orig/001.mgz $(SUBJECTS_DIR)/bert/mri/orig/002.mgz --average 1 --satit --inittp 1 --fixtp --noit --iscale --subsample 200 -mrt_output_dir := $(local_test_base)/$$(mrt_name) -mrt_output_file := rawavg.mgz -mrt_result := $$(mrt_output_dir)/$$(mrt_output_file) -# no --o switch for output -mrt_cmd := $$(mrt_prog) $$(mrt_input) --template $$(mrt_result) -mrt_force_exit_zero := False -$(call test_rule_no_cd,$$(mrt_name),$$(mrt_prog),$$(mrt_output_dir),$$(mrt_cmd),$$(mrt_force_exit_zero)) -endef -short_tests += mri_robust_template - -# mri_seg_diff -# -# mri_seg_diff --debug --seg1 $SUBJECTS_DIR/bert/mri/aseg.auto.mgz --seg2 $SUBJECTS_DIR/bert/mri/aseg.mgz --diff /tmp/aseg_diff_out.mgz - -define test_mri_seg_diff -msd_name := $1 -msd_prog := $$(msd_name) -msd_input := --debug --seg1 $(SUBJECTS_DIR)/bert/mri/aseg.auto.mgz --seg2 $(SUBJECTS_DIR)/bert/mri/aseg.mgz -msd_output_dir := $(local_test_base)/$$(msd_name) -msd_output_file := aseg_diff_out.mgz -msd_result := $$(msd_output_dir)/$$(msd_output_file) -# no --o switch for output -msd_cmd := $$(msd_prog) $$(msd_input) --diff $$(msd_result) -msd_force_exit_zero := False -$(call test_rule_no_cd,$$(msd_name),$$(msd_prog),$$(msd_output_dir),$$(msd_cmd),$$(msd_force_exit_zero)) -endef -short_tests += mri_seg_diff - -# mri_segment -# -# mri_segment $SUBJECTS_DIR/bert/mri/brainmask.mgz /tmp/wm_segment_out.mgz -wlo 80 - -define test_mri_segment -mseg_name := $1 -mseg_prog := $$(mseg_name) -mseg_input := $(SUBJECTS_DIR)/bert/mri/brainmask.mgz -mseg_output_dir := $(local_test_base)/$$(mseg_name) -mseg_output_file := wm_segment_out.mgz -mseg_result := $$(mseg_output_dir)/$$(mseg_output_file) -# no --o switch for output, cannot re-order -wlo 80 to be before output volume -mseg_cmd := $$(mseg_prog) $$(mseg_input) $$(mseg_result) -wlo 80 -mseg_force_exit_zero := False -$(call test_rule_no_cd,$$(mseg_name),$$(mseg_prog),$$(mseg_output_dir),$$(mseg_cmd),$$(mseg_force_exit_zero)) -endef -short_tests += mri_segment - -# mri_stats2seg - -# mri_surf2surf -# fails... -# mri_surf2surf --hemi lh --srcsubject bert --srcsurfval thickness --src_type curv --trgsubject bert --trgicoorder 7 --trgsurfval /tmp/bert-thickness-lh.img --trg_type analyze4d - -define test_mri_surf2surf -ms2s_name := $1 -ms2s_prog := $$(ms2s_name) -ms2s_input := --hemi lh --srcsubject bert --srcsurfval thickness --src_type curv --trgsubject bert --trgicoorder 7 --trg_type analyze4d -ms2s_output_dir := $(local_test_base)/$$(ms2s_name) -ms2s_output_file := bert-thickness-lh.img -ms2s_result := $$(ms2s_output_dir)/$$(ms2s_output_file) -# no --o switch for output -ms2s_cmd := $$(ms2s_prog) $$(ms2s_input) --trgsurfval $$(ms2s_result) -ms2s_force_exit_zero := False -$(call test_rule_no_cd,$$(ms2s_name),$$(ms2s_prog),$$(ms2s_output_dir),$$(ms2s_cmd),$$(ms2s_force_exit_zero)) -endef -short_tests += mri_surf2surf - -# mri_surf2vol - -# mri_surfcluster - -# mri_vol2surf - -# mri_voltovol - -# mri_voldiff - -# mris_diff - -# mris_divide_parcellation - -# mris_label2annot - -# mris_surface_stats - -# mris_thickness - -# mris_thickness_diff - -# mris_topo_fixer - -# pctsurfcon - -# vertexvol - -added_dirs = mri_binarize mri_annotation2label mri_concat mri_diff mri_info mri_label2label mri_label2vol mri_matrix_multiply mri_nu_correct.mni mri_pretess mri_relabel_hypointensities mri_robust_template mri_seg_diff mri_segment mri_surf2surf -# added_dirs = mri_surf2surf - -.PHONY: $(added_dirs) -# create rules for test functions written above -$(foreach dir,$(added_dirs),$(eval $(call test_$(dir),$(dir)))) -# for now, adding in tests with functions above to short tests (as don't take too long) -short_tests += $(added_dirs) -# $(warning short=$(short_tests)) - diff --git a/check_siemens_dir/Makefile.am b/check_siemens_dir/Makefile.am deleted file mode 100644 index 373116f6ce7..00000000000 --- a/check_siemens_dir/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -# Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = check_siemens_dir -check_siemens_dir_SOURCES=check_siemens_dir.c -check_siemens_dir_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -check_siemens_dir_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/config/install-sh b/config/install-sh deleted file mode 100755 index 11870f1b019..00000000000 --- a/config/install-sh +++ /dev/null @@ -1,251 +0,0 @@ -#!/bin/sh -# -# install - install a program, script, or datafile -# This comes from X11R5 (mit/util/scripts/install.sh). -# -# Copyright 1991 by the Massachusetts Institute of Technology -# -# Permission to use, copy, modify, distribute, and sell this software and its -# documentation for any purpose is hereby granted without fee, provided that -# the above copyright notice appear in all copies and that both that -# copyright notice and this permission notice appear in supporting -# documentation, and that the name of M.I.T. not be used in advertising or -# publicity pertaining to distribution of the software without specific, -# written prior permission. M.I.T. makes no representations about the -# suitability of this software for any purpose. It is provided "as is" -# without express or implied warranty. -# -# Calling this script install-sh is preferred over install.sh, to prevent -# `make' implicit rules from creating a file called install from it -# when there is no Makefile. -# -# This script is compatible with the BSD install script, but was written -# from scratch. It can only install one file at a time, a restriction -# shared with many OS's install programs. - - -# set DOITPROG to echo to test this script - -# Don't use :- since 4.3BSD and earlier shells don't like it. -doit="${DOITPROG-}" - - -# put in absolute paths if you don't have them in your path; or use env. vars. - -mvprog="${MVPROG-mv}" -cpprog="${CPPROG-cp}" -chmodprog="${CHMODPROG-chmod}" -chownprog="${CHOWNPROG-chown}" -chgrpprog="${CHGRPPROG-chgrp}" -stripprog="${STRIPPROG-strip}" -rmprog="${RMPROG-rm}" -mkdirprog="${MKDIRPROG-mkdir}" - -transformbasename="" -transform_arg="" -instcmd="$mvprog" -chmodcmd="$chmodprog 0755" -chowncmd="" -chgrpcmd="" -stripcmd="" -rmcmd="$rmprog -f" -mvcmd="$mvprog" -src="" -dst="" -dir_arg="" - -while [ x"$1" != x ]; do - case $1 in - -c) instcmd="$cpprog" - shift - continue;; - - -d) dir_arg=true - shift - continue;; - - -m) chmodcmd="$chmodprog $2" - shift - shift - continue;; - - -o) chowncmd="$chownprog $2" - shift - shift - continue;; - - -g) chgrpcmd="$chgrpprog $2" - shift - shift - continue;; - - -s) stripcmd="$stripprog" - shift - continue;; - - -t=*) transformarg=`echo $1 | sed 's/-t=//'` - shift - continue;; - - -b=*) transformbasename=`echo $1 | sed 's/-b=//'` - shift - continue;; - - *) if [ x"$src" = x ] - then - src=$1 - else - # this colon is to work around a 386BSD /bin/sh bug - : - dst=$1 - fi - shift - continue;; - esac -done - -if [ x"$src" = x ] -then - echo "install: no input file specified" - exit 1 -else - : -fi - -if [ x"$dir_arg" != x ]; then - dst=$src - src="" - - if [ -d $dst ]; then - instcmd=: - chmodcmd="" - else - instcmd=$mkdirprog - fi -else - -# Waiting for this to be detected by the "$instcmd $src $dsttmp" command -# might cause directories to be created, which would be especially bad -# if $src (and thus $dsttmp) contains '*'. - - if [ -f "$src" ] || [ -d "$src" ] - then - : - else - echo "install: $src does not exist" - exit 1 - fi - - if [ x"$dst" = x ] - then - echo "install: no destination specified" - exit 1 - else - : - fi - -# If destination is a directory, append the input filename; if your system -# does not like double slashes in filenames, you may need to add some logic - - if [ -d $dst ] - then - dst="$dst"/`basename $src` - else - : - fi -fi - -## this sed command emulates the dirname command -dstdir=`echo $dst | sed -e 's,[^/]*$,,;s,/$,,;s,^$,.,'` - -# Make sure that the destination directory exists. -# this part is taken from Noah Friedman's mkinstalldirs script - -# Skip lots of stat calls in the usual case. -if [ ! -d "$dstdir" ]; then -defaultIFS=' - ' -IFS="${IFS-${defaultIFS}}" - -oIFS="${IFS}" -# Some sh's can't handle IFS=/ for some reason. -IFS='%' -set - `echo ${dstdir} | sed -e 's@/@%@g' -e 's@^%@/@'` -IFS="${oIFS}" - -pathcomp='' - -while [ $# -ne 0 ] ; do - pathcomp="${pathcomp}${1}" - shift - - if [ ! -d "${pathcomp}" ] ; - then - $mkdirprog "${pathcomp}" - else - : - fi - - pathcomp="${pathcomp}/" -done -fi - -if [ x"$dir_arg" != x ] -then - $doit $instcmd $dst && - - if [ x"$chowncmd" != x ]; then $doit $chowncmd $dst; else : ; fi && - if [ x"$chgrpcmd" != x ]; then $doit $chgrpcmd $dst; else : ; fi && - if [ x"$stripcmd" != x ]; then $doit $stripcmd $dst; else : ; fi && - if [ x"$chmodcmd" != x ]; then $doit $chmodcmd $dst; else : ; fi -else - -# If we're going to rename the final executable, determine the name now. - - if [ x"$transformarg" = x ] - then - dstfile=`basename $dst` - else - dstfile=`basename $dst $transformbasename | - sed $transformarg`$transformbasename - fi - -# don't allow the sed command to completely eliminate the filename - - if [ x"$dstfile" = x ] - then - dstfile=`basename $dst` - else - : - fi - -# Make a temp file name in the proper directory. - - dsttmp=$dstdir/#inst.$$# - -# Move or copy the file name to the temp name - - $doit $instcmd $src $dsttmp && - - trap "rm -f ${dsttmp}" 0 && - -# and set any options; do chmod last to preserve setuid bits - -# If any of these fail, we abort the whole thing. If we want to -# ignore errors from any of these, just make sure not to ignore -# errors from the above "$doit $instcmd $src $dsttmp" command. - - if [ x"$chowncmd" != x ]; then $doit $chowncmd $dsttmp; else :;fi && - if [ x"$chgrpcmd" != x ]; then $doit $chgrpcmd $dsttmp; else :;fi && - if [ x"$stripcmd" != x ]; then $doit $stripcmd $dsttmp; else :;fi && - if [ x"$chmodcmd" != x ]; then $doit $chmodcmd $dsttmp; else :;fi && - -# Now rename the file to the real destination. - - $doit $rmcmd -f $dstdir/$dstfile && - $doit $mvcmd $dsttmp $dstdir/$dstfile - -fi && - - -exit 0 diff --git a/config/mkinstalldirs b/config/mkinstalldirs deleted file mode 100755 index 8ab885ec92d..00000000000 --- a/config/mkinstalldirs +++ /dev/null @@ -1,99 +0,0 @@ -#! /bin/sh -# mkinstalldirs --- make directory hierarchy -# Author: Noah Friedman -# Created: 1993-05-16 -# Public domain - -errstatus=0 -dirmode="" - -usage="\ -Usage: mkinstalldirs [-h] [--help] [-m mode] dir ..." - -# process command line arguments -while test $# -gt 0 ; do - case "${1}" in - -h | --help | --h* ) # -h for help - echo "${usage}" 1>&2; exit 0 ;; - -m ) # -m PERM arg - shift - test $# -eq 0 && { echo "${usage}" 1>&2; exit 1; } - dirmode="${1}" - shift ;; - -- ) shift; break ;; # stop option processing - -* ) echo "${usage}" 1>&2; exit 1 ;; # unknown option - * ) break ;; # first non-opt arg - esac -done - -for file -do - if test -d "$file"; then - shift - else - break - fi -done - -case $# in -0) exit 0 ;; -esac - -case $dirmode in -'') - if mkdir -p -- . 2>/dev/null; then - echo "mkdir -p -- $*" - exec mkdir -p -- "$@" - fi ;; -*) - if mkdir -m "$dirmode" -p -- . 2>/dev/null; then - echo "mkdir -m $dirmode -p -- $*" - exec mkdir -m "$dirmode" -p -- "$@" - fi ;; -esac - -for file -do - set fnord `echo ":$file" | sed -ne 's/^:\//#/;s/^://;s/\// /g;s/^#/\//;p'` - shift - - pathcomp= - for d - do - pathcomp="$pathcomp$d" - case "$pathcomp" in - -* ) pathcomp=./$pathcomp ;; - esac - - if test ! -d "$pathcomp"; then - echo "mkdir $pathcomp" - - mkdir "$pathcomp" || lasterr=$? - - if test ! -d "$pathcomp"; then - errstatus=$lasterr - else - if test ! -z "$dirmode"; then - echo "chmod $dirmode $pathcomp" - - lasterr="" - chmod "$dirmode" "$pathcomp" || lasterr=$? - - if test ! -z "$lasterr"; then - errstatus=$lasterr - fi - fi - fi - fi - - pathcomp="$pathcomp/" - done -done - -exit $errstatus - -# Local Variables: -# mode: shell-script -# sh-indentation: 3 -# End: -# mkinstalldirs ends here diff --git a/configure.in b/configure.in deleted file mode 100644 index 2b9769c1f03..00000000000 --- a/configure.in +++ /dev/null @@ -1,4358 +0,0 @@ -######################################################################## -# -# -*- Autoconf -*- -# configure.in -# by y.tosa -# June 17, 2004 -# -# Process this file with autoconf to produce a configure script. -# See https://devmanual.gentoo.org/general-concepts/autotools/index.html -# -# CVS Revision Info: -# $Author: ah221 $ -# $Date: 2017/02/14 22:38:31 $ -# $Revision: 1.681 $ -# -######################################################################## -AC_PREREQ(2.57) -AC_INIT(Freesurfer, dev, freesurfer@nmr.mgh.harvard.edu) -# if $FREESURFER_HOME is defined, then use that as default install dir: -if test ! 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then - LIB_BLAS="/usr/lib/libblas.a" - fi -fi -AC_SUBST(LIB_BLAS) - -LIB_LAPACK="" -if test -e /usr/local/lib/liblapack.a ; then - LIB_LAPACK="/usr/local/lib/liblapack.a" -elif test -e /usr/lib/liblapack.a ; then - LIB_LAPACK="/usr/lib/liblapack.a" -elif test -e /usr/lib64/liblapack.a ; then - LIB_LAPACK="/usr/lib64/liblapack.a" -elif test -e /usr/lib/lapack/liblapack.a ; then - LIB_LAPACK="/usr/lib/lapack/liblapack.a" -fi -if test "$host" = "powerpc64-suse-linux"; then - if test -e /usr/lib/liblapack.a ; then - LIB_LAPACK="/usr/lib/liblapack.a" - fi -fi -AC_SUBST(LIB_LAPACK) - - -################################################################ -# Most of our scripts use /bin/tcsh, so make sure it exists -################################################################ -AC_CHECK_FILE(/bin/tcsh,[], - [AC_MSG_ERROR([FATAL: /bin/tcsh is required!])]) - -# links with g++ rather than gcc (and check for Intel and AMD Compilers) -# first use $CXX if passed -CCLD=$CXX -if test "x$CCLD" = "x"; 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"$ac_vxl_libraries" = "NO"; then - VXL_LIBS=-L$ac_vxl_libraries - VXL_LIB=$ac_vxl_libraries -fi - -# these are the VXL libs used by freesurfer: -LIBS_VXL="-lvnl_algo -lvnl -lvcl -lnetlib -lv3p_netlib" - -AC_SUBST(VXL_CFLAGS) -AC_SUBST(VXL_LIBS) -AC_SUBST(VXL_LIB) -AC_SUBST(LIBS_VXL) - - -################################################################ -# PETSc -################################################################ -ac_petsc_includes="NO" -ac_petsc_libraries="NO" -ac_petsc_bindir="NO" -ac_petsc_dir="NO" -PETSC_CFLAGS="" -PETSC_LIBS="" -PETSC_LIB="" -PETSC_DIR="" - -AC_MSG_CHECKING(PETSc directory) - -AC_ARG_WITH(petsc-dir, - [ --with-petsc-dir=DIR where the root of PETSc is installed.], - [ petsc_i="$withval"/include - ac_petsc_includes="$petsc_i" - ac_petsc_libraries="$withval"/lib - ac_petsc_bindir="$withval"/bin - ac_petsc_dir="$withval" - PETSC_DIR="$withval" - AC_SUBST(PETSC_DIR) - ]) - -if test "x$PETSC_DIR" = "x"; then - # if a PETSC root was not supplied, but one exists in the - # default packages path at the NMR Center, then use that: - if test -d "${PACKAGES_DIR}/petsc/current" ; then - withval=${PACKAGES_DIR}/petsc/current - PETSC_DIR="$withval" - ac_petsc_dir="$withval" - petsc_i="$withval"/include - ac_petsc_includes="$petsc_i" - ac_petsc_libraries="$withval"/lib - fi -fi - -AC_ARG_WITH(petsc-include, - [ --with-petsc-include=DIR root of PETSc include directory.], - [ ac_petsc_includes="$withval" - ]) - -AC_ARG_WITH(petsc-libraries, - [ --with-petsc-libraries=DIR root of PETSc lib directory.], - [ ac_petsc_libraries="$withval" - ]) - -if test ! "$ac_petsc_includes" = "NO"; then - AC_MSG_RESULT(PETSc directory is $withval) - for item in $ac_petsc_includes; do - PETSC_CFLAGS="${PETSC_CFLAGS} -I${item}" - done - PETSC_DIR=$ac_petsc_dir -else - AC_MSG_RESULT(PETSc directory is not supplied) -fi - -if test ! 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"$ac_mpi_includes" = "NO"; then - AC_MSG_RESULT(MPI directory is $withval) - MPI_CFLAGS=-I$ac_mpi_includes - MPI_DIR=$ac_mpi_dir -else - AC_MSG_RESULT(MPI directory is not supplied) -fi - -if test ! 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"$ac_vtk_includes" = "NO"; then - AC_MSG_RESULT(VTK directory is $withval) - if test -e $ac_vtk_includes/vtk-5.10 ; then - ac_vtk_includes="$ac_vtk_includes/vtk-5.10" - elif test -e $ac_vtk_includes/vtk-5.6 ; then - ac_vtk_includes="$ac_vtk_includes/vtk-5.6" - elif test -e $ac_vtk_includes/vtk-5.5 ; then - ac_vtk_includes="$ac_vtk_includes/vtk-5.5" - elif test -e $ac_vtk_includes/vtk-5.4 ; then - ac_vtk_includes="$ac_vtk_includes/vtk-5.4" - elif test -e $ac_vtk_includes/vtk-5.3 ; then - ac_vtk_includes="$ac_vtk_includes/vtk-5.3" - elif test -e $ac_vtk_includes/vtk-5.2 ; then - ac_vtk_includes="$ac_vtk_includes/vtk-5.2" - elif test -e $ac_vtk_includes/vtk-5.1 ; then - ac_vtk_includes="$ac_vtk_includes/vtk-5.1" - elif test -e $ac_vtk_includes/vtk-5.0 ; then - ac_vtk_includes="$ac_vtk_includes/vtk-5.0" - elif test -e $ac_vtk_includes/vtk ; then - ac_vtk_includes="$ac_vtk_includes/vtk" - fi - VTK_CFLAGS="${VTK_CFLAGS} -I$ac_vtk_includes" - VTK_CXXFLAGS="${VTK_CXXFLAGS} -I$ac_vtk_includes" -fi - -if test ! "$ac_vtk_libraries" = "NO"; then - VTK_LIBS=-L$ac_vtk_libraries - VTK_LIB=$ac_vtk_libraries - if test -e $ac_vtk_libraries/vtk-5.10 ; then - VTK_LIB_VTK="$ac_vtk_libraries/vtk-5.10" - VTK_LIBS=-L$ac_vtk_libraries/vtk-5.10 - VTK_LIB=$ac_vtk_libraries/vtk-5.10 - elif test -e $ac_vtk_libraries/vtk-5.6 ; then - VTK_LIB_VTK="$ac_vtk_libraries/vtk-5.6" - VTK_LIBS=-L$ac_vtk_libraries/vtk-5.6 - VTK_LIB=$ac_vtk_libraries/vtk-5.6 - elif test -e $ac_vtk_libraries/vtk-5.5 ; then - VTK_LIB_VTK="$ac_vtk_libraries/vtk-5.5" - VTK_LIBS=-L$ac_vtk_libraries/vtk-5.5 - VTK_LIB=$ac_vtk_libraries/vtk-5.5 - elif test -e $ac_vtk_libraries/vtk-5.4 ; then - VTK_LIB_VTK="$ac_vtk_libraries/vtk-5.4" - VTK_LIBS=-L$ac_vtk_libraries/vtk-5.4 - VTK_LIB=$ac_vtk_libraries/vtk-5.4 - elif test -e $ac_vtk_libraries/vtk-5.3 ; then - VTK_LIB_VTK="$ac_vtk_libraries/vtk-5.3" - VTK_LIBS=-L$ac_vtk_libraries/vtk-5.3 - VTK_LIB=$ac_vtk_libraries/vtk-5.3 - elif test -e $ac_vtk_libraries/vtk-5.2 ; then - VTK_LIB_VTK="$ac_vtk_libraries/vtk-5.2" - VTK_LIBS=-L$ac_vtk_libraries/vtk-5.2 - VTK_LIB=$ac_vtk_libraries/vtk-5.2 - elif test -e $ac_vtk_libraries/vtk-5.1 ; then - VTK_LIB_VTK="$ac_vtk_libraries/vtk-5.1" - elif test -e $ac_vtk_libraries/vtk-5.0 ; then - VTK_LIB_VTK="$ac_vtk_libraries/vtk-5.0" - elif test -e $ac_vtk_libraries/vtk ; then - VTK_LIB_VTK="$ac_vtk_libraries/vtk" - fi -fi - -AM_CONDITIONAL(HAVE_VTK_LIBS, test ! "x$VTK_DIR" = "x") - -AC_SUBST(VTK_CFLAGS) -AC_SUBST(VTK_CXXFLAGS) -AC_SUBST(VTK_LIBS) -AC_SUBST(VTK_LIB) -AC_SUBST(VTK_LIB_VTK) -AC_SUBST(VTK_DIR) - - -################################################################ -# VTK for Freeview in Mac -################################################################ -# This is a static build of Cocoa VTK because KWWidgets doesn't play -# nice with this VTK. Hence different VTK for different things -ac_vtk_cocoa_includes="NO" -ac_vtk_cocoa_libraries="NO" -ac_vtk_cocoa_dir="NO" -VTK_COCOA_CFLAGS="" -VTK_COCOA_CXXFLAGS="" -VTK_COCOA_LIBS="" -VTK_COCOA_LIB="" -VTK_COCOA_LIB_VTK="" -VTK_COCOA_DIR="" - -AC_MSG_CHECKING(Cocoa VTK config) - -AC_ARG_WITH(vtk-cocoa-dir, - [ --with-vtk-cocoa-dir=DIR where the root of VTK is installed.], - [ ac_vtk_cocoa_includes="$withval/include" - ac_vtk_cocoa_libraries="$withval"/lib - ac_vtk_cocoa_dir="$withval" - VTK_COCOA_DIR=$ac_vtk_cocoa_dir - ]) - -if test ! "$disable_gui_build" = "YES"; then - if test "x$VTK_COCOA_DIR" = "x"; then - # if a VTK cocoa root was not supplied, but one exists in the - # default packages path at the NMR Center, then use that: - if test -d "${PACKAGES_DIR}/vtk/5.6.1_cocoa" ; then - withval=${PACKAGES_DIR}/vtk/5.6.1_cocoa - ac_vtk_cocoa_includes="$withval/include" - ac_vtk_cocoa_libraries="$withval"/lib - ac_vtk_cocoa_dir="$withval" - VTK_COCOA_DIR=$ac_vtk_cocoa_dir - fi - fi -fi - -if test ! "$ac_vtk_cocoa_includes" = "NO"; then - AC_MSG_RESULT(VTK cocoa directory is $withval) - if test -e $ac_vtk_cocoa_includes/vtk-5.10 ; then - ac_vtk_cocoa_includes="$ac_vtk_cocoa_includes/vtk-5.10" - elif test -e $ac_vtk_cocoa_includes/vtk-5.6 ; then - ac_vtk_cocoa_includes="$ac_vtk_cocoa_includes/vtk-5.6" - elif test -e $ac_vtk_cocoa_includes/vtk-5.5 ; then - ac_vtk_cocoa_includes="$ac_vtk_cocoa_includes/vtk-5.5" - elif test -e $ac_vtk_cocoa_includes/vtk-5.4 ; then - ac_vtk_cocoa_includes="$ac_vtk_cocoa_includes/vtk-5.4" - elif test -e $ac_vtk_cocoa_includes/vtk-5.3 ; then - ac_vtk_cocoa_includes="$ac_vtk_cocoa_includes/vtk-5.3" - elif test -e $ac_vtk_cocoa_includes/vtk-5.2 ; then - ac_vtk_cocoa_includes="$ac_vtk_cocoa_includes/vtk-5.2" - elif test -e $ac_vtk_cocoa_includes/vtk-5.1 ; then - ac_vtk_cocoa_includes="$ac_vtk_cocoa_includes/vtk-5.1" - elif test -e $ac_vtk_cocoa_includes/vtk-5.0 ; then - ac_vtk_cocoa_includes="$ac_vtk_cocoa_includes/vtk-5.0" - elif test -e $ac_vtk_cocoa_includes/vtk ; then - ac_vtk_cocoa_includes="$ac_vtk_cocoa_includes/vtk" - fi - VTK_COCOA_CFLAGS="${VTK_COCOA_CFLAGS} -I$ac_vtk_cocoa_includes" - VTK_COCOA_CXXFLAGS="${VTK_COCOA_CXXFLAGS} -I$ac_vtk_cocoa_includes" -fi - -if test ! "$ac_vtk_libraries" = "NO"; then - VTK_COCOA_LIBS=-L$ac_vtk_cocoa_libraries - VTK_COCOA_LIB=$ac_vtk_cocoa_libraries - if test -e $ac_vtk_cocoa_libraries/vtk-5.10 ; then - VTK_COCOA_LIB_VTK="$ac_vtk_cocoa_libraries/vtk-5.10" - VTK_COCOA_LIBS=-L$ac_vtk_cocoa_libraries/vtk-5.10 - VTK_COCOA_LIB=$ac_vtk_cocoa_libraries/vtk-5.10 - elif test -e $ac_vtk_cocoa_libraries/vtk-5.6 ; then - VTK_COCOA_LIB_VTK="$ac_vtk_cocoa_libraries/vtk-5.6" - VTK_COCOA_LIBS=-L$ac_vtk_cocoa_libraries/vtk-5.6 - VTK_COCOA_LIB=$ac_vtk_cocoa_libraries/vtk-5.6 - elif test -e $ac_vtk_cocoa_libraries/vtk-5.5 ; then - VTK_COCOA_LIB_VTK="$ac_vtk_cocoa_libraries/vtk-5.5" - VTK_COCOA_LIBS=-L$ac_vtk_cocoa_libraries/vtk-5.5 - VTK_COCOA_LIB=$ac_vtk_cocoa_libraries/vtk-5.5 - elif test -e $ac_vtk_cocoa_libraries/vtk-5.4 ; then - VTK_COCOA_LIB_VTK="$ac_vtk_cocoa_libraries/vtk-5.4" - VTK_COCOA_LIBS=-L$ac_vtk_cocoa_libraries/vtk-5.4 - VTK_COCOA_LIB=$ac_vtk_cocoa_libraries/vtk-5.4 - elif test -e $ac_vtk_cocoa_libraries/vtk-5.3 ; then - VTK_COCOA_LIB_VTK="$ac_vtk_cocoa_libraries/vtk-5.3" - VTK_COCOA_LIBS=-L$ac_vtk_cocoa_libraries/vtk-5.3 - VTK_COCOA_LIB=$ac_vtk_cocoa_libraries/vtk-5.3 - elif test -e $ac_vtk_cocoa_libraries/vtk-5.2 ; then - VTK_COCOA_LIB_VTK="$ac_vtk_cocoa_libraries/vtk-5.2" - VTK_COCOA_LIBS=-L$ac_vtk_cocoa_libraries/vtk-5.2 - VTK_COCOA_LIB=$ac_vtk_cocoa_libraries/vtk-5.2 - elif test -e $ac_vtk_cocoa_libraries/vtk-5.1 ; then - VTK_COCOA_LIB_VTK="$ac_vtk_cocoa_libraries/vtk-5.1" - elif test -e $ac_vtk_cocoa_libraries/vtk-5.0 ; then - VTK_COCOA_LIB_VTK="$ac_vtk_cocoa_libraries/vtk-5.0" - elif test -e $ac_vtk_cocoa_libraries/vtk ; then - VTK_COCOA_LIB_VTK="$ac_vtk_cocoa_libraries/vtk" - fi -fi - -AM_CONDITIONAL(HAVE_COCOA_VTK_LIBS, test ! "x$VTK_COCOA_DIR" = "x") - -AC_SUBST(VTK_COCOA_CFLAGS) -AC_SUBST(VTK_COCOA_CXXFLAGS) -AC_SUBST(VTK_COCOA_LIBS) -AC_SUBST(VTK_COCOA_LIB) -AC_SUBST(VTK_COCOA_LIB_VTK) -AC_SUBST(VTK_COCOA_DIR) - - -################################################################ -# KWWidgets -################################################################ -ac_kwwidgets_includes="NO" -ac_kwwidgets_libraries="NO" -ac_kwwidgets_dir="NO" -KWWIDGETS_CFLAGS="" -KWWIDGETS_CXXFLAGS="" -KWWIDGETS_LIBS="" -KWWIDGETS_DIR="" - -AC_MSG_CHECKING(KWWidgets config) - -AC_ARG_WITH(kwwidgets-dir, - [ --with-kwwidgets-dir=DIR where the root of KWWidgets is installed.], - [ ac_kwwidgets_includes="$withval"/include/KWWidgets - ac_kwwidgets_libraries="$withval"/lib/KWWidgets - ac_kwwidgets_dir="$withval" - KWWIDGETS_DIR=$ac_kwwidgets_dir - ]) - -if test "x$KWWIDGETS_DIR" = "x"; then - # if a KWWidgets root was not supplied, but one exists in the - # default packages path at the NMR Center, then use that: - if test -d "${PACKAGES_DIR}/KWWidgets/current" ; then - withval=${PACKAGES_DIR}/KWWidgets/current - ac_kwwidgets_includes="$withval"/include/KWWidgets - ac_kwwidgets_libraries="$withval"/lib/KWWidgets - ac_kwwidgets_dir="$withval" - KWWIDGETS_DIR=$ac_kwwidgets_dir - kww_apps="yes" - fi -fi - -if test ! "$ac_kwwidgets_includes" = "NO"; then - AC_MSG_RESULT(KWWidgets directory is $withval) - for item in $ac_kwwidgets_includes; do - KWWIDGETS_CFLAGS="${KWWIDGETS_CFLAGS} -I${item}" - KWWIDGETS_CXXFLAGS="${KWWIDGETS_CXXFLAGS} -I${item}" - done - KWWIDGETS_DIR=$ac_kwwidgets_dir - kww_apps="yes" -fi - -if test ! "$ac_kwwidgets_libraries" = "NO"; then - for item in $ac_kwwidgets_libraries; do - KWWIDGETS_LIBS="${KWWIDGETS_LIBS} -L${item}" - done - KWWIDGETS_LIBS="${KWWIDGETS_LIBS}" - kww_apps="yes" -fi - -AC_ARG_ENABLE(kww-apps, - [ --disable-kww-apps disable building KWWidgets-based apps], - [ kww_apps="NO" - ]) - -if test "$disable_gui_build" = "YES"; then - kww_apps="NO" -fi - -if test "$kww_apps" = "yes"; then - AC_MSG_RESULT([Enabled building of KWWidgets apps.]) - # enable testing for OpenGL libs: - needs_opengl="$needs_opengl kwwapps" -else - AC_MSG_RESULT([Not building KWWidgets apps.]) -fi - -AM_CONDITIONAL(ENABLE_KWWIDGETS_APPS, test "$kww_apps" = "yes") - -AC_SUBST(KWWIDGETS_CFLAGS) -AC_SUBST(KWWIDGETS_CXXFLAGS) -AC_SUBST(KWWIDGETS_LIBS) -AC_SUBST(KWWIDGETS_DIR) - - -################################################################ -# wxWidgets -################################################################ -WXWIDGETS_CFLAGS="" -WXWIDGETS_CXXFLAGS="" -WXWIDGETS_LIBS="" -WXWIDGETS_GL_LIBS="" -WXWIDGETS_OPTIONAL_LIBS="" -WXWIDGETS_DIR="" - -AC_MSG_CHECKING(wxWidgets config) - -AC_ARG_WITH(wxwidgets-dir, - [ --with-wxwidgets-dir=DIR where the root of wxWidgets is installed.], - [ WXWIDGETS_DIR="$withval" - wxw_apps="yes" - ]) - -if test "x$WXWIDGETS_DIR" = "x"; then - # if a wxWidgets root was not supplied, but one exists in the - # default packages path at the NMR Center, then use that: - if test -d "${PACKAGES_DIR}/wxWidgets/current" ; then - WXWIDGETS_DIR=${PACKAGES_DIR}/wxWidgets/current - wxw_apps="yes" - fi -fi - -# use the handy wx-config utility to get the compiler and linker flags -if test ! "x$WXWIDGETS_DIR" = "x"; then - WXCONFIG="${WXWIDGETS_DIR}/bin/wx-config" - WXWIDGETS_CFLAGS="`${WXCONFIG} --cflags`" - WXWIDGETS_CXXFLAGS="`${WXCONFIG} --cxxflags`" - # we want to use the local / static jpeg, tiff and expat libs - WXWIDGETS_LIBS="`${WXCONFIG} --libs | sed 's/-ljpeg/..\/jpeg\/libjpeg.a/g' | sed 's/-ltiff/..\/tiff\/libtiff.a/g' | sed 's/-lexpat/..\/expat\/libexpat.a/g'`" - WXWIDGETS_GL_LIBS="`${WXCONFIG} --libs gl | sed 's/-ljpeg/..\/jpeg\/libjpeg.a/g' | sed 's/-ltiff/..\/tiff\/libtiff.a/g' | sed 's/-lexpat/..\/expat\/libexpat.a/g'`" - - # except wx-config isn't so handy in including some header paths on Linux: - if test -d /usr/include/gtk-2.0 ; then - WXWIDGETS_GTK_CFLAGS="-D__WXGTK20__" - WXWIDGETS_GTK_CFLAGS="$WXWIDGETS_GTK_CFLAGS -I/usr/include/gtk-2.0" - WXWIDGETS_GTK_CFLAGS="$WXWIDGETS_GTK_CFLAGS -I/usr/lib/gtk-2.0/include" - WXWIDGETS_GTK_CFLAGS="$WXWIDGETS_GTK_CFLAGS -I/usr/include/gdk-pixbuf-2.0" - WXWIDGETS_GTK_CFLAGS="$WXWIDGETS_GTK_CFLAGS -I/usr/lib64/gtk-2.0/include" - WXWIDGETS_GTK_CFLAGS="$WXWIDGETS_GTK_CFLAGS -I/usr/include/glib-2.0" - WXWIDGETS_GTK_CFLAGS="$WXWIDGETS_GTK_CFLAGS -I/usr/lib/glib-2.0/include" - WXWIDGETS_GTK_CFLAGS="$WXWIDGETS_GTK_CFLAGS -I/usr/lib64/glib-2.0/include" - WXWIDGETS_GTK_CFLAGS="$WXWIDGETS_GTK_CFLAGS -I/usr/include/pango-1.0" - WXWIDGETS_GTK_CFLAGS="$WXWIDGETS_GTK_CFLAGS -I/usr/include/cairo" - WXWIDGETS_GTK_CFLAGS="$WXWIDGETS_GTK_CFLAGS -I/usr/include/atk-1.0" - WXWIDGETS_CFLAGS="$WXWIDGETS_CFLAGS $WXWIDGETS_GTK_CFLAGS" - WXWIDGETS_CXXFLAGS="$WXWIDGETS_CXXFLAGS $WXWIDGETS_GTK_CFLAGS" - fi - - # seems like we gotta manually check for these... - if test -e ${WXWIDGETS_DIR}/lib/libwx_gtk2_gl-2.8.a ; then - WXWIDGETS_LIBS="$WXWIDGETS_LIBS -lwx_gtk2_gl-2.8" - fi - if test -e ${WXWIDGETS_DIR}/lib/libwx_gtk2u_gl-2.9.a ; then - WXWIDGETS_LIBS="$WXWIDGETS_LIBS -lwx_gtk2u_gl-2.9" - fi - WXWIDGETS_OPTIONAL_LIBS= - if test -e ${WXWIDGETS_DIR}/lib/libwx_gtk2u_aui-2.9.a ; then - WXWIDGETS_LIBS="$WXWIDGETS_LIBS -lwx_gtk2u_aui-2.9" - WXWIDGETS_OPTIONAL_LIBS="`${WXCONFIG} --optional-libs aui`" - fi - if test -e ${WXWIDGETS_DIR}/lib/libwx_gtk2u_core-2.9.a ; then - WXWIDGETS_LIBS="$WXWIDGETS_LIBS -lwx_gtk2u_core-2.9" - fi -fi - -AC_ARG_ENABLE(wxw-apps, - [ --disable-wxw-apps disable building wxWidgets-based apps], - [ wxw_apps="NO" - ]) - -if test "$disable_gui_build" = "YES"; then - wxw_apps="NO" -fi -if test "$wxw_apps" = "yes"; then - AC_MSG_RESULT([Enabled building of wxWidgets apps.]) - # enable testing for OpenGL libs: - needs_opengl="$needs_opengl wxwapps" -else - AC_MSG_RESULT([Not building wxWidgets apps.]) -fi - -AM_CONDITIONAL(ENABLE_WXWIDGETS_APPS, test "$wxw_apps" = "yes") - -AC_SUBST(WXWIDGETS_CFLAGS) -AC_SUBST(WXWIDGETS_CXXFLAGS) -AC_SUBST(WXWIDGETS_LIBS) -AC_SUBST(WXWIDGETS_GL_LIBS) -AC_SUBST(WXWIDGETS_OPTIONAL_LIBS) -AC_SUBST(WXWIDGETS_DIR) - -################################################################ -# GTS -################################################################ -GTS_CFLAGS="" -GTS_LIBS="" -GTS_DIR="" - -AC_MSG_CHECKING(GTS config) - -AC_ARG_WITH(gts-dir, - [ --with-gts-dir=DIR where the root of GTS is installed.], - [ GTS_DIR="$withval" ]) - -if test "x$GTS_DIR" = "x"; then - # if a gts root was not supplied, but one exists in the - # default packages path at the NMR Center, then use that: - if test -d "${PACKAGES_DIR}/gts/current" ; then - GTS_DIR=${PACKAGES_DIR}/gts/current - fi -else - if ! test -d "$GTS_DIR" ; then - GTS_DIR="" - fi -fi - -# use the handy wx-config utility to get the compiler and linker flags -if ! test "x$GTS_DIR" = "x"; then - AC_MSG_RESULT([Enabled building of GTS apps.]) - GTSCONFIG="${GTS_DIR}/bin/gts-config" - GTS_CFLAGS="`${GTSCONFIG} --cflags`" - # we want to use the local / static jpeg, tiff and expat libs - GTS_LIBS="`${GTSCONFIG} --libs`" -else - AC_MSG_RESULT([Not building GTS apps.]) -fi - -AM_CONDITIONAL(HAVE_GTS_LIBS, test ! "x$GTS_DIR" = "x") - -AC_SUBST(GTS_CFLAGS) -AC_SUBST(GTS_LIBS) -AC_SUBST(GTS_DIR) - - -################################################################ -# ITK -################################################################ -ac_itk_includes="NO" -ac_itk_libraries="NO" -ITK_CFLAGS="" -ITK_LIBS="" -ITK_LIB="" -LIBS_ITK="" -ITK_DIR="" -AC_MSG_CHECKING(ITK directory) - -AC_ARG_WITH(itk-dir, - [ --with-itk-dir=DIR where the root of ITK is installed.], - [ itk_i="$withval/include/InsightToolkit" - ac_itk_includes="$itk_i $itk_i/Algorithms \ - $itk_i/BasicFilters \ - $itk_i/Common \ - $itk_i/IO \ - $itk_i/Numerics \ - $itk_i/Numerics/Statistics \ - $itk_i/Review \ - $itk_i/Review/Statistics \ - $itk_i/SpatialObject \ - $itk_i/Utilities" - ac_itk_libraries="$withval"/lib/InsightToolkit - ITK_DIR="$withval" - itk_apps="yes" - AC_SUBST(ITK_DIR) - ]) - -# option to build against ITK v4.13 -AC_ARG_WITH(itk-4.13, - [ --with-itk-4.13=DIR where the root of ITK v4.13 is installed.], - [ ac_itk_includes="$withval"/include/ITK-4.13 - ac_itk_libraries="$withval"/lib - ITK_DIR="$withval" - itk_apps="yes" - itk_413="yes" - AC_SUBST(ITK_DIR) - ]) - -# option to build against ITK v4.5 -AC_ARG_WITH(itk-4.5, - [ --with-itk-4.5=DIR where the root of ITK v4.5 is installed.], - [ ac_itk_includes="$withval"/include/ITK-4.5 - ac_itk_libraries="$withval"/lib - ITK_DIR="$withval" - itk_apps="yes" - itk_45="yes" - AC_SUBST(ITK_DIR) - ]) - -AC_ARG_WITH(itk-include, - [ --with-itk-include=DIR root of ITK include directory.], - [ itk_i="$withval" - ac_itk_includes="$itk_i" - itk_apps="yes" - ]) - -AC_ARG_WITH(itk-libraries, - [ --with-itk-libraries=DIR root of ITK lib directory.], - [ ac_itk_libraries="$withval/InsightToolkit" - itk_apps="yes" - ]) - -# if --without-itk-dir was specified: -if test "x$ITK_DIR" = "xno"; then - itk_apps="NO" -fi - -if test "x$ITK_DIR" = "x"; then - # if an ITK root was not supplied, but one exists in the - # default packages path at the NMR Center, then use that: - if test -d "${PACKAGES_DIR}/itk/current" ; then - withval=${PACKAGES_DIR}/itk/current - itk_i="$withval/include/InsightToolkit" - ac_itk_includes="$itk_i \ - $itk_i/Algorithms \ - $itk_i/BasicFilters \ - $itk_i/Common \ - $itk_i/IO \ - $itk_i/Numerics \ - $itk_i/Numerics/Statistics \ - $itk_i/Review \ - $itk_i/Review/Statistics \ - $itk_i/SpatialObject \ - $itk_i/Utilities" - ac_itk_libraries="$withval"/lib/InsightToolkit - ITK_DIR="$withval" - itk_apps="yes" - AC_SUBST(ITK_DIR) - fi -fi - -if test ! "$ac_itk_includes" = "NO"; then - AC_MSG_RESULT(ITK directory is $withval) - for item in $ac_itk_includes; do - ITK_CFLAGS="${ITK_CFLAGS} -I${item}" - done -fi - -if test ! "$ac_itk_libraries" = "NO"; then - ITK_LIBS=-L$ac_itk_libraries - ITK_LIB=$ac_itk_libraries -fi - -AC_ARG_ENABLE(itk-apps, - [ --disable-itk-apps disable building ITK-based apps], - [ itk_apps="NO" - ac_itk_includes="NO" - ac_itk_libraries="NO" - ITK_CFLAGS="" - ITK_LIBS="" - ITK_LIB="" - LIBS_ITK="" - ITK_DIR="" - ]) - -if test "$itk_apps" = "yes"; then - AC_MSG_RESULT([Enabled building of ITK apps.]) - - # these are the minimum ITK libs necessary to support Nrrd IO, - # notice they are all static (avoiding LD_LIBRARY_PATH usage) - LIBS_ITK="\ - $ac_itk_libraries/libITKIO.a \ - $ac_itk_libraries/libITKAlgorithms.a \ - $ac_itk_libraries/libITKCommon.a \ - $ac_itk_libraries/libITKNumerics.a \ - $ac_itk_libraries/libITKMetaIO.a \ - $ac_itk_libraries/libITKniftiio.a \ - $ac_itk_libraries/libITKNrrdIO.a \ - $ac_itk_libraries/libitkpng.a \ - $ac_itk_libraries/libitksys.a \ - $ac_itk_libraries/libitktiff.a \ - $ac_itk_libraries/libitkv3p_netlib.a \ - $ac_itk_libraries/libitkzlib.a \ - $ac_itk_libraries/libitkgdcm.a \ - $ac_itk_libraries/libitkopenjpeg.a \ - $ac_itk_libraries/libitkjpeg8.a \ - $ac_itk_libraries/libitkjpeg12.a \ - $ac_itk_libraries/libitkjpeg16.a \ - $ac_itk_libraries/libITKDICOMParser.a" - - # ITK 4.13 uses these: - if test "x$itk_413" = "xyes"; then - LIBS_ITK="\ - $ac_itk_libraries/libITKIONRRD-4.13.a \ - $ac_itk_libraries/libITKIOImageBase-4.13.a \ - $ac_itk_libraries/libITKCommon-4.13.a \ - $ac_itk_libraries/libITKMetaIO-4.13.a \ - $ac_itk_libraries/libITKniftiio-4.13.a \ - $ac_itk_libraries/libITKNrrdIO-4.13.a \ - $ac_itk_libraries/libitkpng-4.13.a \ - $ac_itk_libraries/libitksys-4.13.a \ - $ac_itk_libraries/libitktiff-4.13.a \ - $ac_itk_libraries/libitkv3p_netlib-4.13.a \ - $ac_itk_libraries/libitkzlib-4.13.a" -# These aren't installed in v4.13 using options in packages/itk/makefile -# should they be installed separately/referenced in another way? -# $ac_itk_libraries/libitkopenjpeg-4.13.a \ -# $ac_itk_libraries/libITKDICOMParser-4.13.a" - fi - - # ITK 4.5 uses these: - if test "x$itk_45" = "xyes"; then - LIBS_ITK="\ - $ac_itk_libraries/libITKIONRRD-4.5.a \ - $ac_itk_libraries/libITKIOImageBase-4.5.a \ - $ac_itk_libraries/libITKCommon-4.5.a \ - $ac_itk_libraries/libITKMetaIO-4.5.a \ - $ac_itk_libraries/libITKniftiio-4.5.a \ - $ac_itk_libraries/libITKNrrdIO-4.5.a \ - $ac_itk_libraries/libitkpng-4.5.a \ - $ac_itk_libraries/libitksys-4.5.a \ - $ac_itk_libraries/libitktiff-4.5.a \ - $ac_itk_libraries/libitkv3p_netlib-4.5.a \ - $ac_itk_libraries/libitkzlib-4.5.a \ - $ac_itk_libraries/libitkopenjpeg-4.5.a \ - $ac_itk_libraries/libITKDICOMParser-4.5.a" - fi - - # ITK v3.16.0 needs libuuid for function `gdcm::Util::GenerateUUID' - if test -e /usr/lib/libuuid.a ; then - LIB_UUID="/usr/lib/libuuid.a" - AC_SUBST(LIB_UUID) - elif test -e /usr/lib64/libuuid.a ; then - LIB_UUID="/usr/lib64/libuuid.a" - AC_SUBST(LIB_UUID) - elif test -e /usr/lib/x86_64-linux-gnu/libuuid.a ; then - LIB_UUID="/usr/lib/x86_64-linux-gnu/libuuid.a" - AC_SUBST(LIB_UUID) - elif test -e /usr/lib64/libuuid.so ; then - LIB_UUID="/usr/lib64/libuuid.so" - AC_SUBST(LIB_UUID) - fi - LIBS_ITK="$LIBS_ITK $LIB_UUID" -else - AC_MSG_RESULT([Not building ITK apps.]) -fi - -AM_CONDITIONAL(ENABLE_ITK_APPS, test "$itk_apps" = "yes") -AM_CONDITIONAL(HAVE_ITK_LIBS, test "$itk_apps" = "yes") -AM_CONDITIONAL(HAVE_ITK45, test "$itk_45" = "yes") -AM_CONDITIONAL(HAVE_ITK413, test "$itk_413" = "yes") - - -AC_SUBST(ITK_CFLAGS) -AC_SUBST(ITK_LIBS) -AC_SUBST(ITK_LIB) -AC_SUBST(LIBS_ITK) - -################################################################ -# GDCM (Grassroots DICOM) -################################################################ -ac_gdcm_includes="NO" -ac_gdcm_libraries="NO" -GDCM_CFLAGS="" -GDCM_LIBS="" -GDCM_LIB="" -LIBS_GDCM="" -GDCM_DIR="" -AC_MSG_CHECKING(GDCM directory) - -if test "x$GDCM_DIR" = "x"; then - if test -d "${PACKAGES_DIR}/gdcm/current" ; then - withval=${PACKAGES_DIR}/gdcm/current - gdcm_i="$withval/include/gdcm-2.4" - ac_gdcm_includes="$gdcm_i $gdcm_i/gdcmjpeg $gdcm_i/gdcmopenjpeg $gdcm_i/gdcmcharls $gdcm_i/socketxx" - ac_gdcm_libraries="$withval/lib" - GDCM_DIR="$withval" - gdcm_apps="yes" - AC_SUBST(GDCM_DIR) - fi -fi - -if test ! "$ac_gdcm_includes" = "NO"; then - AC_MSG_RESULT(GDCM directory is $withval) - for item in $ac_gdcm_includes; do - GDCM_CFLAGS="${GDCM_CFLAGS} -I${item}" - done -fi - -if test ! "$ac_gdcm_libraries" = "NO"; then - GDCM_LIBS=-L$ac_gdcm_libraries - GDCM_LIB=$ac_gdcm_libraries -fi - -if test "$gdcm_apps" = "yes"; then - AC_MSG_RESULT([Enabled building of GDCM apps.]) - LIBS_GDCM="-lgdcmcharls -lgdcmCommon -lgdcmDICT -lgdcmDSED -lgdcmexpat \ - -lgdcmIOD -lgdcmjpeg12 -lgdcmjpeg16 -lgdcmjpeg8 -lgdcmMEXD \ - -lgdcmMSFF -lgdcmopenjpeg -lgdcmuuid -lgdcmzlib -lsocketxx" - LDFLAGS="$GDCM_LIBS $LDFLAGS" -else - AC_MSG_RESULT([Not building GDCM apps.]) -fi - -AM_CONDITIONAL(ENABLE_GDCM_APPS, test "$gdcm_apps" = "yes") -AM_CONDITIONAL(HAVE_GDCM_LIBS, test "$gdcm_apps" = "yes") - -AC_SUBST(GDCM_CFLAGS) -AC_SUBST(GDCM_LIBS) -AC_SUBST(GDCM_LIB) -AC_SUBST(LIBS_GDCM) - -# OpenGL -##################################################### -AC_MSG_NOTICE(Getting OpenGL info...) -mac_gl_libs= -##### -# GL -##### -ac_gl_includes="NO" -ac_gl_libraries="NO" -ac_gl_bindir="NO" -# these are lower-case because later AX_CHECK_GL trounces -# GL_CLFLAGS and GL_LIBS: -gl_cflags="" -gl_libs="" -AC_MSG_CHECKING(GL directory) - -AC_ARG_WITH(gl-dir, - [ --with-gl-dir=DIR where the root of OpenGL is installed.], - [ ac_gl_includes="$withval"/include - ac_gl_libraries="$withval"/lib - ac_gl_bindir="$withval"/bin - ]) - -if test ! "$ac_gl_includes" = "NO"; then - AC_MSG_RESULT(gl directory is $withval) - gl_cflags=-I$ac_gl_includes -else - AC_MSG_RESULT(OpenGL directory is not supplied) -fi -if test ! "$ac_gl_libraries" = "NO"; then - gl_libs=-L$ac_gl_libraries -fi - -# stupid Mac OS Leopard fix: -if test "$OS" = "Darwin"; then - X_DIR="" - if test -d "/usr/X11R6"; then - X_DIR="/usr/X11R6" - fi - if test -d "/usr/X11"; then - X_DIR="/usr/X11" - fi - if test ! "X$X_DIR" = "X"; then - gl_cflags="-I${X_DIR}/include -I${X_DIR}/include/GL" - gl_libs="-L${X_DIR}/lib $X_LIBS -Wl,-dylib_file,\ -/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib:\ -/System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGL.dylib" - mac_gl_libs=$gl_libs - fi -fi - -AC_SUBST(gl_cflags) -AC_SUBST(gl_libs) - - -##################################################### -# AX_CHECK_GL produces GL_CFLAGS GL_LIBS -ac_save_cflags=$CFLAGS -ac_save_ldflags=$LDFLAGS -CFLAGS="$gl_cflags $CFLAGS" -# bug in AX_CHECK_GL: assumes HAVE_WINDOWS_H is defined, so fix CFLAGS -# (note: Mac doesnt have this bug) -if test ! "$OS" = "Darwin"; then - CFLAGS="-DHAVE_WINDOWS_H=0 $CFLAGS" -fi -LDFLAGS="$gl_libs $LDFLAGS" -AX_CHECK_GL -if test "X$no_gl" = "Xyes"; then - if test ! "X$needs_opengl" = "X"; then - AC_MSG_ERROR([FATAL: GL not found, but needed for $needs_opengl. Use --with-gl-dir=... to specify]) - else - AC_MSG_RESULT([GL not found]) - fi -else - AC_MSG_RESULT([GL found: -Setting GL_CFLAGS='$GL_CFLAGS $gl_cflags' -and GL_LIBS='$GL_LIBS']) - GL_CFLAGS="$GL_CFLAGS $gl_cflags" - LIBS_OPENGL="$GL_LIBS $mac_gl_libs" -fi -if test ! "X$gl_cflags" = "X"; then - GL_CFLAGS="$GL_CFLAGS $gl_cflags" - LIBS_OPENGL="$GL_LIBS $mac_gl_libs" -fi - -CFLAGS="$ac_save_cflags" -LDFLAGS=$ac_save_ldflags -##################################################### -# AX_CHECK_GLU produces GLU_CFLAGS GLU_LIBS -ac_save_cflags=$CFLAGS -ac_save_ldflags=$LDFLAGS -CFLAGS="$gl_cflags $CFLAGS" -LDFLAGS="$gl_libs $LDFLAGS" -AX_CHECK_GLU -if test "X$no_glu" = "Xyes"; then - if test ! "X$needs_opengl" = "X"; then - AC_MSG_ERROR([FATAL: GLu not found but needed for $needs_opengl. Use --with-gl-dir=... to specify]) - else - AC_MSG_RESULT([GLu not found]) - fi -else - AC_MSG_RESULT([GLu found: -Setting GLU_CFLAGS='$GLU_CFLAGS' -and GLU_LIBS='$GLU_LIBS']) - LIBS_OPENGL="$GLU_LIBS $mac_gl_libs" -fi -CFLAGS=$ac_save_cflags -LDFLAGS=$ac_save_ldflags - -AC_SUBST(LIBS_OPENGL) - -################################################################### -# Install NMR Martinos Center files (not included in distribution) -################################################################### -AC_ARG_ENABLE(nmr-install, - [ --enable-nmr-install install NMR Center-only files], - [case "${enableval}" in - yes) nmrinstall=true ;; - no) nmrinstall=false ;; - *) AC_MSG_ERROR(bad value ${enableval} for --enable-nmr-install) ;; - esac], -[nmrinstall=false]) - -if test "x$nmrinstall" = "xtrue"; then - AC_MSG_RESULT([Performing an NMR installation.]) -else - AC_MSG_RESULT([Performing an off-site installation.]) -fi - -AM_CONDITIONAL(NMR_INSTALL, test x$nmrinstall = xtrue) - - -################################################################### -# Temporary build options -################################################################### - -# include Lilla's infant FS scripts and subjects -AC_ARG_ENABLE(infantFS, - [ --enable-infantFS include infantFS in build], - [ AM_CONDITIONAL(INCLUDE_INFANTFS, true) ], - [ AM_CONDITIONAL(INCLUDE_INFANTFS, false) -]) - -################################################ -LIBDIRS_MGH="utils rgb unix dicom hipsstubs" -AC_SUBST(LIBDIRS_MGH) - -# stupid circular dependency on iopen swapInt etc. -LIBS_MGH="\ - utils/libutils.a \ - fsgdf/libfsgdf.a \ - rgb/librgb.a \ - unix/libunix.a \ - dicom/libdicom.a \ - hipsstubs/libhipsstubs.a \ - log/liblog.a \ - xml2/libxml2.a" - -LIBS_CPP="utilscpp/libutilscpp.a" - -# use local libjpeg if --with-jpeg-dir not used: -if test "$ac_jpeg_libraries" = "NO"; then - LIB_JPEG="" - LIBS_MGH="${LIBS_MGH} jpeg/libjpeg.a" -fi -# use local libtiff if --with-tiff-dir not used: -if test "$ac_tiff_libraries" = "NO"; then - LIB_TIFF="" - LIBS_MGH="${LIBS_MGH} tiff/libtiff.a" -fi -# use local libexpat if --with-expat-dir not used: -if test "$ac_expat_libraries" = "NO"; then - LIB_EXPAT="" - LIBS_MGH="${LIBS_MGH} expat/libexpat.a" -fi -# use local minc and netcdf if --with-mni-dir not used: -if test "$ac_mni_libraries" = "no"; then - LIBS_MGH="${LIBS_MGH} ${LIBS_MNI_LOCAL}" -fi - -# to support CUDA, use libutils_cuda instead of libutils: -LIBS_CUDA_MGH=`echo ${LIBS_MGH} | sed 's/libutils/libutils_cuda/g'` - - -AC_SUBST(LIBS_MGH) -AC_SUBST(LIBS_CPP) -AC_SUBST(LIBS_CUDA_MGH) -AC_SUBST(LIB_JPEG) -AC_SUBST(LIB_TIFF) -AC_SUBST(LIB_EXPAT) - - -##################################################### -# generic mods -##################################################### -CPPFLAGS="$CPPFLAGS -D$OS -DANSI $OS_CPPFLAGS" -LDFLAGS="$LDFLAGS $OS_LDFLAGS" - -##################################################### -# link map -##################################################### -# this produces errors on os x -if test ! "$OS" = "Darwin"; then - LDFLAGS="$LDFLAGS -Wl,-Map,ld_map.txt -Wl,--no-demangle" -fi - -##################################################### -# Checks for libraries. -# the order is important -##################################################### -# the entire libs here is passed as LIBS -# thus save the current one, along with flags, which -# are restored upon completion of these checks -ac_save_libs=$LIBS -ac_save_cppflags=$CPPFLAGS -ac_save_ldflags=$LDFLAGS -CPPFLAGS="$CPPFLAGS $EXPAT_CFLAGS $TIFF_CFLAGS $JPEG_CFLAGS \ -$PETSC_CFLAGS $ITK_CFLAGS $ANN_CFLAGS \ -$MNI_CFLAGS $TCL_CFLAGS $CPPUNIT_CFLAGS $VXL_CFLAGS $NIFTI_CFLAGS \ -$GL_CFLAGS $GLU_CFLAGS $VTK_CFLAGS $KWWIDGETS_CFLAGS" -LDFLAGS="$LDFLAGS $MNI_LIBS $TCL_LIBS $VXL_LIBS \ -$EXPAT_LIBS $TIFF_LIBS $JPEG_LIBS \ -$gl_libs $GL_LIBS $GLU_LIBS $VTK_LIBS $ITK_LIBS $KWWIDGETS_LIBS \ -$PETSC_LIBS $NIFTI_LIBS $XAWPLUS_LIBS $ANN_LIBS" -AC_MSG_NOTICE(Making sure that all libraries can be compiled...) -# AC_MSG_NOTICE(CPPFLAGS: $CPPFLAGS) -# AC_MSG_NOTICE(LDFLAGS: $LDFLAGS) -AC_CHECK_LIB([m], [floor]) -AC_CHECK_LIB([z], [gzopen]) -AC_CHECK_LIB([crypt], [crypt],[],[echo "(Note: Mac OS X doesn't use crypt)"]) -LIB_CRYPT="-lcrypt" -if test "$OS" = "Darwin"; then - LIB_CRYPT="" -fi -AC_SUBST(LIB_CRYPT) - -# test for libtiff only if --with-tiff-dir was used: -if test ! "$ac_tiff_libraries" = "NO"; then - CPPFLAGS="$CPPFLAGS $TIFF_CFLAGS" - LDFLAGS="$LDFLAGS $TIFF_LIBS" - AC_CHECK_LIB([tiff], [TIFFGetVersion],[], - [AC_MSG_ERROR([FATAL: tiff lib not found. \ -Please install tiff header files and libs.])] ) -fi - -# test for libjpeg only if --with-jpeg-dir was used: -if test ! "$ac_jpeg_libraries" = "NO"; then - CPPFLAGS="$CPPFLAGS $JPEG_CFLAGS" - LDFLAGS="$LDFLAGS $JPEG_LIBS" - AC_CHECK_LIB([jpeg], [jpeg_start_compress],[], - [AC_MSG_ERROR([FATAL: jpeg lib not found. Please install jpeg lib.])] ) -fi - -# three mni libs -if test ! "x$MNI_DIR" = "xno"; then - AC_CHECK_LIB([netcdf], [nccreate],[], - [AC_MSG_ERROR([FATAL: netcdf lib not found. \ - Set LDFLAGS or --with-mni-dir.])] ) - if test "x$MINC2" = "xYES"; then - # check for newer build of mni tools - AC_CHECK_LIB([minc2 -lhdf5], [miopen], [], - [AC_MSG_ERROR([FATAL: minc2 lib not found. \ - Set LDFLAGS or --with-mni-dir.])] ) - AC_CHECK_LIB([volume_io2], [transform_point],[], - [AC_MSG_ERROR([FATAL: volume_io2 lib not found. \ - Set LDFLAGS or --with-mni-dir.])] ) - else - AC_CHECK_LIB([minc], [miopen], [], - [AC_MSG_ERROR([FATAL: minc lib not found. \ - Set LDFLAGS or --with-mni-dir.])] ) - AC_CHECK_LIB([volume_io], [transform_point],[], - [AC_MSG_ERROR([FATAL: volume_io lib not found. \ - Set LDFLAGS or --with-mni-dir.])] ) - fi -fi - -# VXL check -AC_CHECK_FILE($VXL_LIB/libvnl$DYNAMIC_LIB_EXT, - [if test "x$LD_LIBRARY_PATH" = "x"; then - export LD_LIBRARY_PATH=$VXL_LIB - else - export LD_LIBRARY_PATH="$VXL_LIB":"$LD_LIBRARY_PATH" - fi],[]) -AC_CHECK_LIB([vnl], [main],[], - [AC_MSG_ERROR([FATAL: vnl lib not found. Set LDFLAGS or --with-vxl-dir.])] ) -AC_CHECK_LIB([vnl_algo], [main],[], - [AC_MSG_ERROR([FATAL: vnl_algo lib not found. Set LDFLAGS or --with-vxl-dir.])] ) - -# ANN check -if test ! "x$ac_ann_dir" = "xNO"; then - # if --with-ann-dir was used, make sure necessary libs exist - AC_CHECK_LIB([ANN], [main],[], - [AC_MSG_ERROR([FATAL: ANN Approximate Nearest Neighbors lib not found. \ - Set LDFLAGS or --with-ann-dir.])] ) -fi - -# PETSc check -if test ! "x$ac_petsc_dir" = "xNO"; then - # if --with-petsc-dir was used, make sure necessary libs exist - if test "$OS" = "Darwin"; then - PMPICH=-lpmpich - else - PMPICH= - fi - AC_CHECK_LIB([petsc -lmpich -lpthread ${PMPICH}], [PetscInitialize],[], - [AC_MSG_ERROR([FATAL: petsc lib not found. \ - Set LDFLAGS or --with-petsc-dir.])] ) -fi - -# BOOST check -BOOST_PO_LIB="" -# if --with-boost-dir was used, make sure necessary lib(s) exist, -# namely, boost_program_options, used by fem_elastic build dir -if test ! "x$ac_boost_dir" = "xNO"; then - BOOST_PO_LIB="${BOOST_LIBS} -lboost_program_options-mt" - if test -e ${BOOST_LIB}/libboost_program_options-mt.a ; then - BOOST_PO_LIB=${BOOST_LIB}/libboost_program_options-mt.a - AC_MSG_RESULT([found '$BOOST_PO_LIB']) - else - if test -e ${BOOST_LIB}/libboost_program_options.a ; then - BOOST_PO_LIB=${BOOST_LIB}/libboost_program_options.a - AC_MSG_RESULT([found '$BOOST_PO_LIB']) - fi - fi -else - # else check for native install of boost program options lib - if test -e /usr/lib/libboost_program_options.a ; then - BOOST_PO_LIB=/usr/lib/libboost_program_options.a - AC_MSG_RESULT([found '$BOOST_PO_LIB']) - AM_CONDITIONAL(HAVE_BOOST_LIBS, ! test "x$BOOST_PO_LIB" = "xNO") - fi - if test -e /usr/lib64/libboost_program_options.a ; then - BOOST_PO_LIB=/usr/lib64/libboost_program_options.a - BOOST_LIB=/usr/lib64 - BOOST_LIBS=-L/usr/lib64 - AC_SUBST(BOOST_LIB) - AC_SUBST(BOOST_LIBS) - AC_MSG_RESULT([found '$BOOST_PO_LIB']) - AM_CONDITIONAL(HAVE_BOOST_LIBS, ! test "x$BOOST_PO_LIB" = "xNO") - else - if test -e /usr/lib64/libboost_program_options.so ; then - # note: centos 6 doesnt have the .a lib, so the shared is used instead - BOOST_PO_LIB=-lboost_program_options - BOOST_LIB=/usr/lib64 - BOOST_LIBS=-L/usr/lib64 - AC_SUBST(BOOST_LIB) - AC_SUBST(BOOST_LIBS) - AC_MSG_RESULT([found '$BOOST_PO_LIB']) - AM_CONDITIONAL(HAVE_BOOST_LIBS, ! test "x$BOOST_PO_LIB" = "xNO") - fi - fi -fi -AC_SUBST(BOOST_PO_LIB) - -# NIfTI check -if test ! "x$ac_nifti_dir" = "xNO"; then - # if --with-nifti-dir was used, make sure necessary libs exist - AC_CHECK_LIB([znz], [znzread],[], - [AC_MSG_ERROR([FATAL: NIfTI znz lib not found. \ - Set LDFLAGS or --with-nifti-dir.])] ) - AC_CHECK_LIB([niftiio -lznz], [is_nifti_file],[], - [AC_MSG_ERROR([FATAL: niftiio lib not found. \ - Set LDFLAGS or --with-nifti-dir.])] ) - LIBS_NIFTI="-lznz -lniftiio" -else - # check if libs installed natively somewhere - AC_CHECK_LIB([znz], [znzread], - [AC_CHECK_LIB([niftiio -lznz], [is_nifti_file], - [AM_CONDITIONAL(HAVE_NIFTI_LIBS, test "1" = "1") - LIBS_NIFTI="-lznz -lniftiio"],[])], []) -fi -AC_SUBST(LIBS_NIFTI) - -# test for vtk versions of system libs, and if not found (ie, not -# built when vtk was built), then use the system lib - -# use local libexpat if --with-expat-dir not used: -if test "$ac_expat_libraries" = "NO"; then - if test ! "$OS" = "Darwin"; then - VTK_EXPAT_LIB=../expat/libexpat.a - else - # else use whatever we can find - AC_CHECK_LIB([vtkexpat], [main], - [VTK_EXPAT_LIB="-lvtkexpat"], - [AC_CHECK_LIB([expat],[main],[VTK_EXPAT_LIB="-lexpat"], - [AC_MSG_ERROR([FATAL: libvtkexpat or libexpat not found.])])]) - fi -fi -AC_SUBST(VTK_EXPAT_LIB) - -AC_CHECK_LIB([vtkfreetype], [FTC_Manager_LookupSize], - [VTK_FREETYPE_LIB="-lvtkfreetype"], - [AC_CHECK_LIB([vtkfreetype], [vtk_freetype_FTC_Manager_LookupSize], [VTK_FREETYPE_LIB="-lvtkfreetype"], - [AC_CHECK_LIB([freetype],[FTC_Manager_LookupSize],[VTK_FREETYPE_LIB="-lfreetype"], - [AC_MSG_ERROR([FATAL: libvtkfreetype or libfreetype not found.])])])]) -AC_SUBST(VTK_FREETYPE_LIB) - -AC_CHECK_LIB([vtkzlib], [gzopen], - [VTK_Z_LIB="-lvtkzlib"], - [AC_CHECK_LIB([z],[gzopen],[VTK_Z_LIB="-lz"], - [AC_MSG_ERROR([FATAL: libvtkzlib or libz not found.])])]) -AC_SUBST(VTK_Z_LIB) - -# use local libjpeg if --with-jpeg-dir not used: -if test "$ac_jpeg_libraries" = "NO"; then - if test ! "$OS" = "Darwin"; then - VTK_JPEG_LIB=../jpeg/libjpeg.a - else - # else use whatever we can find - AC_CHECK_LIB([vtkjpeg], [vtk_jpeg_start_compress], - [VTK_JPEG_LIB="-lvtkjpeg"], - [VTK_JPEG_LIB="-ljpeg"]) - fi -fi -AC_SUBST(VTK_JPEG_LIB) - -# use local libtiff if --with-tiff-dir not used: -if test "$ac_tiff_libraries" = "NO"; then - if test ! "$OS" = "Darwin"; then - VTK_TIFF_LIB=../tiff/libtiff.a - else - # else use whatever we can find - AC_CHECK_LIB([vtktiff $VTK_JPEG_LIB $VTK_Z_LIB], [vtk_TIFFGetVersion], - [VTK_TIFF_LIB="-lvtktiff"], - [VTK_TIFF_LIB="-ltiff"]) - fi -fi -AC_SUBST(VTK_TIFF_LIB) - -AC_CHECK_LIB([vtkpng $VTK_Z_LIB], [main], - [VTK_PNG_LIB="-lvtkpng"], - [AC_CHECK_LIB([png],[main],[VTK_PNG_LIB="-lpng"], - [AC_MSG_ERROR([FATAL: libvtkpng or libpng not found.])])]) -AC_SUBST(VTK_PNG_LIB) - -# check for VTK libs -AC_CHECK_FILE($VTK_LIB/libvtkCommon$DYNAMIC_LIB_EXT, - [if test "x$LD_LIBRARY_PATH" = "x"; then - export LD_LIBRARY_PATH=$VTK_LIB - else - export LD_LIBRARY_PATH="$VTK_LIB":"$LD_LIBRARY_PATH" - fi],[]) -AC_CHECK_LIB([vtkCommon -lstdc++], [main],[], - [AC_MSG_RESULT([INFO: vtkCommon lib not found. \ -Try setting LDFLAGS, LD_LIBRARY_PATH and-or --with-vtk-dir.])] ) - -# libverdict appeared in VTK v5.1.0, and is required by libvtkHybrid, -# and libvtkGraphics (in v5.2.0), but doesnt exist in earlier versions of VTK -VTK_VERDICT_LIB="" -AC_CHECK_LIB([verdict], [main], [VTK_VERDICT_LIB="-lverdict"], - [AC_CHECK_LIB([vtkverdict], [main], [VTK_VERDICT_LIB="-lvtkverdict"], [])]) -AC_SUBST(VTK_VERDICT_LIB) - -# ditto for libvtksqlite -VTK_SQLITE_LIB="" -AC_CHECK_LIB([vtksqlite], [main], [VTK_SQLITE_LIB="-lvtksqlite"], []) -AC_SUBST(VTK_SQLITE_LIB) - -# libvtkMPEG2Encode disappeared from VTK v5.1.0, so test for it -VTK_MPEG2ENCODE_LIB="" -AC_CHECK_LIB([vtkMPEG2Encode], [main], - [VTK_MPEG2ENCODE_LIB="-lvtkMPEG2Encode"], []) -AC_SUBST(VTK_MPEG2ENCODE_LIB) - -# libvtkmetaio appeared in VTK v5.1.0, so check for it -# and, ugggg... it requires vtkpng and vtkzlib -VTK_METAIO_LIB="" -AC_CHECK_LIB([vtkmetaio], [main], [VTK_METAIO_LIB="-lvtkmetaio" - AC_CHECK_LIB([vtkpng], [main], [VTK_PNG_LIB="-lvtkpng"], []) - AC_CHECK_LIB([vtkzlib], [main], [VTK_Z_LIB="-lvtkzlib"], []) -], []) -AC_SUBST(VTK_METAIO_LIB) - -# vtkhdf5, vtkNetCDF_cxx and LSDyna appeared in VTK v5.10.0, so check for them -VTK_HDF5_LIB="" -AC_CHECK_LIB([vtkhdf5], [main], [VTK_HDF5_LIB="-lvtkhdf5_hl -lvtkhdf5"], []) -AC_SUBST(VTK_HDF5_LIB) -VTK_NETCDFCXX_LIB="" -AC_CHECK_LIB([vtkNetCDF_cxx], [main], [VTK_NETCDFCXX_LIB="-lvtkNetCDF_cxx"], []) -AC_SUBST(VTK_NETCDFCXX_LIB) -VTK_LSDYNA_LIB="" -AC_CHECK_LIB([LSDyna], [main], [VTK_LSDYNA_LIB="-lLSDyna"], []) -AC_SUBST(VTK_LSDYNA_LIB) - -# -# check tcl/tk/tix/blt only if tcl/tk apps are enabled -# -if test "x$tcltk_apps" = "xyes"; then - ################## Tcl - # check tcl8.5 - # NJS NOTE! here temp changed to 8.4 until tcl8.5 works - AC_CHECK_LIB([tcl8.4],[Tcl_Init], - [LIB_TCL=-ltcl8.4], - # check tcl8.4 - [ - AC_CHECK_LIB([tcl8.4],[Tcl_Init], - [LIB_TCL=-ltcl8.4], - # check tcl8.3 - [ - AC_CHECK_LIB([tcl8.3],[Tcl_Init], - [LIB_TCL=-ltcl8.3], - # check tcl83 - [ - AC_CHECK_LIB([tcl83],[Tcl_Init], - [LIB_TCL=-ltcl83], - # check tcl - [ AC_CHECK_LIB([tcl],[Tcl_Init], - [LIB_TCL=-ltcl], - # check tclstub - [ AC_CHECK_LIB([tclstub],[Tcl_Init], - [LIB_TCL=-ltclstub], - [AC_MSG_ERROR([FATAL: libtcl not found. \ -Check config.log. Set LDFLAGS or --with-tcl-dir.]) - ]) - ]) - ]) - ]) - ]) - ]) - AC_SUBST(LIB_TCL) - - #################### Tk needs X11 (or Aqua) - LIBS="$X_LIBS $LIBS" - CPPFLAGS="$GL_CFLAGS $CPPFLAGS" - LDFLAGS="$X_LIBS $LDFLAGS" - # check tk8.5 - # NJS NOTE! here temp changed to 8.4 until tcl8.5 works - AC_CHECK_LIB([tk8.4],[Tk_Init], - [LIB_TK=-ltk8.4], - # check tk8.4 - [ - AC_CHECK_LIB([tk8.4],[Tk_Init], - [LIB_TK=-ltk8.4], - # check tk8.3 - [ - AC_CHECK_LIB([tk8.3],[Tk_Init], - [LIB_TK=-ltk8.3], - # check tk83 - [ - AC_CHECK_LIB([tk83],[Tk_Init], - [LIB_TK=-ltk83], - # check tk - [ - AC_CHECK_LIB([tk],[Tk_Init], - [LIB_TK=-ltk], - [AC_MSG_ERROR([FATAL: libtk not found. \ -Check config.log. Set LDFLAGS or --with-tcl-dir.]) - ]) - ]) - ]) - ]) - ]) - AC_SUBST(LIB_TK) - - ##################### Tix - LIBS="$X_LIBS $LIB_TK $LIB_TCL $LIBS" - # check Tix8.4.2 first, as that is known to work best with tcl/tk 8.5 - AC_CHECK_LIB([Tix8.4.2], [Tix_Init], - [LIB_TIX=-lTix8.4.2], - [ - # check tix8.1.8.4, as that is known to work best with tcl/tk 8.4 - AC_CHECK_LIB([tix8.1.8.4], [Tix_Init], - [LIB_TIX=-ltix8.1.8.4], - [ - # check tix8.1.8.3 - AC_CHECK_LIB([tix8.1.8.3], [Tix_Init], - [LIB_TIX=-ltix8.1.8.3], - [ - # check tix8183 - AC_CHECK_LIB([tix8183], [Tix_Init], - [LIB_TIX=-ltix8183], - [ - # check tix8.4 - AC_CHECK_LIB([Tix8.4], [Tix_Init], - [LIB_TIX=-lTix8.4], - [ - # check tix - AC_CHECK_LIB([tix],[Tix_Init], - [LIB_TIX=-ltix], - [AC_MSG_ERROR([FATAL: libtix not found. \ -Check config.log. Set LDFLAGS or --with-tcl-dir.]) - ]) - ]) - ]) - ]) - ]) - ]) - AC_SUBST(LIB_TIX) - - ######## BLT (we cannot build BLT in Aqua) must use X11 - AC_CHECK_LIB([BLT25 $LIB_BLT_JPEG],[Blt_Init], - [LIB_BLT=-lBLT25], - [ - AC_CHECK_LIB([BLT $LIB_BLT_JPEG],[Blt_Init], - [LIB_BLT=-lBLT], - # check BLT.2 (MacOSX) - [ - AC_CHECK_LIB([BLT.2 $LIB_BLT_JPEG],[Blt_Init], - [LIB_BLT=-lBLT.2], - [ - # check BLT24 (Fedora) - AC_CHECK_LIB([BLT24 $LIB_BLT_JPEG],[Blt_Init], - [LIB_BLT=-lBLT24], - [AC_MSG_NOTICE([FATAL: libBLT not found. \ -Check config.log. Set LDFLAGS or --with-BLT-dir.]) - ]) - ]) - ]) - ]) - AC_SUBST(LIB_BLT) -fi - -# check for KWWidget libs only if kww app building is enabled -if test ! "x$kww_apps" = "xNO"; then - LDFLAGS="$LDFLAGS $LIB_TCL" - AC_CHECK_LIB([KWWidgets], [main],[], - [AC_MSG_ERROR([FATAL: KWWidgets lib not found. \ - Set LDFLAGS or --with-KWWidgets-dir.])] ) -fi - -# check for XawPlus lib only if xawplus app building is enabled -if test ! "x$xawplus_apps" = "xNO"; then - # with and without libXpm (Centos 6 doesnt have it) - AC_CHECK_LIB( - [XawPlus], - [XawInitializeWidgetSet], - [LIBS_XAWPLUS="-lXawPlus -lXt -lXpm -lX11"], - [AC_CHECK_LIB( - [XawPlus], - [XawInitializeWidgetSet], - [LIBS_XAWPLUS="-lXawPlus -lXt -lX11"], - [AC_MSG_ERROR([FATAL: XawPlus lib not found. Set LDFLAGS or --with-xawplus-dir.])], - [-lXt -lX11] - ) - ], - [-lXt -lXpm -lX11]) - AC_SUBST(LIBS_XAWPLUS) -fi - - -########################################################### -# More Intel C/C++ compiler stuff -########################################################### -LIBS_ICC="" -if test "x$CC" = "xicc"; then - AC_MSG_NOTICE(Setting Intel Compiler libs...) - LIBS_ICC="-lirc -lsvml -limf" -fi - -AC_SUBST(LIBS_ICC) -AM_CONDITIONAL(HAVE_INTEL_COMPILER, test "x$CC" = "xicc" ) - - -# -# recover previous settings, from prior to checks. -# let each Makefile.am set as appropriate, choose from: -# MNI_CFLAGS, MNI_LIBS -# JPEG_CFLAGS, JPEG_LIBS -# TIFF_CFLAGS, TIFF_LIBS -# TCL_CFLAGS, TCL_LIBS, LIB_TCL, ENABLE_TCLTK_APPS -# TK_CFLAGS, TK_LIBS, LIB_TK, LIB_TIX -# BLT_CFLAGS, BLT_LIBS, LIB_BLT -# GL_CFLAGS, GL_LIBS -# GLU_CFLAGS, GLU_LIBS -# VXL_CFLAGS, VXL_LIBS -# VTK_CFLAGS, VTK_LIBS -# KWWIDGETS_CFLAGS, KWWIDGETS_LIBS, ENABLE_KWWIDGETS_APPS -# ITK_CFLAGS, ITK_LIBS -LIBS=$ac_save_libs -CPPFLAGS=$ac_save_cppflags -LDFLAGS=$ac_save_ldflags - -# ...or use combined flags -LDFLAGS_TCL="$BLT_LIBS $TCL_LIBS" -if test "$OS" = "Darwin"; then - LDFLAGS_TCL="-bind_at_load $LDFLAGS_TCL" -fi -LIBS_TCL="$LIB_BLT $LIB_TIX $LIB_TK $LIB_TCL" -LIBS_TCL_OPENGL="$LIBS_TCL $LIBS_OPENGL" -AC_SUBST(LDFLAGS_TCL) -AC_SUBST(LIBS_TCL) -AC_SUBST(LIBS_TCL_OPENGL) - -# if using the Intel compiler, enable additional interprocedural -# optimizations for single file compilation, and enable auto-parallelization. -# this is done here because if added earlier -ipo breaks the OpenGL check -if test "x$CC" = "xicc"; then - AC_MSG_NOTICE(Setting Intel Compiler optimizations...) - CPPFLAGS="$CPPFLAGS -ip" - if test "x$ac_have_avx2" = "xyes"; then - CPPFLAGS="$CPPFLAGS -axCORE-AVX2" - fi - CPPFLAGS="$CPPFLAGS -parallel" - CPPFLAGS="$CPPFLAGS -qopt-report=5" # -guide-par - LDFLAGS="$LDFLAGS -ip" -fi -if test "x$F77" = "xifort"; then - if test "x$ac_have_avx2" = "xyes"; then - FFLAGS="$FFLAGS -xCORE-AVX2" - fi -fi - -########################################################### -# some common flags and libs -########################################################### -CPPFLAGS="$CPPFLAGS $MNI_CFLAGS" -LDFLAGS="$LDFLAGS $JPEG_LIBS $TIFF_LIBS $MNI_LIBS $VXL_LIBS $NIFTI_LIBS \ -$ITK_LIBS $EXPAT_LIBS" -# The order is important here. When adding or removing a lib, be sure -# to test the link line to make sure you don't need to adjust the -# order. -ac_use_mkl=no -if test "x$CC" = "xicc"; then - # was yes, but that assumed MKL was installed, which is not guaranteed - ac_use_mkl=no -fi -AC_ARG_ENABLE(icc, - [ --enable-mkl enable use of the Intel Math Kernel Library], - [case "${enableval}" in - yes) ac_enable_icc=yes ;; - no) ;; - *) AC_MSG_ERROR([bad value ${enableval} for --enable-mkl]) ;; - esac]) -if test "$ac_use_mkl" = "yes"; then - AC_MSG_NOTICE(Using Intel Math Kernel Library) - MATH_LIBS="-lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core" - MATH_LIBS="$MATH_LIBS -liomp5 -lm" -else - MATH_LIBS="-lm" -fi -LIBS="-lz $MATH_LIBS $LIB_CRYPT -ldl -lpthread $LIBS" -# librt is not available on osx -if test ! "$OS" = "Darwin"; then - LIBS="-lrt $LIBS" -fi -LIBS="$LIBS $LIB_JPEG" -LIBS="$LIBS $LIB_TIFF" -LIBS="$LIBS $LIB_EXPAT" -LIBS="$LIBS $LIBS_MNI" -LIBS="$LIBS $LIBS_VXL" -LIBS="$LIBS $LIBS_NIFTI" -LIBS="$LIBS_ITK $LIBS" -LIBS="$LIBS_ICC $LIBS" -LIBS="$LIBS_OPEN64 $LIBS" - -AC_SUBST(CPPFLAGS) -AC_SUBST(LDFLAGS) -AC_SUBST(LIBS) - - -######################################################################## -# check whether needs Itcl_Init() and Itk_Init() -# except when using Tcl8.4, which doesn't contain Itcl_Init or Itk_Init -######################################################################## -if test "x$tcltk_apps" = "xyes"; then - # NJS NOTE! tcl8.5 doesnt work yet with freesurfer (blt/tix) -# if ! test "$LIB_TCL" = "-ltcl8.5"; then - if ! test "$LIB_TCL" = "-ltcl8.4"; then - if ! test "$LIB_TCL" = "-ltcl83"; then - AX_TIX_INITCHECK($TCL_CFLAGS, $LDFLAGS_TCL, $LIBS_TCL) - fi -# fi - fi -fi - - -######################################################################## -# Indicate whether we have OpenGL or we don't need it in the build -# (HAVE_OPENGL is undefined if not) -######################################################################## -HAVE_OPENGL="-DHAVE_OPENGL" -if test "x$GL_LIBS" = "x"; then - HAVE_OPENGL="" -fi -if test "$disable_gui_build" = "YES"; then - HAVE_OPENGL="" -fi -AC_SUBST(HAVE_OPENGL) -AM_CONDITIONAL(HAVE_OPENGL_LIBS, ! test "X$HAVE_OPENGL" = "X") - - -######################################################################### -# 'make check' environment setup -######################################################################### -# -# When 'make check' is run, the tests specified in TESTS will inherit -# these environment variable. The first one bypasses the need for a -# license in FREESURFER_HOME, the others specify necessary libs. -# -TESTS_ENVIRONMENT="SURFER_FRONTDOOR=1 LD_LIBRARY_PATH=$TCL_LIB:$VTK_LIB" -if (! test "x$ac_cppunit_dir" = "xNO"); then - TESTS_ENVIRONMENT="$TESTS_ENVIRONMENT:$CPPUNIT_LIB" -fi -AC_SUBST(TESTS_ENVIRONMENT) - -######################################################################### -# output Makefiles in this list. Note that the top-level Makefile.am -# lists the subdirectories (SUBDIRS) to make, so that drives a build -######################################################################### - -AC_CONFIG_FILES([ - Makefile - Makefile.smalldist - ThalamicNuclei/Makefile - ThalamicNuclei/linux_x86_64/Makefile - ThalamicNuclei/mac_osx/Makefile - BrainstemSS/Makefile - BrainstemSS/linux_x86_64/Makefile - BrainstemSS/mac_osx/Makefile - HippoSF/Makefile - HippoSF/linux_x86_64/Makefile - HippoSF/mac_osx/Makefile - check_siemens_dir/Makefile - connectgraph/Makefile - cudatest/Makefile - cudatest/gcatest/Makefile - cudatest/mrilabeltest/Makefile - cudatest/volumecopy/Makefile - dicom/Makefile - distribution/Makefile - distribution/average/Buckner_JNeurophysiol11_MNI152/Makefile - distribution/average/Choi_JNeurophysiol12_MNI152/Makefile - distribution/average/Makefile - distribution/average/Yeo_JNeurophysiol11_MNI152/Makefile - distribution/average/samseg/Makefile - distribution/average/surf/Makefile - distribution/diffusion/Makefile - distribution/diffusion/mgh-dti-seqpack/Makefile - distribution/docs/Makefile - distribution/fsafd/Makefile - distribution/fsl-extra/Makefile - distribution/lib/Makefile - distribution/lib/bem/Makefile - distribution/sessions/Makefile - distribution/subjects/Makefile - distribution/trctrain/Makefile - dmri_tensoreig/Makefile - dngtester/Makefile - dummy/Makefile - dummy_qt/Makefile - expat/Makefile - fem_elastic/Makefile - freeview/Makefile - fsfast/Makefile - fsfast/bin/Makefile - fsfast/docs/Makefile - fsfast/toolbox/Makefile - fsgdf/Makefile - fslutils/Makefile - glut/Makefile - gpu_utils/Makefile - hiam_make_surfaces/Makefile - hiam_make_template/Makefile - hiam_register/Makefile - hipsstubs/Makefile - histo_compute_joint_density/Makefile - histo_fix_topology/Makefile - histo_register/Makefile - histo_register/ParticleVideoLib/Makefile - histo_register/SimpleBaseLib/Makefile - histo_register_block/Makefile - histo_segment/Makefile - histo_synthesize/Makefile - images/Makefile - include/Makefile - include/NrrdIO/Makefile - include/dicom/Makefile - include/fs_vnl/Makefile - include/pixrect/Makefile - include/sys/Makefile - include/topology/Makefile - include/xview/Makefile - itkio/Makefile - itkutils/Makefile - jpeg/Makefile - label2flat/Makefile - label2patch/Makefile - label_area/Makefile - label_border/Makefile - lineprof/Makefile - log/Makefile - lta_convert/Makefile - matlab/Makefile - minc_1_5_1/Makefile - mkxsubjreg/Makefile - mri_add_xform_to_header/Makefile - mri_and/Makefile - mri_annotation2label/Makefile - mri_aparc2aseg/Makefile - mri_aparc2wmseg/Makefile - mri_apply_inu_correction/Makefile - mri_aseg_edit_reclassify/Makefile - mri_aseg_edit_train/Makefile - mri_auto_fill/Makefile - mri_average/Makefile - mri_bc_sc_bias_correct/Makefile - mri_bias/Makefile - mri_binarize/Makefile - mri_build_priors/Makefile - mri_ca_label/Makefile - mri_ca_normalize/Makefile - mri_ca_register/Makefile - mri_ca_tissue_parms/Makefile - mri_ca_train/Makefile - mri_cal_renormalize_gca/Makefile - 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mri_extract_label/Makefile - mri_extract_largest_CC/Makefile - mri_fcili/Makefile - mri_fdr/Makefile - mri_fieldsign/Makefile - mri_fill/Makefile - mri_fit_bias/Makefile - mri_fslmat_to_lta/Makefile - mri_fuse_intensity_images/Makefile - mri_fuse_segmentations/Makefile - mri_fwhm/Makefile - mri_gca_ambiguous/Makefile - mri_gcab_train/Makefile - mri_gcut/Makefile - mri_gdfglm/Makefile - mri_glmfit/Makefile - mri_gtmpvc/Makefile - mri_gtmseg/Makefile - mri_hausdorff_dist/Makefile - mri_head/Makefile - mri_hires_register/Makefile - mri_histo_eq/Makefile - mri_histo_normalize/Makefile - mri_ibmc/Makefile - mri_iic/Makefile - mri_info/Makefile - mri_interpolate/Makefile - mri_jacobian/Makefile - mri_joint_density/Makefile - mri_label2label/Makefile - mri_label2vol/Makefile - mri_label_accuracy/Makefile - mri_label_histo/Makefile - mri_label_vals/Makefile - mri_label_volume/Makefile - mri_linear_register/Makefile - mri_log_likelihood/Makefile - mri_make_bem_surfaces/Makefile - mri_make_density_map/Makefile - 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mri_watershed/Makefile - mri_watershed/brain_volume/Makefile - mri_wbc/Makefile - mri_wmfilter/Makefile - mri_xcorr/Makefile - mri_xvolavg/Makefile - mri_z2p/Makefile - mris2rgb/Makefile - mris_BA_segment/Makefile - mris_add_template/Makefile - mris_anatomical_stats/Makefile - mris_annot_to_segmentation/Makefile - mris_apply_reg/Makefile - mris_aseg_distance/Makefile - mris_average_curvature/Makefile - mris_average_parcellation/Makefile - mris_ca_label/Makefile - mris_ca_train/Makefile - mris_calc/Makefile - mris_classify_thickness/Makefile - mris_compute_acorr/Makefile - mris_compute_lgi/Makefile - mris_compute_optimal_kernel/Makefile - mris_compute_overlap/Makefile - mris_compute_parc_overlap/Makefile - mris_compute_volume_fractions/Makefile - mris_congeal/Makefile - mris_convert/Makefile - mris_copy_header/Makefile - mris_curvature/Makefile - mris_curvature_stats/Makefile - mris_decimate/Makefile - mris_decimate_gui/Makefile - mris_deform/Makefile - mris_density/Makefile - mris_diff/Makefile - 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mris_mesh_subdivide/Makefile - mris_morph_stats/Makefile - mris_ms_refine/Makefile - mris_ms_surface_CNR/Makefile - mris_multiscale_stats/Makefile - mris_niters2fwhm/Makefile - mris_parcellate_connectivity/Makefile - mris_pmake/Makefile - mris_register/Makefile - mris_register_label_map/Makefile - mris_register_to_volume/Makefile - mris_remove_variance/Makefile - mris_resample/Makefile - mris_rescale/Makefile - mris_reverse/Makefile - mris_rf_label/Makefile - mris_rf_train/Makefile - mris_rotate/Makefile - mris_sample_label/Makefile - mris_sample_parc/Makefile - mris_seg2annot/Makefile - mris_segment/Makefile - mris_segment_vals/Makefile - mris_segmentation_stats/Makefile - mris_shrinkwrap/Makefile - mris_simulate_atrophy/Makefile - mris_smooth/Makefile - mris_sphere/Makefile - mris_spherical_average/Makefile - mris_surface_change/Makefile - mris_surface_stats/Makefile - mris_surface_to_vol_distances/Makefile - mris_svm_classify/Makefile - mris_svm_train/Makefile - mris_talairach/Makefile - mris_thickness/Makefile - mris_thickness_comparison/Makefile - mris_thickness_diff/Makefile - mris_topo_fixer/Makefile - mris_transform/Makefile - mris_translate_annotation/Makefile - mris_transmantle_dysplasia_paths/Makefile - mris_twoclass/Makefile - mris_volmask/Makefile - mris_volume/Makefile - mris_w_to_curv/Makefile - mris_warp/Makefile - mris_watershed/Makefile - mrisp_paint/Makefile - mrisp_write/Makefile - netcdf_3_6_0_p1/Makefile - oct_register_mosaic/Makefile - oct_train/Makefile - opencl_algorithms/Makefile - optseq2/Makefile - qdec/Makefile - qdec_glmfit/Makefile - qdecproject/Makefile - rbftest/Makefile - regdat2xfm/Makefile - repair_siemens_file/Makefile - rgb/Makefile - scripts/InfantFS/Makefile - scripts/Makefile - spherical_stats/Makefile - spline3/Makefile - stat_normalize/Makefile - stim_polar/Makefile - svm-lib/Makefile - swi_processing/Makefile - talairach_afd/Makefile - talairach_avi/Makefile - template/Makefile - test_makevol/Makefile - tetgen/Makefile - tiff/Makefile - tkmedit/Makefile - tkregister2/Makefile - tkregister2/cmdl/Makefile - tksurfer/Makefile - trc/Makefile - tridec/Makefile - unix/Makefile - utils/Makefile - utils/NrrdIO/Makefile - utils/cephes/Makefile - utils/test/MRIScomputeBorderValues/Makefile - utils/test/MRISpositionSurface/Makefile - utils/test/Makefile - utils/test/mriBuildVoronoiDiagramFloat/Makefile - utils/test/mriSoapBubbleFloat/Makefile - utils/test/mrishash/Makefile - utilscpp/Makefile - utilscpp/test/Makefile - vtkfsio/Makefile - vtkutils/Makefile - xml2/Makefile - ]) -# generate Makefiles from list in AC_CONFIG_FILES: -AC_OUTPUT() - -# if --enable-small-dist was used, then replace Makefile with the small-build version -if test "x$BUILD_SMALLDIST" = "xyes"; then - AC_MSG_NOTICE(Replaced Makefile with Makefile.smalldist for minimal build) - cp Makefile.smalldist Makefile -fi - - -######################################################################## - -builddir=`pwd` -AC_MSG_RESULT( -[ -FreeSurfer is now configured for ${host} - - Source directory: ${srcdir} - Build directory: ${builddir} - Install directory: ${prefix} - - C compiler: ${CC} ${CPPFLAGS} ${CFLAGS} - C++ compiler: ${CXX} ${CPPFLAGS} ${CXXFLAGS} - Fortran: ${F77} ${FFLAGS} - Linker: ${LD} ${LDFLAGS} - Libs: ${LIBS} -]) diff --git a/connectgraph/Makefile.am b/connectgraph/Makefile.am deleted file mode 100644 index 9d4896e432f..00000000000 --- a/connectgraph/Makefile.am +++ /dev/null @@ -1,20 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = connectgraph -connectgraph_SOURCES =\ - connectgraph.cpp \ - MyCmdLineParser.cpp \ - MyCmdLineParser.h -connectgraph_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -connectgraph_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/cudatest/Makefile.am b/cudatest/Makefile.am deleted file mode 100644 index 998f2bae070..00000000000 --- a/cudatest/Makefile.am +++ /dev/null @@ -1,495 +0,0 @@ -SUBDIRS = gcatest \ - volumecopy \ - mrilabeltest - -AM_CFLAGS=-I$(top_srcdir)/include $(BOOST_CFLAGS) - -AM_CXXFLAGS=-I$(top_srcdir)/include $(BOOST_CFLAGS) -Wall -Wextra - -AM_LDFLAGS= - -## ---- -## CUDA -## ---- - -if HAVE_BOOST_LIBS - -# BUILDCUDA is defined if configure.in finds CUDA -if BUILDCUDA - -if HAVE_FERMI_GPU -NVCCFLAGS += -g -arch sm_20 --ptxas-options=-v - -CUDA_CFLAGS += -DGCAMORPH_ON_GPU -endif - -# rules for building cuda files -.cu.o: - $(NVCC) -o $@ -c $< $(NVCCFLAGS) $(CUDA_CFLAGS) $(AM_CFLAGS) $(MNI_CFLAGS) - - -bin_PROGRAMS = gcamCompare\ - mri2nc\ - gcam_write_test gcam_write_test_cuda\ - conv1d_test conv1d_test_cuda\ - convgaussian_test convgaussian_test_cuda\ - gcam_cmp_test gcam_cmp_test_cuda\ - gcam_lle_test gcam_lle_test_cuda\ - gcam_jacobenergy_test gcam_jacobenergy_test_cuda\ - gcam_labelenergy_test gcam_labelenergy_test_cuda\ - gcam_smoothnessenergy_test gcam_smoothnessenergy_test_cuda\ - gcam_clear_test gcam_clear_test_cuda\ - gcam_applygradient_test gcam_applygradient_test_cuda\ - gcam_undogradient_test gcam_undogradient_test_cuda\ - meanfilter_test meanfilter_test_cuda\ - gcam_smoothnessterm_test gcam_smoothnessterm_test_cuda\ - gcam_jacobterm_test gcam_jacobterm_test_cuda\ - gcam_llterm_test gcam_llterm_test_cuda\ - gcam_addstatus_test gcam_addstatus_test_cuda\ - gcam_removestatus_test gcam_removestatus_test_cuda\ - gcam_labelterm_final_test gcam_labelterm_final_test_cuda\ - gcam_labelterm_postantconsist_test gcam_labelterm_postantconsist_test_cuda\ - gcam_labelterm_copydeltas_test gcam_labelterm_copydeltas_test_cuda\ - gcam_labelterm_removeoutliers_test gcam_labelterm_removeoutliers_test_cuda\ - gcam_labelterm_mainloop_test gcam_labelterm_mainloop_test_cuda\ - gcam_labelterm_test gcam_labelterm_test_cuda\ - gcam_smoothgradient_test gcam_smoothgradient_test_cuda\ - gcam_removesingularities_test gcam_removesingularities_test_cuda - - -gcamCompare_SOURCES = gcamCompare.cpp kahan.hpp -gcamCompare_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(BOOST_PO_LIB) -gcamCompare_LDFLAGS=$(OS_LDFLAGS) - -# -- - -gcam_write_test_SOURCES = gcam_write_test.cpp -gcam_write_test_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(BOOST_PO_LIB) -gcam_write_test_LDFLAGS=$(OS_LDFLAGS) - -gcam_write_test_cuda_SOURCES = gcam_write_test.cpp -gcam_write_test_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_write_test_cuda_CXXFLAGS = $(CUDA_CXXFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_write_test_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) $(BOOST_PO_LIB) -gcam_write_test_cuda_LDFLAGS = $(OS_LDFLAGS) -gcam_write_test_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gcam_write_test_cuda_CFLAGS) \ - $(CFLAGS) $(gcam_write_test_cuda_LDFLAGS) $(LDFLAGS) -o $@ - - -# -- - -mri2nc_SOURCES = mri2nc.cpp -mri2nc_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(BOOST_PO_LIB) -mri2nc_LDFLAGS=$(OS_LDFLAGS) - -# -- - -conv1d_test_SOURCES = conv1d_test.cpp -conv1d_test_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(BOOST_PO_LIB) -conv1d_test_LDFLAGS=$(OS_LDFLAGS) - - -conv1d_test_cuda_SOURCES = conv1d_test.cpp -conv1d_test_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -conv1d_test_cuda_CXXFLAGS = $(CUDA_CXXFLAGS) $(AM_CFLAGS) -DFS_CUDA -conv1d_test_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) $(BOOST_PO_LIB) -conv1d_test_cuda_LDFLAGS = $(OS_LDFLAGS) -conv1d_test_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(conv1d_test_cuda_CFLAGS) \ - $(CFLAGS) $(conv1d_test_cuda_LDFLAGS) $(LDFLAGS) -o $@ - -# -- - -convgaussian_test_SOURCES = convgaussian_test.cpp -convgaussian_test_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(BOOST_PO_LIB) -convgaussian_test_LDFLAGS=$(OS_LDFLAGS) - - -convgaussian_test_cuda_SOURCES = convgaussian_test.cpp -convgaussian_test_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -convgaussian_test_cuda_CXXFLAGS = $(CUDA_CXXFLAGS) $(AM_CFLAGS) -DFS_CUDA -convgaussian_test_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) $(BOOST_PO_LIB) -convgaussian_test_cuda_LDFLAGS = $(OS_LDFLAGS) -convgaussian_test_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(convgaussian_test_cuda_CFLAGS) \ - $(CFLAGS) $(convgaussian_test_cuda_LDFLAGS) $(LDFLAGS) -o $@ - -# -- - -gcam_cmp_test_SOURCES = gcam_cmp_test.cpp -gcam_cmp_test_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(BOOST_PO_LIB) -gcam_cmp_test_LDFLAGS=$(OS_LDFLAGS) - - -gcam_cmp_test_cuda_SOURCES = gcam_cmp_test.cpp -gcam_cmp_test_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_cmp_test_cuda_CXXFLAGS = $(CUDA_CXXFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_cmp_test_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) $(BOOST_PO_LIB) -gcam_cmp_test_cuda_LDFLAGS = $(OS_LDFLAGS) -gcam_cmp_test_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gcam_cmp_test_cuda_CFLAGS) \ - $(CFLAGS) $(gcam_cmp_test_cuda_LDFLAGS) $(LDFLAGS) -o $@ - -# -- - -gcam_lle_test_SOURCES = gcam_lle_test.cpp -gcam_lle_test_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(BOOST_PO_LIB) -gcam_lle_test_LDFLAGS=$(OS_LDFLAGS) - - -gcam_lle_test_cuda_SOURCES = gcam_lle_test.cpp -gcam_lle_test_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_lle_test_cuda_CXXFLAGS = $(CUDA_CXXFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_lle_test_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) $(BOOST_PO_LIB) -gcam_lle_test_cuda_LDFLAGS = $(OS_LDFLAGS) -gcam_lle_test_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gcam_lle_test_cuda_CFLAGS) \ - $(CFLAGS) $(gcam_lle_test_cuda_LDFLAGS) $(LDFLAGS) -o $@ - -# -- - -gcam_jacobenergy_test_SOURCES = gcam_jacobenergy_test.cpp -gcam_jacobenergy_test_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(BOOST_PO_LIB) -gcam_jacobenergy_test_LDFLAGS=$(OS_LDFLAGS) - - -gcam_jacobenergy_test_cuda_SOURCES = gcam_jacobenergy_test.cpp -gcam_jacobenergy_test_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_jacobenergy_test_cuda_CXXFLAGS = $(CUDA_CXXFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_jacobenergy_test_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) $(BOOST_PO_LIB) -gcam_jacobenergy_test_cuda_LDFLAGS = $(OS_LDFLAGS) -gcam_jacobenergy_test_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gcam_jacobenergy_test_cuda_CFLAGS) \ - $(CFLAGS) $(gcam_jacobenergy_test_cuda_LDFLAGS) $(LDFLAGS) -o $@ - -# -- - -gcam_labelenergy_test_SOURCES = gcam_labelenergy_test.cpp -gcam_labelenergy_test_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(BOOST_PO_LIB) -gcam_labelenergy_test_LDFLAGS=$(OS_LDFLAGS) - - -gcam_labelenergy_test_cuda_SOURCES = gcam_labelenergy_test.cpp -gcam_labelenergy_test_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_labelenergy_test_cuda_CXXFLAGS = $(CUDA_CXXFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_labelenergy_test_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) $(BOOST_PO_LIB) -gcam_labelenergy_test_cuda_LDFLAGS = $(OS_LDFLAGS) -gcam_labelenergy_test_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gcam_labelenergy_test_cuda_CFLAGS) \ - $(CFLAGS) $(gcam_labelenergy_test_cuda_LDFLAGS) $(LDFLAGS) -o $@ - - -# -- - -gcam_smoothnessenergy_test_SOURCES = gcam_smoothnessenergy_test.cpp -gcam_smoothnessenergy_test_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(BOOST_PO_LIB) -gcam_smoothnessenergy_test_LDFLAGS=$(OS_LDFLAGS) - - -gcam_smoothnessenergy_test_cuda_SOURCES = gcam_smoothnessenergy_test.cpp -gcam_smoothnessenergy_test_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_smoothnessenergy_test_cuda_CXXFLAGS = $(CUDA_CXXFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_smoothnessenergy_test_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) $(BOOST_PO_LIB) -gcam_smoothnessenergy_test_cuda_LDFLAGS = $(OS_LDFLAGS) -gcam_smoothnessenergy_test_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gcam_smoothnessenergy_test_cuda_CFLAGS) \ - $(CFLAGS) $(gcam_smoothnessenergy_test_cuda_LDFLAGS) $(LDFLAGS) -o $@ - - -# -- - -gcam_clear_test_SOURCES = gcam_clear_test.cpp -gcam_clear_test_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(BOOST_PO_LIB) -gcam_clear_test_LDFLAGS=$(OS_LDFLAGS) - - -gcam_clear_test_cuda_SOURCES = gcam_clear_test.cpp -gcam_clear_test_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_clear_test_cuda_CXXFLAGS = $(CUDA_CXXFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_clear_test_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) $(BOOST_PO_LIB) -gcam_clear_test_cuda_LDFLAGS = $(OS_LDFLAGS) -gcam_clear_test_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gcam_clear_test_cuda_CFLAGS) \ - $(CFLAGS) $(gcam_clear_test_cuda_LDFLAGS) $(LDFLAGS) -o $@ - - -# -- - -gcam_applygradient_test_SOURCES = gcam_applygradient_test.cpp -gcam_applygradient_test_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(BOOST_PO_LIB) -gcam_applygradient_test_LDFLAGS=$(OS_LDFLAGS) - - -gcam_applygradient_test_cuda_SOURCES = gcam_applygradient_test.cpp -gcam_applygradient_test_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_applygradient_test_cuda_CXXFLAGS = $(CUDA_CXXFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_applygradient_test_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) $(BOOST_PO_LIB) -gcam_applygradient_test_cuda_LDFLAGS = $(OS_LDFLAGS) -gcam_applygradient_test_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gcam_applygradient_test_cuda_CFLAGS) \ - $(CFLAGS) $(gcam_applygradient_test_cuda_LDFLAGS) $(LDFLAGS) -o $@ - -# -- - -gcam_undogradient_test_SOURCES = gcam_undogradient_test.cpp -gcam_undogradient_test_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(BOOST_PO_LIB) -gcam_undogradient_test_LDFLAGS=$(OS_LDFLAGS) - - -gcam_undogradient_test_cuda_SOURCES = gcam_undogradient_test.cpp -gcam_undogradient_test_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_undogradient_test_cuda_CXXFLAGS = $(CUDA_CXXFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_undogradient_test_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) $(BOOST_PO_LIB) -gcam_undogradient_test_cuda_LDFLAGS = $(OS_LDFLAGS) -gcam_undogradient_test_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gcam_undogradient_test_cuda_CFLAGS) \ - $(CFLAGS) $(gcam_undogradient_test_cuda_LDFLAGS) $(LDFLAGS) -o $@ - -# -- - -meanfilter_test_SOURCES=meanfilter_test.cpp -meanfilter_test_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(BOOST_PO_LIB) -meanfilter_test_LDFLAGS=$(OS_LDFLAGS) - -meanfilter_test_cuda_SOURCES = meanfilter_test.cpp -meanfilter_test_cuda_CFLAGS = $(AM_CFLAGS) $(CUDA_CFLAGS) -DFS_CUDA -meanfilter_test_cuda_CXXFLAGS = $(CUDA_CXXFLAGS) $(AM_CFLAGS) -DFS_CUDA -meanfilter_test_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) $(BOOST_PO_LIB) -meanfilter_test_cuda_LDFLAGS = $(OS_LDFLAGS) -meanfilter_test_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(meanfilter_test_cuda_CFLAGS) \ - $(CFLAGS) $(meanfilter_test_cuda_LDFLAGS) $(LDFLAGS) -o $@ - - -# -- - -gcam_smoothnessterm_test_SOURCES = gcam_smoothnessterm_test.cpp -gcam_smoothnessterm_test_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(BOOST_PO_LIB) -gcam_smoothnessterm_test_LDFLAGS=$(OS_LDFLAGS) - - -gcam_smoothnessterm_test_cuda_SOURCES = gcam_smoothnessterm_test.cpp -gcam_smoothnessterm_test_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_smoothnessterm_test_cuda_CXXFLAGS = $(CUDA_CXXFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_smoothnessterm_test_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) $(BOOST_PO_LIB) -gcam_smoothnessterm_test_cuda_LDFLAGS = $(OS_LDFLAGS) -gcam_smoothnessterm_test_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gcam_smoothnessterm_test_cuda_CFLAGS) \ - $(CFLAGS) $(gcam_smoothnessterm_test_cuda_LDFLAGS) $(LDFLAGS) -o $@ - -# -- - -gcam_jacobterm_test_SOURCES = gcam_jacobterm_test.cpp -gcam_jacobterm_test_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(BOOST_PO_LIB) -gcam_jacobterm_test_LDFLAGS=$(OS_LDFLAGS) - - -gcam_jacobterm_test_cuda_SOURCES = gcam_jacobterm_test.cpp -gcam_jacobterm_test_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_jacobterm_test_cuda_CXXFLAGS = $(CUDA_CXXFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_jacobterm_test_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) $(BOOST_PO_LIB) -gcam_jacobterm_test_cuda_LDFLAGS = $(OS_LDFLAGS) -gcam_jacobterm_test_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gcam_jacobterm_test_cuda_CFLAGS) \ - $(CFLAGS) $(gcam_jacobterm_test_cuda_LDFLAGS) $(LDFLAGS) -o $@ - -# -- - -gcam_llterm_test_SOURCES = gcam_llterm_test.cpp -gcam_llterm_test_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(BOOST_PO_LIB) -gcam_llterm_test_LDFLAGS=$(OS_LDFLAGS) - 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$(LIBTOOLFLAGS) --mode=link $(CCLD) $(gcam_labelterm_final_test_cuda_CFLAGS) \ - $(CFLAGS) $(gcam_labelterm_final_test_cuda_LDFLAGS) $(LDFLAGS) -o $@ - - -# -- - -gcam_labelterm_postantconsist_test_SOURCES = gcam_labelterm_postantconsist_test.cpp -gcam_labelterm_postantconsist_test_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(BOOST_PO_LIB) -gcam_labelterm_postantconsist_test_LDFLAGS=$(OS_LDFLAGS) - - -gcam_labelterm_postantconsist_test_cuda_SOURCES = gcam_labelterm_postantconsist_test.cpp -gcam_labelterm_postantconsist_test_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_labelterm_postantconsist_test_cuda_CXXFLAGS = $(CUDA_CXXFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_labelterm_postantconsist_test_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) $(BOOST_PO_LIB) -gcam_labelterm_postantconsist_test_cuda_LDFLAGS = $(OS_LDFLAGS) -gcam_labelterm_postantconsist_test_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gcam_labelterm_postantconsist_test_cuda_CFLAGS) \ - $(CFLAGS) $(gcam_labelterm_postantconsist_test_cuda_LDFLAGS) $(LDFLAGS) -o $@ - -# -- - -gcam_labelterm_copydeltas_test_SOURCES = gcam_labelterm_copydeltas_test.cpp -gcam_labelterm_copydeltas_test_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(BOOST_PO_LIB) -gcam_labelterm_copydeltas_test_LDFLAGS=$(OS_LDFLAGS) - - -gcam_labelterm_copydeltas_test_cuda_SOURCES = gcam_labelterm_copydeltas_test.cpp -gcam_labelterm_copydeltas_test_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_labelterm_copydeltas_test_cuda_CXXFLAGS = $(CUDA_CXXFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_labelterm_copydeltas_test_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) $(BOOST_PO_LIB) -gcam_labelterm_copydeltas_test_cuda_LDFLAGS = $(OS_LDFLAGS) -gcam_labelterm_copydeltas_test_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gcam_labelterm_copydeltas_test_cuda_CFLAGS) \ - $(CFLAGS) $(gcam_labelterm_copydeltas_test_cuda_LDFLAGS) $(LDFLAGS) -o $@ - - -# -- - -gcam_labelterm_removeoutliers_test_SOURCES = gcam_labelterm_removeoutliers_test.cpp -gcam_labelterm_removeoutliers_test_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(BOOST_PO_LIB) -gcam_labelterm_removeoutliers_test_LDFLAGS=$(OS_LDFLAGS) - - -gcam_labelterm_removeoutliers_test_cuda_SOURCES = gcam_labelterm_removeoutliers_test.cpp -gcam_labelterm_removeoutliers_test_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_labelterm_removeoutliers_test_cuda_CXXFLAGS = $(CUDA_CXXFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_labelterm_removeoutliers_test_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) $(BOOST_PO_LIB) -gcam_labelterm_removeoutliers_test_cuda_LDFLAGS = $(OS_LDFLAGS) -gcam_labelterm_removeoutliers_test_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gcam_labelterm_removeoutliers_test_cuda_CFLAGS) \ - $(CFLAGS) $(gcam_labelterm_removeoutliers_test_cuda_LDFLAGS) $(LDFLAGS) -o $@ - - -# -- - -gcam_labelterm_mainloop_test_SOURCES = gcam_labelterm_mainloop_test.cpp -gcam_labelterm_mainloop_test_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(BOOST_PO_LIB) -gcam_labelterm_mainloop_test_LDFLAGS=$(OS_LDFLAGS) - - -gcam_labelterm_mainloop_test_cuda_SOURCES = gcam_labelterm_mainloop_test.cpp -gcam_labelterm_mainloop_test_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_labelterm_mainloop_test_cuda_CXXFLAGS = $(CUDA_CXXFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_labelterm_mainloop_test_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) $(BOOST_PO_LIB) -gcam_labelterm_mainloop_test_cuda_LDFLAGS = $(OS_LDFLAGS) -gcam_labelterm_mainloop_test_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gcam_labelterm_mainloop_test_cuda_CFLAGS) \ - $(CFLAGS) $(gcam_labelterm_mainloop_test_cuda_LDFLAGS) $(LDFLAGS) -o $@ - - - -# -- - -gcam_labelterm_test_SOURCES = gcam_labelterm_test.cpp -gcam_labelterm_test_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(BOOST_PO_LIB) -gcam_labelterm_test_LDFLAGS=$(OS_LDFLAGS) - - -gcam_labelterm_test_cuda_SOURCES = gcam_labelterm_test.cpp -gcam_labelterm_test_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_labelterm_test_cuda_CXXFLAGS = $(CUDA_CXXFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_labelterm_test_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) $(BOOST_PO_LIB) -gcam_labelterm_test_cuda_LDFLAGS = $(OS_LDFLAGS) -gcam_labelterm_test_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gcam_labelterm_test_cuda_CFLAGS) \ - $(CFLAGS) $(gcam_labelterm_test_cuda_LDFLAGS) $(LDFLAGS) -o $@ - - - -# -- - -gcam_addstatus_test_SOURCES = gcam_addstatus_test.cpp -gcam_addstatus_test_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(BOOST_PO_LIB) -gcam_addstatus_test_LDFLAGS=$(OS_LDFLAGS) - - -gcam_addstatus_test_cuda_SOURCES = gcam_addstatus_test.cpp -gcam_addstatus_test_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_addstatus_test_cuda_CXXFLAGS = $(CUDA_CXXFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_addstatus_test_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) $(BOOST_PO_LIB) -gcam_addstatus_test_cuda_LDFLAGS = $(OS_LDFLAGS) -gcam_addstatus_test_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gcam_addstatus_test_cuda_CFLAGS) \ - $(CFLAGS) $(gcam_addstatus_test_cuda_LDFLAGS) $(LDFLAGS) -o $@ - - -# -- - -gcam_removestatus_test_SOURCES = gcam_removestatus_test.cpp -gcam_removestatus_test_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(BOOST_PO_LIB) -gcam_removestatus_test_LDFLAGS=$(OS_LDFLAGS) - - -gcam_removestatus_test_cuda_SOURCES = gcam_removestatus_test.cpp -gcam_removestatus_test_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_removestatus_test_cuda_CXXFLAGS = $(CUDA_CXXFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_removestatus_test_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) $(BOOST_PO_LIB) -gcam_removestatus_test_cuda_LDFLAGS = $(OS_LDFLAGS) -gcam_removestatus_test_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gcam_removestatus_test_cuda_CFLAGS) \ - $(CFLAGS) $(gcam_removestatus_test_cuda_LDFLAGS) $(LDFLAGS) -o $@ - -# -- - -gcam_smoothgradient_test_SOURCES = gcam_smoothgradient_test.cpp -gcam_smoothgradient_test_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(BOOST_PO_LIB) -gcam_smoothgradient_test_LDFLAGS=$(OS_LDFLAGS) - - -gcam_smoothgradient_test_cuda_SOURCES = gcam_smoothgradient_test.cpp -gcam_smoothgradient_test_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_smoothgradient_test_cuda_CXXFLAGS = $(CUDA_CXXFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_smoothgradient_test_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) $(BOOST_PO_LIB) -gcam_smoothgradient_test_cuda_LDFLAGS = $(OS_LDFLAGS) -gcam_smoothgradient_test_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gcam_smoothgradient_test_cuda_CFLAGS) \ - $(CFLAGS) $(gcam_smoothgradient_test_cuda_LDFLAGS) $(LDFLAGS) -o $@ - -# -- - -gcam_removesingularities_test_SOURCES = gcam_removesingularities_test.cpp -gcam_removesingularities_test_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(BOOST_PO_LIB) -gcam_removesingularities_test_LDFLAGS=$(OS_LDFLAGS) - - -gcam_removesingularities_test_cuda_SOURCES = gcam_removesingularities_test.cpp -gcam_removesingularities_test_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_removesingularities_test_cuda_CXXFLAGS = $(CUDA_CXXFLAGS) $(AM_CFLAGS) -DFS_CUDA -gcam_removesingularities_test_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) $(BOOST_PO_LIB) -gcam_removesingularities_test_cuda_LDFLAGS = $(OS_LDFLAGS) -gcam_removesingularities_test_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(gcam_removesingularities_test_cuda_CFLAGS) \ - $(CFLAGS) $(gcam_removesingularities_test_cuda_LDFLAGS) $(LDFLAGS) -o $@ - - - -endif -# endif BUILDCUDA - -endif -#endif HAVE_BOOST_LIBS - - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - diff --git a/cudatest/gcatest/Makefile.am b/cudatest/gcatest/Makefile.am deleted file mode 100644 index ac80981c9cb..00000000000 --- a/cudatest/gcatest/Makefile.am +++ /dev/null @@ -1,43 +0,0 @@ -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom\ - $(BOOST_CFLAGS)\ - -Wall -Wextra -AM_LDFLAGS= - -## ---- -## CUDA -## ---- - -if HAVE_BOOST_LIBS - -# BUILDCUDA is defined if configure.in finds CUDA -if BUILDCUDA - -NVCCFLAGS += -g -arch sm_20 --ptxas-options=-v - -CUDA_CFLAGS += -DGCAMORPH_ON_GPU - -# rules for building cuda files -.cu.o: - $(NVCC) -o $@ -c $< $(NVCCFLAGS) $(CUDA_CFLAGS) $(AM_CFLAGS) $(MNI_CFLAGS) - -bin_PROGRAMS = gca_read_test - -gca_read_test_SOURCES = gca_read_test.cpp -gca_read_test_LDADD = $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(BOOST_PO_LIB) -gca_read_test_LDFLAGS = $(OS_LDFLAGS) - -endif -# endif BUILDCUDA - -endif -# endif HAVE_BOOST_LIBS - - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - diff --git a/cudatest/mrilabeltest/Makefile.am b/cudatest/mrilabeltest/Makefile.am deleted file mode 100644 index dca167d7181..00000000000 --- a/cudatest/mrilabeltest/Makefile.am +++ /dev/null @@ -1,72 +0,0 @@ -AM_CFLAGS=-I$(top_srcdir)/include - -AM_CXXFLAGS=-I$(top_srcdir)/include\ - $(BOOST_CFLAGS)\ - -Wall -Wextra - -AM_LDFLAGS= - -## ---- -## CUDA -## ---- - -if HAVE_BOOST_LIBS - -# BUILDCUDA is defined if configure.in finds CUDA -if BUILDCUDA - -NVCCFLAGS += -g -arch sm_20 --ptxas-options=-v - -CUDA_CFLAGS += -DGCAMORPH_ON_GPU - -# rules for building cuda files -.cu.o: - $(NVCC) -o $@ -c $< $(NVCCFLAGS) $(CUDA_CFLAGS) $(AM_CFLAGS) $(MNI_CFLAGS) - - -bin_PROGRAMS = mriMarkLabelBorderVoxelTest mriMarkLabelBorderVoxelTest_cuda\ - mriVoxInLabelPartialVolumeTest mriVoxInLabelPartialVolumeTest_cuda - -# --- - -mriMarkLabelBorderVoxelTest_SOURCES = mriMarkLabelBorderVoxelTest.cpp -mriMarkLabelBorderVoxelTest_LDADD = $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(BOOST_PO_LIB) -mriMarkLabelBorderVoxelTest_LDFLAGS = $(OS_LDFLAGS) - -mriMarkLabelBorderVoxelTest_cuda_SOURCES = mriMarkLabelBorderVoxelTest.cpp -mriMarkLabelBorderVoxelTest_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) $(BOOST_CFLAGS) -DFS_CUDA -mriMarkLabelBorderVoxelTest_cuda_CXXFLAGS = $(CUDA_CXXFLAGS) $(AM_CFLAGS) $(BOOST_CFLAGS) -DFS_CUDA -mriMarkLabelBorderVoxelTest_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) $(BOOST_PO_LIB) -mriMarkLabelBorderVoxelTest_cuda_LDFLAGS = $(OS_LDFLAGS) -mriMarkLabelBorderVoxelTest_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(mriMarkLabelBorderVoxelTest_cuda_CFLAGS) \ - $(CFLAGS) $(mriMarkLabelBorderVoxelTest_cuda_LDFLAGS) $(LDFLAGS) -o $@ -# --- - -# --- - -mriVoxInLabelPartialVolumeTest_SOURCES = mriVoxInLabelPartialVolumeTest.cpp -mriVoxInLabelPartialVolumeTest_LDADD = $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(BOOST_PO_LIB) -mriVoxInLabelPartialVolumeTest_LDFLAGS = $(OS_LDFLAGS) - -mriVoxInLabelPartialVolumeTest_cuda_SOURCES = mriVoxInLabelPartialVolumeTest.cpp -mriVoxInLabelPartialVolumeTest_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) $(BOOST_CFLAGS) -DFS_CUDA -mriVoxInLabelPartialVolumeTest_cuda_CXXFLAGS = $(CUDA_CXXFLAGS) $(AM_CFLAGS) $(BOOST_CFLAGS) -DFS_CUDA -mriVoxInLabelPartialVolumeTest_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) $(BOOST_PO_LIB) -mriVoxInLabelPartialVolumeTest_cuda_LDFLAGS = $(OS_LDFLAGS) -mriVoxInLabelPartialVolumeTest_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(mriVoxInLabelPartialVolumeTest_cuda_CFLAGS) \ - $(CFLAGS) $(mriVoxInLabelParialVolumeTest_cuda_LDFLAGS) $(LDFLAGS) -o $@ - -endif -# endif BUILDCUDA - -endif -# endif HAVE_BOOST_LIBS - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - diff --git a/cudatest/volumecopy/Makefile.am b/cudatest/volumecopy/Makefile.am deleted file mode 100644 index 72e992b1e2a..00000000000 --- a/cudatest/volumecopy/Makefile.am +++ /dev/null @@ -1,40 +0,0 @@ -AM_CFLAGS=-I$(top_srcdir)/include - -AM_CXXFLAGS=-I$(top_srcdir)/include $(BOOST_CFLAGS) -Wall -Wextra - -AM_LDFLAGS= - -## ---- -## CUDA -## ---- - -if HAVE_BOOST_LIBS - -# BUILDCUDA is defined if configure.in finds CUDA -if BUILDCUDA - -CUDA_CFLAGS += -DGCAMORPH_ON_GPU - -# rules for building cuda files -.cu.o: - $(NVCC) -o $@ -c $< $(NVCCFLAGS) $(CUDA_CFLAGS) $(AM_CFLAGS) $(MNI_CFLAGS) - -bin_PROGRAMS = volume_copy_test_cuda - -volume_copy_test_cuda_SOURCES = volume_copy_test.cpp\ - volcopy.cu volcopy.hpp -volume_copy_test_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) $(BOOST_PO_LIB) -volume_copy_test_cuda_LDFLAGS = $(OS_LDFLAGS) - -endif -# endif BUILDCUDA - -endif -# endif HAVE_BOOST_LIBS - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - diff --git a/dicom/Makefile.am b/dicom/Makefile.am deleted file mode 100644 index 60d1768a4e0..00000000000 --- a/dicom/Makefile.am +++ /dev/null @@ -1,21 +0,0 @@ -# -# Makefile.am -# - -AM_CPPFLAGS=-I$(top_srcdir)/include \ - -I$(top_srcdir)/include/dicom - -AM_LDFLAGS= - -noinst_LIBRARIES= libdicom.a - -libdicom_a_SOURCES = condition.c dcmcond.c lst.c \ - ctnthread.c dcmdict.c dcm.c dcmsupport.c - -EXTRA_DIST= - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/distribution/Makefile.am b/distribution/Makefile.am deleted file mode 100644 index af79f3ba5af..00000000000 --- a/distribution/Makefile.am +++ /dev/null @@ -1,35 +0,0 @@ -# -# Makefile.am -# - -if SMALL_DIST_INSTALL -SUBDIRS=average lib docs fsafd subjects -else -SUBDIRS=average lib docs \ - fsafd subjects sessions diffusion fsl-extra trctrain -endif - -foodir=$(prefix) -foo_DATA= \ - tkmeditParcColorsCMA \ - Simple_surface_labels2005.txt \ - Simple_surface_labels2009.txt \ - FreeSurferColorLUT.txt \ - WMParcStatsLUT.txt \ - ASegStatsLUT.txt \ - DefectLUT.txt \ - SegmentNoLUT.txt - -foo_SCRIPTS= \ - FreeSurferEnv.csh \ - SetUpFreeSurfer.csh \ - sources.csh \ - FreeSurferEnv.sh \ - SetUpFreeSurfer.sh \ - sources.sh - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES=.license .xdebug_tk* error.log surfer.log csurf.log -include $(top_srcdir)/Makefile.extra diff --git a/distribution/average/Buckner_JNeurophysiol11_MNI152/Makefile.am b/distribution/average/Buckner_JNeurophysiol11_MNI152/Makefile.am deleted file mode 100644 index ab43a5f4221..00000000000 --- a/distribution/average/Buckner_JNeurophysiol11_MNI152/Makefile.am +++ /dev/null @@ -1,29 +0,0 @@ -# -# Makefile.am -# - -foodir=$(prefix)/average/Buckner_JNeurophysiol11_MNI152 - -foo_datafiles=Buckner2011_17Networks_ColorLUT.txt \ -Buckner2011_17NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz \ -Buckner2011_17NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz \ -Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz \ -Buckner2011_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz \ -Buckner2011_7Networks_ColorLUT.txt \ -Buckner2011_7NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz \ -Buckner2011_7NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz \ -Buckner2011_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz \ -Buckner2011_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz \ -FSL_MNI152_FreeSurferConformed_1mm.nii.gz \ -Buckner_JNeurophysiol11_MNI152_README - - -install-data-local: - test -z $(DESTDIR)$(foodir) || $(mkdir_p) $(DESTDIR)$(foodir) - $(INSTALL_DATA) $(foo_datafiles) $(DESTDIR)$(foodir) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/distribution/average/Choi_JNeurophysiol12_MNI152/Makefile.am b/distribution/average/Choi_JNeurophysiol12_MNI152/Makefile.am deleted file mode 100644 index dbb0d3e21b7..00000000000 --- a/distribution/average/Choi_JNeurophysiol12_MNI152/Makefile.am +++ /dev/null @@ -1,28 +0,0 @@ -# -# Makefile.am -# - -foodir=$(prefix)/average/Choi_JNeurophysiol12_MNI152 - -foo_datafiles=Choi2012_17Networks_ColorLUT.txt \ -Choi2012_17NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz \ -Choi2012_17NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz \ -Choi2012_17Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz \ -Choi2012_17Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz \ -Choi2012_7Networks_ColorLUT.txt \ -Choi2012_7NetworksConfidence_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz \ -Choi2012_7NetworksConfidence_MNI152_FreeSurferConformed1mm_TightMask.nii.gz \ -Choi2012_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz \ -Choi2012_7Networks_MNI152_FreeSurferConformed1mm_TightMask.nii.gz \ -Choi_JNeurophysiol12_MNI152_README \ -FSL_MNI152_FreeSurferConformed_1mm.nii.gz - -install-data-local: - test -z $(DESTDIR)$(foodir) || $(mkdir_p) $(DESTDIR)$(foodir) - $(INSTALL_DATA) $(foo_datafiles) $(DESTDIR)$(foodir) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/distribution/average/Makefile.am b/distribution/average/Makefile.am deleted file mode 100644 index ca8a3027406..00000000000 --- a/distribution/average/Makefile.am +++ /dev/null @@ -1,252 +0,0 @@ -# -# Makefile.am -# -SUBDIRS=surf \ - Yeo_JNeurophysiol11_MNI152 \ - Buckner_JNeurophysiol11_MNI152 \ - Choi_JNeurophysiol12_MNI152 \ - samseg - -foodir=$(prefix)/average - -GCA=\ - face.gca \ - RB_all_2016-05-10.vc700.gca \ - RB_all_withskull_2016-05-10.vc700.gca \ - talairach_mixed_with_skull.gca \ - wmsa_new_eesmith.gca \ - aseg+spmhead.ixi.gca \ - aseg+spmhead+vermis+pons.ixi.gca \ - pons.mni152.2mm.mgz - -GCS=\ - lh.atlas2002_simple.gcs \ - lh.atlas2005_simple.gcs \ - lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs \ - lh_trans_toSulc.gcs \ - lh.destrieux.simple.2009-07-29.gcs \ - rh.atlas2002_simple.gcs \ - rh.atlas2005_simple.gcs \ - rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs \ - rh_trans_toSulc.gcs \ - rh.destrieux.simple.2009-07-29.gcs \ - rh.DKTatlas40.gcs \ - lh.DKTatlas40.gcs \ - rh.DKTatlas100.gcs \ - lh.DKTatlas100.gcs \ - lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs \ - rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs \ - lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs \ - rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs \ - lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs \ - rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs - -TIF=\ - lh.average.curvature.filled.buckner40.tif \ - lh.average.CURVATURE.tif \ - lh.average.tif \ - rh.average.curvature.filled.buckner40.tif \ - rh.average.CURVATURE.tif \ - rh.average.tif \ - rigidly_aligned_brain_template.tif \ - lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif \ - rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif - -TXT=\ - colortable_desikan_killiany.txt \ - colortable_BA.txt \ - tissue_parms.txt - -MGZ=\ - HPMarch022005_ras.mgz \ - mni305.cor.mgz \ - mni305.cor.subfov1.mgz \ - mni305.cor.subfov2.mgz \ - mni305.mask.cor.mgz - -if NMR_INSTALL -foo_datafiles=\ - $(GCA) \ - $(GCS) \ - $(TIF) \ - $(TXT) \ - $(MGZ) \ - label_scales.dat \ - mni305.cor.readme \ - mni305.cor.subfov1.reg \ - mni305.cor.subfov2.reg \ - mni152.register.dat \ - mni152.1mm.register.dat \ - mni152.mni305.cor.subfov1.dat \ - mni152.mni305.cor.subfov2.dat \ - RB_all_2008-03-26.mni152.2mm.lta -else -foo_datafiles=\ - $(GCA) \ - $(GCS) \ - $(TIF) \ - $(TXT) \ - label_scales.dat \ - mni305.cor.mgz \ - mni305.cor.readme \ - mni305.mask.cor.mgz \ - mni305.cor.subfov1.mgz \ - mni305.cor.subfov2.mgz \ - mni305.cor.subfov1.reg \ - mni305.cor.subfov2.reg \ - mni152.register.dat \ - mni152.mni305.cor.subfov1.dat \ - mni152.mni305.cor.subfov2.dat \ - RB_all_2008-03-26.mni152.2mm.lta -endif - -foo_otherdatafiles=fsaverage.tar.gz fsaverage_sym.tar.gz \ - V1_average.tar.gz \ - fsaverage3.tar.gz fsaverage4.tar.gz \ - fsaverage5.tar.gz fsaverage6.tar.gz fsaverage7.tar.gz \ - EC_average.tar.gz mult-comp-cor.tar.gz Yeo_Brainmap_MNI152.tar.gz \ - build_gcs_morph.csh cvs_avg35.tar.gz cvs_avg35_inMNI152.tar.gz - -if INCLUDE_INFANTFS -install_CNYBCH=true -foo_otherdatafiles += CNYBCH.tar.gz -endif - -if SMALL_DIST_INSTALL -foo_datafiles=\ - RB_all_2016-05-10.vc700.gca \ - RB_all_withskull_2016-05-10.vc700.gca \ - lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs \ - rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs \ - lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs \ - rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs \ - lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs \ - rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs \ - lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif \ - rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif \ - rigidly_aligned_brain_template.tif \ - mni305.cor.mgz \ - mni305.cor.subfov1.mgz \ - mni305.cor.subfov2.mgz \ - mni305.mask.cor.mgz \ - colortable_desikan_killiany.txt \ - colortable_BA.txt -endif - -install: - test -z $(DESTDIR)$(foodir) || $(mkdir_p) $(DESTDIR)$(foodir) - $(INSTALL_DATA) $(foo_datafiles) $(DESTDIR)$(foodir) - mkdir -p $(DESTDIR)$(prefix)/subjects - rm -Rf $(DESTDIR)$(prefix)/subjects/fsaverage - rm -Rf $(top_builddir)/distribution/average/fsaverage - gunzip -c $(top_srcdir)/distribution/average/fsaverage.tar.gz | tar xvf - - mv $(top_builddir)/distribution/average/fsaverage \ - $(DESTDIR)$(prefix)/subjects - chmod -R 775 $(DESTDIR)$(prefix)/subjects/fsaverage -if SMALL_DIST_INSTALL -else - rm -Rf $(DESTDIR)$(prefix)/subjects/cvs_avg35 - rm -Rf $(top_builddir)/distribution/average/cvs_avg35 - gunzip -c $(top_srcdir)/distribution/average/cvs_avg35.tar.gz | tar xvf - - mv $(top_builddir)/distribution/average/cvs_avg35 \ - $(DESTDIR)$(prefix)/subjects - rm -Rf $(DESTDIR)$(prefix)/subjects/cvs_avg35_inMNI152 - rm -Rf $(top_builddir)/distribution/average/cvs_avg35_inMNI152 - gunzip -c $(top_srcdir)/distribution/average/cvs_avg35_inMNI152.tar.gz | tar xvf - - mv $(top_builddir)/distribution/average/cvs_avg35_inMNI152 \ - $(DESTDIR)$(prefix)/subjects - rm -Rf $(DESTDIR)$(prefix)/subjects/fsaverage_sym - rm -Rf $(top_builddir)/distribution/average/fsaverage_sym - gunzip -c $(top_srcdir)/distribution/average/fsaverage_sym.tar.gz | tar xvf - - mv $(top_builddir)/distribution/average/fsaverage_sym \ - $(DESTDIR)$(prefix)/subjects - chmod -R 775 $(DESTDIR)$(prefix)/subjects/fsaverage_sym - rm -Rf $(DESTDIR)$(prefix)/subjects/V1_average - rm -Rf $(top_builddir)/distribution/average/V1_average - gunzip -c $(top_srcdir)/distribution/average/V1_average.tar.gz | tar xvf - - cp -f $(top_builddir)/distribution/average/V1_average/scripts/predict_v1.sh \ - $(DESTDIR)$(bindir) - mv $(top_builddir)/distribution/average/V1_average \ - $(DESTDIR)$(prefix)/subjects - chmod -R 775 $(DESTDIR)$(prefix)/subjects/V1_average - rm -Rf $(DESTDIR)$(prefix)/subjects/fsaverage3 - rm -Rf $(top_builddir)/distribution/average/fsaverage3 - gunzip -c $(top_srcdir)/distribution/average/fsaverage3.tar.gz | tar xvf - - mv $(top_builddir)/distribution/average/fsaverage3 \ - $(DESTDIR)$(prefix)/subjects - chmod -R 775 $(DESTDIR)$(prefix)/subjects/fsaverage3 - rm -Rf $(DESTDIR)$(prefix)/subjects/fsaverage4 - rm -Rf $(top_builddir)/distribution/average/fsaverage4 - gunzip -c $(top_srcdir)/distribution/average/fsaverage4.tar.gz | tar xvf - - mv $(top_builddir)/distribution/average/fsaverage4 \ - $(DESTDIR)$(prefix)/subjects - chmod -R 775 $(DESTDIR)$(prefix)/subjects/fsaverage4 - rm -Rf $(DESTDIR)$(prefix)/subjects/fsaverage5 - rm -Rf $(top_builddir)/distribution/average/fsaverage5 - gunzip -c $(top_srcdir)/distribution/average/fsaverage5.tar.gz | tar xvf - - mv $(top_builddir)/distribution/average/fsaverage5 \ - $(DESTDIR)$(prefix)/subjects - chmod -R 775 $(DESTDIR)$(prefix)/subjects/fsaverage5 - rm -Rf $(DESTDIR)$(prefix)/subjects/fsaverage6 - rm -Rf $(top_builddir)/distribution/average/fsaverage6 - gunzip -c $(top_srcdir)/distribution/average/fsaverage6.tar.gz | tar xvf - - mv $(top_builddir)/distribution/average/fsaverage6 \ - $(DESTDIR)$(prefix)/subjects - chmod -R 775 $(DESTDIR)$(prefix)/subjects/fsaverage6 - rm -Rf $(DESTDIR)$(prefix)/subjects/?h.EC_average - rm -Rf $(top_builddir)/distribution/average/?h.EC_average - gunzip -c $(top_srcdir)/distribution/average/EC_average.tar.gz | tar xvf - - mv $(top_builddir)/distribution/average/?h.EC_average \ - $(DESTDIR)$(prefix)/subjects - chmod -R 775 $(DESTDIR)$(prefix)/subjects/?h.EC_average - rm -Rf $(DESTDIR)$(prefix)/average/mult-comp-cor - rm -Rf $(top_builddir)/distribution/average/mult-comp-cor - gunzip -c $(top_srcdir)/distribution/average/mult-comp-cor.tar.gz | tar xvf - - pwd - mv $(top_builddir)/distribution/average/mult-comp-cor \ - $(DESTDIR)$(prefix)/average - chmod -R 775 $(DESTDIR)$(prefix)/average/mult-comp-cor - rm -Rf $(DESTDIR)$(prefix)/average/Yeo_Brainmap_MNI152 - rm -Rf $(top_builddir)/distribution/average/Yeo_Brainmap_MNI152 - gunzip -c $(top_srcdir)/distribution/average/Yeo_Brainmap_MNI152.tar.gz | tar xvf - - pwd - mv $(top_builddir)/distribution/average/Yeo_Brainmap_MNI152 \ - $(DESTDIR)$(prefix)/average - chmod -R 775 $(DESTDIR)$(prefix)/average/Yeo_Brainmap_MNI152 - cd surf; make install - cd Yeo_JNeurophysiol11_MNI152; make install - cd Buckner_JNeurophysiol11_MNI152; make install - cd Choi_JNeurophysiol12_MNI152; make install - cd samseg; make install - if [ "$(install_CNYBCH)" = "true" ]; then \ - rm -Rf $(DESTDIR)$(prefix)/average/CNYBCH ;\ - rm -Rf $(top_builddir)/distribution/average/CNYBCH ;\ - gunzip -c $(top_srcdir)/distribution/average/CNYBCH.tar.gz | tar xvf - ;\ - pwd ;\ - mv $(top_builddir)/distribution/average/CNYBCH $(DESTDIR)$(prefix)/average ;\ - chmod -R 775 $(DESTDIR)$(prefix)/average/CNYBCH ;\ - fi - -endif - -uninstall-hook: - rm -Rf $(DESTDIR)$(prefix)/subjects/cvs_avg35 - rm -Rf $(DESTDIR)$(prefix)/subjects/cvs_avg35_inMNI152 - rm -Rf $(DESTDIR)$(prefix)/subjects/fsaverage - rm -Rf $(DESTDIR)$(prefix)/subjects/fsaverage_sym - rm -Rf $(DESTDIR)$(prefix)/subjects/fsaverage3 - rm -Rf $(DESTDIR)$(prefix)/subjects/fsaverage4 - rm -Rf $(DESTDIR)$(prefix)/subjects/fsaverage5 - rm -Rf $(DESTDIR)$(prefix)/subjects/fsaverage6 - rm -Rf $(DESTDIR)$(prefix)/subjects/?h.EC_average - rm -Rf $(DESTDIR)$(prefix)/subjects/V1_average - rm -f $(DESTDIR)$(bindir)/predict_v1.sh - rm -Rf $(DESTDIR)$(prefix)/average/mult-comp-cor - rm -Rf $(DESTDIR)$(prefix)/average/Yeo_Brainmap_MNI152 - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="HPMarch022005_ras.mgz" - -include $(top_srcdir)/Makefile.extra diff --git a/distribution/average/Yeo_JNeurophysiol11_MNI152/Makefile.am b/distribution/average/Yeo_JNeurophysiol11_MNI152/Makefile.am deleted file mode 100644 index a34bb287b39..00000000000 --- a/distribution/average/Yeo_JNeurophysiol11_MNI152/Makefile.am +++ /dev/null @@ -1,20 +0,0 @@ -# -# Makefile.am -# - -foodir=$(prefix)/average/Yeo_JNeurophysiol11_MNI152 - -foo_datafiles=Yeo_JNeurophysiol11_MNI152_README FSL_MNI152_FreeSurferConformed_1mm.nii.gz \ -Yeo2011_17Networks_ColorLUT.txt Yeo2011_17Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz \ -Yeo2011_17Networks_MNI152_FreeSurferConformed1mm.nii.gz Yeo2011_7Networks_ColorLUT.txt \ -Yeo2011_7Networks_MNI152_FreeSurferConformed1mm_LiberalMask.nii.gz Yeo2011_7Networks_MNI152_FreeSurferConformed1mm.nii.gz - -install-data-local: - test -z $(DESTDIR)$(foodir) || $(mkdir_p) $(DESTDIR)$(foodir) - $(INSTALL_DATA) $(foo_datafiles) $(DESTDIR)$(foodir) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/distribution/average/samseg/Makefile.am b/distribution/average/samseg/Makefile.am deleted file mode 100644 index 7a095732ee1..00000000000 --- a/distribution/average/samseg/Makefile.am +++ /dev/null @@ -1,19 +0,0 @@ -# -# Makefile.am -# - -foodir=$(prefix)/average/samseg - -foo_tarballs=20Subjects_smoothing2_down2_smoothingForAffine2.tar.gz - -install-data-local: - test -z $(DESTDIR)$(foodir) || $(mkdir_p) $(DESTDIR)$(foodir) - for tarball in $(foo_tarballs); do \ - gunzip -c $(top_srcdir)/distribution/average/samseg/$$tarball | tar xvf - -C $(foodir);\ - done - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/distribution/average/surf/Makefile.am b/distribution/average/surf/Makefile.am deleted file mode 100644 index 0b7f37318b8..00000000000 --- a/distribution/average/surf/Makefile.am +++ /dev/null @@ -1,21 +0,0 @@ -# -# Makefile.am -# - -foodir=$(prefix)/average/surf - -foo_datafiles=README lh.sphere.reg rh.sphere.reg \ -lh.sphere.ico0.reg lh.sphere.ico4.reg rh.sphere.ico0.reg rh.sphere.ico4.reg \ -lh.sphere.ico1.reg lh.sphere.ico5.reg rh.sphere.ico1.reg rh.sphere.ico5.reg \ -lh.sphere.ico2.reg lh.sphere.ico6.reg rh.sphere.ico2.reg rh.sphere.ico6.reg \ -lh.sphere.ico3.reg lh.sphere.ico7.reg rh.sphere.ico3.reg rh.sphere.ico7.reg - -install-data-local: - test -z $(DESTDIR)$(foodir) || $(mkdir_p) $(DESTDIR)$(foodir) - $(INSTALL_DATA) $(foo_datafiles) $(DESTDIR)$(foodir) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/distribution/diffusion/Makefile.am b/distribution/diffusion/Makefile.am deleted file mode 100644 index 476d80b7d21..00000000000 --- a/distribution/diffusion/Makefile.am +++ /dev/null @@ -1,14 +0,0 @@ -# -# Makefile.am -# - -SUBDIRS=mgh-dti-seqpack - -EXTRA_DIST= - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - diff --git a/distribution/diffusion/mgh-dti-seqpack/Makefile.am b/distribution/diffusion/mgh-dti-seqpack/Makefile.am deleted file mode 100644 index 28fc2142fda..00000000000 --- a/distribution/diffusion/mgh-dti-seqpack/Makefile.am +++ /dev/null @@ -1,66 +0,0 @@ -# -# Makefile.am -# - -foodir=$(prefix)/diffusion/mgh-dti-seqpack -foo_DATA=README \ - gradient_mgh_dti6.gdt gradient_mgh_dti12.gdt \ - gradient_mgh_dti13.gdt gradient_mgh_dti57.gdt \ - gradient_mgh_dti14.gdt gradient_mgh_dti58.gdt \ - gradient_mgh_dti15.gdt gradient_mgh_dti59.gdt \ - gradient_mgh_dti16.gdt gradient_mgh_dti60.gdt \ - gradient_mgh_dti17.gdt gradient_mgh_dti61.gdt \ - gradient_mgh_dti18.gdt gradient_mgh_dti62.gdt \ - gradient_mgh_dti19.gdt gradient_mgh_dti63.gdt \ - gradient_mgh_dti20.gdt gradient_mgh_dti64.gdt \ - gradient_mgh_dti21.gdt gradient_mgh_dti65.gdt \ - gradient_mgh_dti22.gdt gradient_mgh_dti66.gdt \ - gradient_mgh_dti23.gdt gradient_mgh_dti67.gdt \ - gradient_mgh_dti24.gdt gradient_mgh_dti68.gdt \ - gradient_mgh_dti25.gdt gradient_mgh_dti69.gdt \ - gradient_mgh_dti26.gdt gradient_mgh_dti70.gdt \ - gradient_mgh_dti27.gdt gradient_mgh_dti71.gdt \ - gradient_mgh_dti28.gdt gradient_mgh_dti72.gdt \ - gradient_mgh_dti29.gdt gradient_mgh_dti73.gdt \ - gradient_mgh_dti30.gdt gradient_mgh_dti74.gdt \ - gradient_mgh_dti31.gdt gradient_mgh_dti75.gdt \ - gradient_mgh_dti32.gdt gradient_mgh_dti76.gdt \ - gradient_mgh_dti33.gdt gradient_mgh_dti77.gdt \ - gradient_mgh_dti34.gdt gradient_mgh_dti78.gdt \ - gradient_mgh_dti35.gdt gradient_mgh_dti79.gdt \ - gradient_mgh_dti36.gdt gradient_mgh_dti80.gdt \ - gradient_mgh_dti37.gdt gradient_mgh_dti81.gdt \ - gradient_mgh_dti38.gdt gradient_mgh_dti82.gdt \ - gradient_mgh_dti39.gdt gradient_mgh_dti83.gdt \ - gradient_mgh_dti40.gdt gradient_mgh_dti84.gdt \ - gradient_mgh_dti41.gdt gradient_mgh_dti85.gdt \ - gradient_mgh_dti42.gdt gradient_mgh_dti86.gdt \ - gradient_mgh_dti43.gdt gradient_mgh_dti87.gdt \ - gradient_mgh_dti44.gdt gradient_mgh_dti88.gdt \ - gradient_mgh_dti45.gdt gradient_mgh_dti89.gdt \ - gradient_mgh_dti46.gdt gradient_mgh_dti90.gdt \ - gradient_mgh_dti47.gdt gradient_mgh_dti91.gdt \ - gradient_mgh_dti48.gdt gradient_mgh_dti92.gdt \ - gradient_mgh_dti49.gdt gradient_mgh_dti93.gdt \ - gradient_mgh_dti50.gdt gradient_mgh_dti94.gdt \ - gradient_mgh_dti51.gdt gradient_mgh_dti95.gdt \ - gradient_mgh_dti52.gdt gradient_mgh_dti96.gdt \ - gradient_mgh_dti53.gdt gradient_mgh_dti97.gdt \ - gradient_mgh_dti54.gdt gradient_mgh_dti98.gdt \ - gradient_mgh_dti55.gdt gradient_mgh_dti99.gdt \ - gradient_mgh_dti56.gdt \ - gradient_mgh_dti06.gdt gradient_mgh_dti240.gdt - -EXTRA_DIST=$(foo_DATA) - -install: - rm -Rf $(DESTDIR)$(prefix)/diffusion/mgh-dti-seqpack/ - mkdir -p $(DESTDIR)$(prefix)/diffusion/mgh-dti-seqpack/ - cd $(top_srcdir)/distribution/diffusion/mgh-dti-seqpack/; cp $(foo_DATA) \ -$(DESTDIR)$(prefix)/diffusion/mgh-dti-seqpack/ - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/distribution/docs/Makefile.am b/distribution/docs/Makefile.am deleted file mode 100644 index 841c7488834..00000000000 --- a/distribution/docs/Makefile.am +++ /dev/null @@ -1,40 +0,0 @@ -# -# Makefile.am -# - -foodir=$(prefix)/docs -foo_DATA=\ - license.freesurfer_SLA.txt \ - license.minc.txt \ - license.fsl.txt \ - license.tcltk.txt \ - license.tix.txt \ - license.blt.txt \ - license.swig.txt \ - license.vxl.txt \ - license.thrust.txt \ - license.qt.txt \ - license.vtk.txt \ - license.itk.txt \ - license.petsc.txt \ - license.boost.txt \ - license.nrrdio.txt \ - license.nifti.txt \ - license.gifti.txt \ - license.cuda.txt \ - license.dcmtk.txt \ - license.lapack.txt - -if SMALL_DIST_INSTALL -else -poodir=$(prefix)/tktools -poo_DATA=license.cortechs.txt -endif - -EXTRA_DIST=$(foo_DATA) $(poo_DATA) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/distribution/fsafd/Makefile.am b/distribution/fsafd/Makefile.am deleted file mode 100644 index 5df4ca1d307..00000000000 --- a/distribution/fsafd/Makefile.am +++ /dev/null @@ -1,34 +0,0 @@ -# -# Makefile.am -# - -SUBDIRS= - -foodir=$(prefix)/fsafd - -foo_datafiles=TalairachingCovariance.adf \ - TalairachingMean.adf \ - TalairachingProbas.adf - -# not yet used: -# lh.CorpusCallosumCutDice.adf \ -# lh.CorticalLabelingPercentArea_txt.adf \ -# lh.SurfRegistrationResidualVar.adf \ -# PonsCutDice.adf \ -# rh.CorpusCallosumCutDice.adf \ -# rh.CorticalLabelingPercentArea_txt.adf \ -# RibbonPlacementDice.adf \ -# SubcorticalLabelingPercentVol.adf \ -# WMsegmentationDice.adf \ -# lh.EV90.mgh \ -# lh.ThicknessMatrix.mgh - -install-data-local: - test -z $(DESTDIR)$(foodir) || $(mkdir_p) $(DESTDIR)$(foodir) - $(INSTALL_DATA) $(foo_datafiles) $(DESTDIR)$(foodir) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/distribution/fsl-extra/Makefile.am b/distribution/fsl-extra/Makefile.am deleted file mode 100644 index 9faa08e16e8..00000000000 --- a/distribution/fsl-extra/Makefile.am +++ /dev/null @@ -1,14 +0,0 @@ -# -# Makefile.am -# - -foodir=$(bindir) -foo_DATA=flirt.newdefault.20080811.sch - -EXTRA_DIST=$(foo_DATA) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/distribution/lib/Makefile.am b/distribution/lib/Makefile.am deleted file mode 100644 index d35befe883f..00000000000 --- a/distribution/lib/Makefile.am +++ /dev/null @@ -1,10 +0,0 @@ -# -# Makefile.am -# -SUBDIRS=bem - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/distribution/lib/bem/Makefile.am b/distribution/lib/bem/Makefile.am deleted file mode 100644 index ae9a26712c1..00000000000 --- a/distribution/lib/bem/Makefile.am +++ /dev/null @@ -1,18 +0,0 @@ -# -# Makefile.am -# - -foodir=$(prefix)/lib/bem -foo_datafiles=\ - ic0.tri ic2.tri ic4.tri ic6.tri ic1.tri ic3.tri ic5.tri ic7.tri \ - inner_skull.dat outer_skull.dat outer_skin.dat - -install-data-local: - test -z $(DESTDIR)$(foodir) || $(mkdir_p) $(DESTDIR)$(foodir) - $(INSTALL_DATA) $(foo_datafiles) $(DESTDIR)$(foodir) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/distribution/sessions/Makefile.am b/distribution/sessions/Makefile.am deleted file mode 100644 index a4accf0c15d..00000000000 --- a/distribution/sessions/Makefile.am +++ /dev/null @@ -1,13 +0,0 @@ -# -# Makefile.am -# -foodir=$(prefix)/sessions -foo_DATA=README - -EXTRA_DIST=$(foo_DATA) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/distribution/subjects/Makefile.am b/distribution/subjects/Makefile.am deleted file mode 100644 index 5c6aa635223..00000000000 --- a/distribution/subjects/Makefile.am +++ /dev/null @@ -1,16 +0,0 @@ -# -# Makefile.am -# - -foodir=$(prefix)/subjects -foo_datafiles=README sample-001.mgz sample-002.mgz - -install-data-local: - test -z $(DESTDIR)$(foodir) || $(mkdir_p) $(DESTDIR)$(foodir) - $(INSTALL_DATA) $(foo_datafiles) $(DESTDIR)$(foodir) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/distribution/trctrain/Makefile.am b/distribution/trctrain/Makefile.am deleted file mode 100644 index f87dcc4270d..00000000000 --- a/distribution/trctrain/Makefile.am +++ /dev/null @@ -1,32 +0,0 @@ -# -# Makefile.am -# - -foodir=$(prefix)/trctrain - -install: trctraindata.tar.gz - rm -Rf $(DESTDIR)$(prefix)/trctrain - rm -Rf $(top_builddir)/distribution/trctrain/trc??? - rm -Rf $(top_builddir)/distribution/trctrain/README - rm -Rf $(top_builddir)/distribution/trctrain/trainlist.txt - gunzip -c $(top_srcdir)/distribution/trctrain/trctraindata.tar.gz | tar xvf - - mkdir -p $(DESTDIR)$(prefix)/trctrain - mv -v $(top_builddir)/distribution/trctrain/trc??? \ - $(DESTDIR)$(prefix)/trctrain - mv -v $(top_builddir)/distribution/trctrain/README \ - $(DESTDIR)$(prefix)/trctrain - mv -v $(top_builddir)/distribution/trctrain/trainlist.txt \ - $(DESTDIR)$(prefix)/trctrain - chmod -R 775 $(DESTDIR)$(prefix)/trctrain - -uninstall-hook: - rm -Rf $(DESTDIR)$(prefix)/trctrain - -EXTRA_DIST=trctraindata.tar.gz - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= - -include $(top_srcdir)/Makefile.extra diff --git a/dmri_poistats/Makefile.am b/dmri_poistats/Makefile.am deleted file mode 100644 index fe0cfbe974c..00000000000 --- a/dmri_poistats/Makefile.am +++ /dev/null @@ -1,199 +0,0 @@ -# -# Makefile.am for poistats -# - -#itk is required for building poistats -# add ITK -if HAVE_ITK_LIBS - -ITK_THINGS=$(ITK_CFLAGS) -DHAVE_ITK_LIBS - -DATAMODEL_SRCS = \ - datamodel/PoistatsModel.cxx \ - datamodel/PoistatsModel.h - -DATA_SRCS = \ - datamodel/data/PoistatsReplica.cxx \ - datamodel/data/PoistatsReplica.h \ - datamodel/data/PoistatsReplicas.cxx \ - datamodel/data/PoistatsReplicas.h - -EVENTS_SRCS = \ - datamodel/events/PoistatsEvents.h \ - datamodel/events/CommandUpdate.cxx \ - datamodel/events/CommandUpdate.h - -UTILS_SRCS = \ - datamodel/utils/itkPoistatsFilter.txx \ - datamodel/utils/itkPoistatsFilter.h \ - datamodel/utils/InitializePath.cxx \ - datamodel/utils/InitializePath.h \ - datamodel/utils/EigenVectorInitPathStrategy.cxx \ - datamodel/utils/EigenVectorInitPathStrategy.h \ - datamodel/utils/FieldLineInitPathStrategy.cxx \ - datamodel/utils/FieldLineInitPathStrategy.h - -IO_SRCS = \ - io/AsymmetricTensorReaderStrategy.cxx \ - io/AsymmetricTensorReaderStrategy.h \ - io/AsymmetricTensorVectorReaderStrategy.cxx \ - io/AsymmetricTensorVectorReaderStrategy.h \ - io/SymmetricTensorReaderStrategy.cxx \ - io/SymmetricTensorReaderStrategy.h \ - io/TensorReaderStrategy.cxx \ - io/TensorReaderStrategy.h - -AM_CPPFLAGS = $(X_CFLAGS) $(VXL_CFLAGS) \ - -I$(top_srcdir)/dmri_poistats \ - -I$(top_srcdir)/include \ - -I$(top_srcdir)/itkio \ - -I$(top_srcdir)/itkutils \ - $(ITK_THINGS) -DHAVE_ZLIB - -bin_PROGRAMS = \ - dmri_poistats \ - dmri_initialize_path \ - dmri_mask - -# poistats -dmri_poistats_SOURCES = \ - $(DATAMODEL_SRCS) \ - $(DATA_SRCS) \ - $(EVENTS_SRCS) \ - $(UTILS_SRCS) \ - $(IO_SRCS) \ - dmri_poistats.cxx -dmri_poistats_LDADD = $(LIBS_ITK) \ - $(top_builddir)/itkio/libitkio.a \ - $(top_builddir)/itkutils/libitkutils.a \ - -lITKBasicFilters -litkgdcm -litkpng -litktiff -lITKSpatialObject \ - -lITKNumerics -litkvnl_inst -litkvnl_algo -litkv3p_netlib \ - -litkvnl -litkvcl \ - -lITKMetaIO -litksys -lITKEXPAT -lITKniftiio -lITKznz -litkzlib \ - $(addprefix $(top_builddir)/, $(LIBS_MGH) ) -dmri_poistats_LDFLAGS = $(OS_LDFLAGS) -dmri_poistats_CXXFLAGS = - -# initialize poistats path stuff -dmri_initialize_path_SOURCES = \ - $(DATAMODEL_SRCS) \ - $(UTILS_SRCS) \ - dmri_initialize_path.cxx -dmri_initialize_path_LDADD = $(LIBS_ITK) \ - $(top_builddir)/itkutils/libitkutils.a \ - -lITKBasicFilters -litkgdcm -litkpng -litktiff -lITKSpatialObject \ - -lITKNumerics -litkvnl_inst -litkvnl_algo -litkv3p_netlib \ - -litkvnl -litkvcl \ - -lITKMetaIO -litksys -lITKEXPAT -lITKniftiio -lITKznz -litkzlib \ - $(addprefix $(top_builddir)/, $(LIBS_MGH) ) -dmri_initialize_path_LDFLAGS = $(OS_LDFLAGS) -dmri_initialize_path_CXXFLAGS = - -# mask path -dmri_mask_SOURCES = \ - dmri_mask.cxx -dmri_mask_LDADD = $(addprefix $(top_builddir)/, $(LIBS_MGH) ) \ - $(top_builddir)/itkutils/libitkutils.a -dmri_mask_LDFLAGS = $(OS_LDFLAGS) -dmri_mask_CXXFLAGS = - -# trick to get test data into the build directory -foo_SOURCES= -foo: - if ! test -f "$(top_builddir)/dmri_poistats/test/data/Path.nii.gz"; then \ - mkdir -p $(top_builddir)/dmri_poistats/test/data/; \ - cp -v $(top_srcdir)/dmri_poistats/test/data/*.nii.gz \ - $(top_builddir)/dmri_poistats/test/data/; fi; - -# tests -if HAVE_CPPUNIT - -check_PROGRAMS = \ - foo \ - TestPoistatsReplica \ - TestPoistatsReplicas \ - TestPoistats - -TESTS = \ - TestPoistatsReplica \ - TestPoistatsReplicas \ - TestPoistats - -# TestPoistatsReplica -TestPoistatsReplica_SOURCES= \ - $(DATAMODEL_SRCS) \ - $(DATA_SRCS) \ - $(EVENTS_SRCS) \ - $(UTILS_SRCS) \ - TestPoistatsReplica.cxx - -TestPoistatsReplica_CXXFLAGS=$(CPPUNIT_CFLAGS) -Wno-non-virtual-dtor - -TestPoistatsReplica_LDADD=$(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(top_builddir)/itkio/libitkio.a \ - $(top_builddir)/itkutils/libitkutils.a \ - $(CPPUNIT_LIBS) -lcppunit -ldl \ - -lITKBasicFilters -litkgdcm -litkpng -litktiff -lITKSpatialObject \ - -lITKNumerics -litkvnl_inst -litkvnl_algo -litkv3p_netlib \ - -litkvnl -litkvcl -lITKMetaIO -litksys -lITKEXPAT -lITKniftiio \ - -lITKznz -litkzlib - -# TestPoistatsReplicas -TestPoistatsReplicas_SOURCES= \ - $(DATAMODEL_SRCS) \ - $(DATA_SRCS) \ - $(EVENTS_SRCS) \ - $(UTILS_SRCS) \ - TestPoistatsReplicas.cxx - -TestPoistatsReplicas_CXXFLAGS=$(CPPUNIT_CFLAGS) -Wno-non-virtual-dtor - -TestPoistatsReplicas_LDADD=$(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(top_builddir)/itkio/libitkio.a \ - $(top_builddir)/itkutils/libitkutils.a \ - $(CPPUNIT_LIBS) -lcppunit -ldl \ - -lITKBasicFilters -litkgdcm -litkpng -litktiff -lITKSpatialObject \ - -lITKNumerics -litkvnl_inst -litkvnl_algo -litkv3p_netlib \ - -litkvnl -litkvcl -lITKMetaIO -litksys -lITKEXPAT -lITKniftiio \ - -lITKznz -litkzlib - -# TestPoistats -TestPoistats_SOURCES= \ - $(DATAMODEL_SRCS) \ - $(DATA_SRCS) \ - $(EVENTS_SRCS) \ - $(UTILS_SRCS) \ - $(IO_SRCS) \ - TestPoistats.cxx - -TestPoistats_CXXFLAGS=$(CPPUNIT_CFLAGS) -Wno-non-virtual-dtor - -TestPoistats_LDADD= \ - $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(top_builddir)/itkio/libitkio.a \ - $(top_builddir)/itkutils/libitkutils.a \ - $(LIBS_ITK) \ - $(CPPUNIT_LIBS) -lcppunit \ - -lITKBasicFilters -litkgdcm -litkpng -litktiff -lITKSpatialObject \ - -lITKNumerics -litkvnl_inst -litkvnl_algo -litkv3p_netlib -litkvnl -litkvcl \ - -lITKIO -lITKMetaIO -litksys -lITKEXPAT -lITKniftiio -lITKznz -litkzlib - -TestPoistats_LDFLAGS = $(OS_LDFLAGS) -endif -#end cppunit - -endif -#end itk - -EXTRA_DIST=test/data/FinalSeeds.nii.gz \ - test/data/Path.nii.gz \ - test/data/HelixTensors.nii.gz - - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES=io/CVS datamodel/CVS datamodel/utils/CVS datamodel/events/CVS \ -datamodel/data/CVS test/CVS test/data/CVS - -include $(top_srcdir)/Makefile.extra diff --git a/dmri_tensoreig/Makefile.am b/dmri_tensoreig/Makefile.am deleted file mode 100644 index f6ff48bafc3..00000000000 --- a/dmri_tensoreig/Makefile.am +++ /dev/null @@ -1,13 +0,0 @@ - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = dmri_tensoreig -dmri_tensoreig_SOURCES=dmri_tensoreig.c -dmri_tensoreig_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -dmri_tensoreig_LDFLAGS=$(OS_LDFLAGS) - -EXTRA_DIST=do.sh - -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/dngtester/Makefile.am b/dngtester/Makefile.am deleted file mode 100644 index 334a5dfb295..00000000000 --- a/dngtester/Makefile.am +++ /dev/null @@ -1,38 +0,0 @@ -## -## Makefile.am -## - -if HAVE_ITK_LIBS -ITK_THINGS=$(ITK_CFLAGS) \ - -I$(ITK_DIR)/include/InsightToolkit/Utilities/vxl/core \ - -I$(ITK_DIR)/include/InsightToolkit/Utilities/vxl/vcl \ - -DHAVE_ITK_LIBS -endif - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -O0 -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -O0 $(ITK_THINGS) - -dngtester_SOURCES=dngtester.c -dngtester_LDADD= $(top_builddir)/fsgdf/libfsgdf.a \ - $(addprefix $(top_builddir)/, $(LIBS_MGH)) -dngtester_LDFLAGS=$(OS_LDFLAGS) - -cpptester_SOURCES=cpptester.cpp -cpptester_LDADD= $(top_builddir)/fsgdf/libfsgdf.a \ - $(addprefix $(top_builddir)/, $(LIBS_MGH)) -cpptester_LDFLAGS=$(OS_LDFLAGS) - -# only compile cpptester if ITK is enabled -if HAVE_ITK_LIBS -bin_PROGRAMS = dngtester cpptester -else -bin_PROGRAMS = dngtester -endif - -install: - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/doxy-file-header b/doxy-file-header deleted file mode 100644 index a14d7e2d26f..00000000000 --- a/doxy-file-header +++ /dev/null @@ -1,24 +0,0 @@ -/** - * @file REPLACE_WITH_FILENAME - * @brief REPLACE_WITH_ONE_LINE_SHORT_DESCRIPTION - * - * REPLACE_WITH_LONG_DESCRIPTION_OR_REFERENCE - */ -/* - * Original Author: REPLACE_WITH_FULL_NAME_OF_CREATING_AUTHOR - * CVS Revision Info: - * $Author: nicks $ - * $Date: 2014/08/13 21:14:13 $ - * $Revision: 1.13 $ - * - * Copyright © 2014 The General Hospital Corporation (Boston, MA) "MGH" - * - * Terms and conditions for use, reproduction, distribution and contribution - * are found in the 'FreeSurfer Software License Agreement' contained - * in the file 'LICENSE' found in the FreeSurfer distribution, and here: - * - * https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense - * - * Reporting: freesurfer@nmr.mgh.harvard.edu - * - */ diff --git a/dummy/Makefile.am b/dummy/Makefile.am deleted file mode 100644 index 32ff5c83fc5..00000000000 --- a/dummy/Makefile.am +++ /dev/null @@ -1,69 +0,0 @@ -## -## Makefile.am -## - -####################################################################### -# When you create your own program directory, copy the 'from' to the -# 'to' lines to your Makefile.am and change dummy to your program name. -# -# 0. mkdir dev/yourdir and put .c file in there -# 1. modify dev/configure.in to have yourdir/Makefile -# 2. modify dev/Makefile.am to have yourdir as one of SUBDIRS -# 3. create dev/yourdir/Makefile.am (follow dummy/Makefile.am) -# i.e. replace dummy with your program name. -# -# 4. ./setup_configure at the top directory, i.e. dev/ (which will create -# Makefile.in in yourdir directory and configure from configure.in) -# 5. ./configure .... and make to make sure that your new thing is working -# 6. try make to make sure that yourthing is compiled. -# -# After confirming everything working: -# 7. checkin yourdir/Makefile.am, yourdir/yourprog.c or cpp. -# (Don't checkin Makefile or Makefile.in.) -# 8. commit dev/configure.in, dev/Makefile.am -# -# 9. lastly, delete this help text from your own Makefile.am! -# -# If you have problems, please let us know (zkaufman@nmr.mgh.harvard.edu -# or nicks@nmr.mgh.harvard.edu). -######################################################################### -# from ------------------------------------------------ - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = dummy -dummy_SOURCES=dummy.c -dummy_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -dummy_LDFLAGS=$(OS_LDFLAGS) - -# to -------------------------------------------------- -# -# Where $(OS_LDFLAGS) is to compile programs statically for Linux. -# -# You can have multiple bin_PROGRAMS in the same directory. -# -######################################################################## -# When you want to create your program to test, use the following -# framework: -# You can have as many programs (separated by space) in check_PROGRAMS. -# Your program can consist of many sources (you add to _SOURCES= line). -# You can do "make myown" to compile. The default CFLAGS="-g -O2", but -# you can do "make CFLAGS=-g myown" to create a debugging version. -# -# The program listed as check_PROGRAMS are not compiled under standard -# "make". Only "make check" will compile them. See mri_convert's -# Makefile.am for an example of its 'make check' test setup. -# -# Please don't remove myown.c from this dummy directory. -######################################################################## -#check_PROGRAMS=myown - -#myown_SOURCES=myown.c -#myown_LDADD=$(addprefix $(top_builddir)/, $(LIBS_MGH)) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/dummy_qt/Makefile.am b/dummy_qt/Makefile.am deleted file mode 100644 index b20d884857b..00000000000 --- a/dummy_qt/Makefile.am +++ /dev/null @@ -1,108 +0,0 @@ -if ENABLE_QT_APPS - -include $(top_srcdir)/build-aux/autotroll.mk - -bin_PROGRAMS = dummy_qt - -BUILT_SOURCES = ui_MainWindow.h \ - moc_MainWindow.cpp \ - qrc_dummy_qt.cpp - -dummy_qt_SOURCES = $(BUILT_SOURCES) \ - MainWindow.cpp \ - main.cpp \ - dummy_qt.qrc - -qrc_dummy_qt.cpp: dummy_qt.qrc - $(RCC) $< -o $@ - -if HAVE_MAC_OSX -AM_CXXFLAGS=\ - -fno-strict-aliasing \ - -Wno-deprecated \ - -Wno-unused \ - -Wno-uninitialized \ - -Wno-return-type \ - -Wno-reorder \ - -Wno-sign-compare \ - -I$(top_srcdir)/include \ - $(GL_CFLAGS) - - -dummy_qt_CXXFLAGS = $(QT_CXXFLAGS) $(AM_CXXFLAGS) -dummy_qt_CPPFLAGS = $(QT_CPPFLAGS) $(AM_CPPFLAGS) -dummy_qt_LDFLAGS = $(QT_LDFLAGS) $(OS_LDFLAGS) -framework Cocoa -framework IOKit -dummy_qt_LDADD = $(QT_LIBS) \ - $(addprefix $(top_builddir)/, $(LIBS_MGH)) - -# need to create a bundle for Macs -install-exec-hook:dummy_qt - mkdir -p $(DESTDIR)$(bindir)/DummyQt.app - mkdir -p $(DESTDIR)$(bindir)/DummyQt.app/Contents - mkdir -p $(DESTDIR)$(bindir)/DummyQt.app/Contents/MacOS - mkdir -p $(DESTDIR)$(bindir)/DummyQt.app/Contents/Resources - mkdir -p $(DESTDIR)$(bindir)/DummyQt.app/Contents/Resources/English.lproj -# mkdir -p $(DESTDIR)$(bindir)/DummyQt.app/Contents/Frameworks - cp $(top_builddir)/dummy_qt/Info.plist $(DESTDIR)$(bindir)/DummyQt.app/Contents - echo -n 'APPL????' > $(DESTDIR)$(bindir)/DummyQt.app/Contents/PkgInfo - cp $(top_builddir)/dummy_qt/dummy_qt $(DESTDIR)$(bindir)/DummyQt.app/Contents/MacOS/dummy_qt.bin - echo "#!/bin/tcsh -ef" > $(DESTDIR)$(bindir)/dummy_qt -# echo "source \$$FREESURFER_HOME/bin/tcl_setup" \ - >> $(DESTDIR)$(bindir)/dummy_qt - echo "source \$$FREESURFER_HOME/bin/qt_setup" \ - >> $(DESTDIR)$(bindir)/dummy_qt - echo "exec $(DESTDIR)$(bindir)/DummyQt.app/Contents/MacOS/dummy_qt.bin \$$*" >> $(DESTDIR)$(bindir)/dummy_qt - chmod a+x $(DESTDIR)$(bindir)/dummy_qt -# ./mac_package_dylibs.sh $(WXWIDGETS_DIR)lib $(DESTDIR)$(bindir)/Freeview.app/Contents/Frameworks $(DESTDIR)$(bindir)/Freeview.app/Contents/MacOS/freeview.bin - if [[ -f /usr/pubsw/bin/chrpath ]]; then \ - /usr/pubsw/bin/chrpath -d $(DESTDIR)$(bindir)/DummyQt.App/Contents/MacOS/dummy_qt.bin; fi - -uninstall-hook: - rm -f $(DESTDIR)$(bindir)/dummy_qt - rm -rf $(DESTDIR)$(bindir)/DummyQt.app - -else - -AM_CXXFLAGS=\ - -fno-strict-aliasing \ - -Wno-deprecated \ - -Wno-unused \ - -Wno-uninitialized \ - -Wno-return-type \ - -Wno-reorder \ - -Wno-sign-compare \ - -I$(top_srcdir)/include \ - $(GL_CFLAGS) - - -dummy_qt_CXXFLAGS = $(QT_CXXFLAGS) $(AM_CXXFLAGS) -dummy_qt_CPPFLAGS = $(QT_CPPFLAGS) $(AM_CPPFLAGS) -dummy_qt_LDFLAGS = $(QT_LDFLAGS) $(OS_LDFLAGS) -dummy_qt_LDADD = $(QT_LIBS) \ - $(addprefix $(top_builddir)/, $(LIBS_MGH)) - -# put a wrapper around the bin, used to setup tcltktixblt,vtk,kww enviro vars -# and if the OS is MACOSX have a different install-hook to create a bundle -install-exec-hook:dummy_qt - cp $(top_builddir)/dummy_qt/dummy_qt $(DESTDIR)$(bindir)/dummy_qt.bin - echo "#!/bin/tcsh -ef" > $(DESTDIR)$(bindir)/dummy_qt - echo "source \$$FREESURFER_HOME/bin/tcl_setup" \ - >> $(DESTDIR)$(bindir)/dummy_qt - echo "source \$$FREESURFER_HOME/bin/vtk_setup" \ - >> $(DESTDIR)$(bindir)/dummy_qt - echo "source \$$FREESURFER_HOME/bin/qt_setup" \ - >> $(DESTDIR)$(bindir)/dummy_qt - echo "dummy_qt.bin \$$argv" >> $(DESTDIR)$(bindir)/dummy_qt - chmod a+x $(DESTDIR)$(bindir)/dummy_qt - if [[ -f /usr/pubsw/bin/chrpath ]]; then \ - /usr/pubsw/bin/chrpath -d $(DESTDIR)$(bindir)/dummy_qt.bin; fi - -uninstall-hook: - rm -f $(DESTDIR)$(bindir)/dummy_qt.bin -endif -endif - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=MainWindow.ui MainWindow.h dummy_qt.pro diff --git a/fem_elastic/Makefile.am b/fem_elastic/Makefile.am deleted file mode 100644 index 35eb56e9596..00000000000 --- a/fem_elastic/Makefile.am +++ /dev/null @@ -1,107 +0,0 @@ -# -# Makefile.am -# - -if HAVE_ITK_LIBS -if HAVE_PETSC_LIBS -if HAVE_BOOST_LIBS -AM_CPPFLAGS=\ - -I$(top_srcdir)/include \ - -I$(top_srcdir)/tetgen \ - $(VXL_CFLAGS) \ - $(ITK_CFLAGS) -DHAVE_ITK_LIBS \ - $(PETSC_CFLAGS) \ - $(BOOST_CFLAGS) - -if HAVE_MAC_OSX -AM_LDFLAGS=$(OS_LDFLAGS) -framework Accelerate -else -AM_LDFLAGS=$(OS_LDFLAGS) -z muldefs -endif - -common3d_SOURCES=\ - fem_3d.cpp fem_3d.h solver.h \ - misc.h mesh.h toctree.hpp node.h simple_timer.h tag_fio.h \ - coords.h material.h element.h gmpError.h streamIoMisc.h stl_utils.hpp \ - small_matrix.cpp small_matrix.h \ - morph.cpp morph.h \ - morph_utils.cpp morph_utils.h - -bin_PROGRAMS=createMorph applyMorph exportGcam surf2vol - -createMorph_SOURCES=\ - $(common3d_SOURCES) \ - fcreateMorph.cpp \ - misc_maths.cpp misc_maths.h \ - transformUtils.cpp transformUtils.h \ - surf_utils.cpp surf_utils.h \ - ZlibStringCompressor.cpp ZlibStringCompressor.h - -createMorph_LDADD=\ - $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(top_builddir)/tetgen/libtetgen.a $(BOOST_PO_LIB) - -applyMorph_SOURCES=\ - $(common3d_SOURCES) \ - fapplyMorph.cpp \ - misc_maths.cpp misc_maths.h \ - transformUtils.cpp transformUtils.h \ - surf_utils.cpp surf_utils.h \ - ZlibStringCompressor.cpp ZlibStringCompressor.h - -applyMorph_LDADD=\ - $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(top_builddir)/tetgen/libtetgen.a $(BOOST_PO_LIB) - -exportGcam_SOURCES=\ - $(common3d_SOURCES) \ - exportGcam.cpp \ - ZlibStringCompressor.cpp ZlibStringCompressor.h - -exportGcam_LDADD=\ - $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(top_builddir)/tetgen/libtetgen.a $(BOOST_PO_LIB) - -surf2vol_SOURCES=\ - $(common3d_SOURCES) \ - fsurf2vol.cpp cstats.h surf_types.h \ - surf_powell.cpp surf_powell.h \ - surf_energy.cpp surf_energy.h \ - misc_maths.cpp \ - transformUtils.cpp \ - surf_utils.cpp \ - ZlibStringCompressor.cpp \ - pbCluster_mesh_crop.cpp pbCluster_mesh_crop.h mesh_bfs.h \ - untangler.cpp untangler.h pbmesh_crop.h - -if HAVE_MAC_OSX -surf2vol_LDADD=\ - $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(top_builddir)/tetgen/libtetgen.a \ - $(PETSC_LIBS) -lpetscts -lpetscsnes -lpetscksp -lpetscdm -lpetscmat \ - -lpetscvec -lpetsc -lmpich -lpmpich -else -surf2vol_LDADD=\ - $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(top_builddir)/tetgen/libtetgen.a \ - $(PETSC_LIBS) -lpetscts -lpetscsnes -lpetscksp -lpetscdm -lpetscmat \ - -lpetscvec -lpetsc -lmpich \ - $(LIB_GFORTRAN) $(LIB_LAPACK) $(LIB_BLAS) $(LIB_G2C_A) $(LIB_GFORTRAN) -endif - - -# build library... -noinst_LIBRARIES= libfem_elastic.a -libfem_elastic_a_SOURCES = $(createMorph_SOURCES) $(applyMorph_SOURCES) - -endif -endif -endif - -EXTRA_DIST= - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/freeview/Makefile.am b/freeview/Makefile.am deleted file mode 100644 index b725b7c2499..00000000000 --- a/freeview/Makefile.am +++ /dev/null @@ -1,728 +0,0 @@ -if ENABLE_QT_APPS - -include $(top_srcdir)/build-aux/autotroll.mk - -bin_PROGRAMS = freeview - -BUILT_SOURCES = \ - ui_MainWindow.h \ - ui_PanelVolume.h \ - ui_PanelSurface.h \ - ui_PanelROI.h \ - ui_PanelPointSet.h \ - ui_DialogLoadVolume.h \ - ui_DialogPreferences.h \ - ui_ToolWindowMeasure.h \ - ui_ToolWindowEdit.h \ - ui_DialogNewVolume.h \ - ui_DialogNewROI.h \ - ui_DialogNewPointSet.h \ - ui_ToolWindowROIEdit.h \ - ui_DialogLoadPointSet.h \ - ui_DialogLoadDTI.h \ - ui_WindowConfigureOverlay.h \ - ui_DialogTransformVolume.h \ - ui_DialogCropVolume.h \ - ui_DialogSaveScreenshot.h \ - ui_DialogVolumeFilter.h \ - ui_DialogAbout.h \ - ui_DialogWriteMovieFrames.h \ - ui_DialogGradientFilter.h \ - ui_WindowQuickReference.h \ - ui_FloatingStatusBar.h \ - ui_TermWidget.h \ - ui_PanelTrack.h \ - ui_DialogSavePointSet.h \ - ui_DialogSaveVolume.h \ - ui_DialogReplaceLabel.h \ - ui_DialogRepositionSurface.h \ - ui_WindowTimeCourse.h \ - ui_DialogLabelStats.h \ - ui_WindowGroupPlot.h \ - ui_DialogLoadSurfaceOverlay.h \ - ui_DialogReloadLayer.h \ - ui_DialogSmoothSurface.h \ - ui_DialogLineProfile.h \ - ui_DialogLoadConnectome.h \ - ui_PanelConnectomeMatrix.h \ - ui_PanelAllLayers.h \ - ui_DialogLoadSurface.h \ - ui_PanelFCD.h \ - ui_DialogLoadFCD.h \ - ui_DialogSetCamera.h \ - ui_DialogThresholdVolume.h \ - ui_DialogVolumeSegmentation.h \ - ui_DialogLoadTransform.h \ - ui_DialogAddPointSetStat.h \ - ui_DialogSelectSplines.h \ - ui_DialogCustomFill.h \ - qtcolorpicker.moc \ - moc_BrushProperty.cpp \ - moc_CommandEdit.cpp \ - moc_Contour2D.cpp \ - moc_Cursor2D.cpp \ - moc_Cursor3D.cpp \ - moc_DialogAbout.cpp \ - moc_DialogCropVolume.cpp \ - moc_DialogGradientFilter.cpp \ - moc_DialogLoadDTI.cpp \ - moc_DialogLoadPointSet.cpp \ - moc_DialogLoadVolume.cpp \ - moc_DialogPreferences.cpp \ - moc_DialogNewPointSet.cpp \ - moc_DialogNewROI.cpp \ - moc_DialogNewVolume.cpp \ - moc_DialogSavePointSet.cpp \ - moc_DialogSaveScreenshot.cpp \ - moc_DialogTransformVolume.cpp \ - moc_DialogVolumeFilter.cpp \ - moc_DialogWriteMovieFrames.cpp \ - moc_FloatingStatusBar.cpp \ - moc_FSLabel.cpp \ - moc_FSSurface.cpp \ - moc_FSVolume.cpp \ - moc_GenericRenderView.cpp \ - moc_InfoTreeWidget.cpp \ - moc_Interactor.cpp \ - moc_Interactor2D.cpp \ - moc_Interactor2DNavigate.cpp \ - moc_Interactor2DMeasure.cpp \ - moc_Interactor2DVolumeCrop.cpp \ - moc_Interactor2DVolumeEdit.cpp \ - moc_Interactor3D.cpp \ - moc_Interactor3DMeasure.cpp \ - moc_Interactor3DROIEdit.cpp \ - moc_Interactor3DPathEdit.cpp \ - moc_Layer.cpp \ - moc_LayerCollection.cpp \ - moc_LayerDTI.cpp \ - moc_LayerEditable.cpp \ - moc_LayerPLabel.cpp \ - moc_LayerPointSet.cpp \ - moc_LayerProperty.cpp \ - moc_LayerPropertyDTI.cpp \ - moc_LayerPropertyMRI.cpp \ - moc_LayerPropertyPointSet.cpp \ - moc_LayerPropertyROI.cpp \ - moc_LayerPropertySurface.cpp \ - moc_LayerROI.cpp \ - moc_LayerSurface.cpp \ - moc_LayerTreeWidget.cpp \ - moc_LabelTreeWidget.cpp \ - moc_SplineTreeWidget.cpp \ - moc_LayerVolumeBase.cpp \ - moc_LayerMRI.cpp \ - moc_MainWindow.cpp \ - moc_PanelLayer.cpp \ - moc_PanelPointSet.cpp \ - moc_PanelROI.cpp \ - moc_PanelSurface.cpp \ - moc_PanelVolume.cpp \ - moc_qtcolorpicker.cpp \ - moc_QVTKWidget.cpp \ - moc_Region2D.cpp \ - moc_RenderView.cpp \ - moc_RenderView2D.cpp \ - moc_RenderView3D.cpp \ - moc_SurfaceLabel.cpp \ - moc_SurfaceOverlay.cpp \ - moc_SurfaceOverlayProperty.cpp \ - moc_SurfaceRegion.cpp \ - moc_SurfaceRegionGroups.cpp \ - moc_TermWidget.cpp \ - moc_ThreadBuildContour.cpp \ - moc_ThreadIOWorker.cpp \ - moc_ToolWindowEdit.cpp \ - moc_ToolWindowMeasure.cpp \ - moc_ToolWindowROIEdit.cpp \ - moc_VolumeCropper.cpp \ - moc_VolumeFilter.cpp \ - moc_WidgetHistogram.cpp \ - moc_WindowConfigureOverlay.cpp \ - moc_WindowQuickReference.cpp \ - moc_FSTrack.cpp \ - moc_TrackData.cpp \ - moc_LayerTrack.cpp \ - moc_TrackGroup.cpp \ - moc_PanelTrack.cpp \ - moc_LayerPropertyTrack.cpp \ - moc_DialogSaveVolume.cpp \ - moc_DialogReplaceLabel.cpp \ - moc_LayerVolumeTrack.cpp \ - moc_LayerLandmarks.cpp \ - moc_SurfaceROI.cpp \ - moc_SurfacePath.cpp \ - moc_MainApplication.cpp \ - moc_DialogRepositionSurface.cpp \ - moc_WindowTimeCourse.cpp \ - moc_WidgetTimeCoursePlot.cpp \ - moc_LayerMRIWorkerThread.cpp \ - moc_DialogLabelStats.cpp \ - moc_VolumeFilterWorkerThread.cpp \ - moc_FSGroupDescriptor.cpp \ - moc_WindowGroupPlot.cpp \ - moc_WidgetGroupPlot.cpp \ - moc_SurfaceSpline.cpp \ - moc_DialogLoadSurfaceOverlay.cpp \ - moc_DialogReloadLayer.cpp \ - moc_DialogSmoothSurface.cpp \ - moc_DialogLineProfile.cpp \ - moc_LayerLineProfile.cpp \ - moc_LayerPropertyLineProfile.cpp \ - moc_DialogLoadConnectome.cpp \ - moc_LayerConnectomeMatrix.cpp \ - moc_LayerPropertyConnectomeMatrix.cpp \ - moc_PanelConnectomeMatrix.cpp \ - moc_PanelAllLayers.cpp \ - moc_Annotation2D.cpp \ - moc_DialogLoadSurface.cpp \ - moc_PanelFCD.cpp \ - moc_LayerFCD.cpp \ - moc_LayerPropertyFCD.cpp \ - moc_DialogLoadFCD.cpp \ - moc_LayerFCDWorkerThread.cpp \ - moc_DialogSetCamera.cpp \ - moc_DialogThresholdVolume.cpp \ - moc_DialogVolumeSegmentation.cpp \ - moc_DialogLoadTransform.cpp \ - moc_DialogAddPointSetStat.cpp \ - moc_BinaryTreeEdge.cpp \ - moc_BinaryTreeNode.cpp \ - moc_BinaryTreeView.cpp \ - moc_DialogSelectSplines.cpp \ - moc_DialogCustomFill.cpp \ - qrc_freeview.cpp - -if USING_QT_5 -JSON_SOURCES = -JSON_INCLUDE = -else -JSON_SOURCES = \ - json/qjson.cpp \ - json/qjsonarray.cpp \ - json/qjsondocument.cpp \ - json/qjsonobject.cpp \ - json/qjsonparser.cpp \ - json/qjsonvalue.cpp \ - json/qjsonwriter.cpp \ - json/qjson_p.h \ - json/qjsonarray.h \ - json/qjsondocument.h \ - json/qjsonobject.h \ - json/qjsonparser_p.h \ - json/qjsonvalue.h \ - json/qjsonwriter_p.h -JSON_INCLUDE = \ - -Ijson -endif - -freeview_SOURCES = $(BUILT_SOURCES) $(JSON_SOURCES) \ - Annotation2D.cpp \ - CommandEdit.cpp \ - Contour2D.cpp \ - Cursor2D.cpp \ - Cursor3D.cpp \ - CursorFactory.cpp \ - BrushProperty.cpp \ - DialogAbout.cpp \ - DialogCropVolume.cpp \ - DialogGradientFilter.cpp \ - DialogLoadDTI.cpp \ - DialogLoadPointSet.cpp \ - DialogLoadVolume.cpp \ - DialogNewROI.cpp \ - DialogNewPointSet.cpp \ - DialogNewVolume.cpp \ - DialogPreferences.cpp \ - DialogSavePointSet.cpp \ - DialogSaveScreenshot.cpp \ - DialogTransformVolume.cpp \ - DialogVolumeFilter.cpp \ - DialogWriteMovieFrames.cpp \ - FloatingStatusBar.cpp \ - FSLabel.cpp\ - FSPointSet.cpp \ - FSSurface.cpp \ - FSVolume.cpp \ - GenericRenderView.cpp \ - InfoTreeWidget.cpp \ - Interactor.cpp \ - Interactor2D.cpp \ - Interactor2DMeasure.cpp \ - Interactor2DNavigate.cpp \ - Interactor2DPointSetEdit.cpp \ - Interactor2DROIEdit.cpp \ - Interactor2DVolumeCrop.cpp \ - Interactor2DVolumeEdit.cpp \ - Interactor2DVoxelEdit.cpp \ - Interactor3D.cpp \ - Interactor3DMeasure.cpp \ - Interactor3DNavigate.cpp \ - Interactor3DVolumeCrop.cpp \ - Interactor3DROIEdit.cpp \ - Interactor3DPathEdit.cpp \ - Layer.cpp \ - LayerCollection.cpp \ - LayerDTI.cpp \ - LayerEditable.cpp \ - LayerMRI.cpp \ - LayerPLabel.cpp \ - LayerPointSet.cpp \ - LayerProperty.cpp \ - LayerPropertyDTI.cpp \ - LayerPropertyMRI.cpp \ - LayerPropertyPointSet.cpp \ - LayerPropertyROI.cpp \ - LayerPropertySurface.cpp \ - LayerROI.cpp \ - LayerSurface.cpp \ - LayerTreeWidget.cpp \ - LayerVolumeBase.cpp \ - LabelTreeWidget.cpp \ - SplineTreeWidget.cpp \ - LivewireTool.cpp \ - LUTDataHolder.cpp \ - main.cpp \ - MyCmdLineParser.cpp \ - MyUtils.cpp \ - MyVTKUtils.cpp \ - PanelLayer.cpp \ - PanelPointSet.cpp \ - PanelROI.cpp \ - PanelSurface.cpp \ - PanelVolume.cpp \ - qtcolorpicker.cpp \ - QVTKWidget.cxx \ - QVTKWidget.h \ - QVTKPaintEngine.cxx \ - QVTKPaintEngine.h \ - QVTKWin32Header.h \ - Region2D.cpp \ - Region2DLine.cpp \ - Region2DPolyline.cpp \ - Region2DRectangle.cpp \ - RenderView.cpp \ - RenderView2D.cpp \ - RenderView3D.cpp \ - SurfaceAnnotation.cpp \ - SurfaceLabel.cpp \ - SurfaceOverlay.cpp \ - SurfaceOverlayProperty.cpp \ - SurfaceRegion.cpp \ - SurfaceRegionGroups.cpp \ - TermWidget.cpp \ - ThreadBuildContour.cpp \ - ThreadIOWorker.cpp \ - ToolWindowEdit.cpp \ - ToolWindowMeasure.cpp \ - ToolWindowROIEdit.cpp \ - UIUpdateHelper.cpp \ - VolumeCropper.cpp \ - VolumeFilter.cpp \ - VolumeFilter.h \ - VolumeFilterConvolve.cpp \ - VolumeFilterConvolve.h \ - VolumeFilterGradient.cpp \ - VolumeFilterGradient.h \ - VolumeFilterMean.cpp \ - VolumeFilterMean.h \ - VolumeFilterMedian.cpp \ - VolumeFilterMedian.h \ - VolumeFilterSobel.cpp \ - VolumeFilterSobel.h \ - VolumeFilterErode.cpp \ - VolumeFilterErode.h \ - VolumeFilterDilate.cpp \ - VolumeFilterDilate.h \ - VolumeFilterOpen.cpp \ - VolumeFilterOpen.h \ - VolumeFilterClose.cpp \ - VolumeFilterClose.h \ - vtkSimpleLabelEdgeFilter.cpp \ - WidgetHistogram.cpp \ - WindowConfigureOverlay.cpp \ - WindowQuickReference.cpp \ - FSTrack.cpp \ - track_io/TrackIO.cpp \ - track_io/TrackIO.h \ - track_io/ByteSwap.h \ - track_io/ErrorCode.h \ - TrackData.cpp \ - Track.cpp \ - Track.h \ - LayerTrack.cpp \ - TrackGroup.cpp \ - PanelTrack.cpp \ - LayerPropertyTrack.cpp \ - DialogSaveVolume.cpp \ - MainWindow.cpp \ - Annotation2D.h \ - BrushProperty.h \ - CommandEdit.h \ - CommonDataStruct.h \ - Contour2D.h \ - Cursor2D.h \ - Cursor3D.h \ - CursorFactory.h \ - DialogAbout.h \ - DialogCropVolume.h \ - DialogGradientFilter.h \ - DialogLoadDTI.h \ - DialogLoadPointSet.h \ - DialogLoadVolume.h \ - DialogPreferences.h \ - DialogNewPointSet.h \ - DialogNewROI.h \ - DialogNewVolume.h \ - DialogSavePointSet.h \ - DialogSaveScreenshot.h \ - DialogTransformVolume.h \ - DialogVolumeFilter.h \ - DialogWriteMovieFrames.h \ - FloatingStatusBar.h \ - FSLabel.h \ - FSPointSet.h \ - FSSurface.h \ - FSVolume.h \ - GenericRenderView.h \ - InfoTreeWidget.h \ - Interactor.h \ - Interactor2D.h \ - Interactor2DMeasure.h \ - Interactor2DNavigate.h \ - Interactor2DPointSetEdit.h \ - Interactor2DROIEdit.h \ - Interactor2DVolumeCrop.h \ - Interactor2DVolumeEdit.h \ - Interactor2DVoxelEdit.h \ - Interactor3D.h \ - Interactor3DMeasure.h \ - Interactor3DNavigate.h \ - Interactor3DVolumeCrop.h \ - Interactor3DROIEdit.h \ - Interactor3DPathEdit.h \ - Layer.h \ - LayerCollection.h \ - LayerDTI.h \ - LayerEditable.h \ - LayerPLabel.h \ - LayerPointSet.h \ - LayerProperty.h \ - LayerPropertyDTI.h \ - LayerPropertyMRI.h \ - LayerPropertyPointSet.h \ - LayerPropertyROI.h \ - LayerPropertySurface.h \ - StockColorMap.h \ - LayerROI.h \ - LayerSurface.h \ - LayerTreeWidget.h \ - LabelTreeWidget.h \ - SplineTreeWidget.h \ - LayerVolumeBase.h \ - LayerMRI.h \ - LivewireTool.h \ - LUTDataHolder.h \ - MainWindow.h \ - MyCmdLineParser.h \ - MyUtils.h \ - MyVTKUtils.h \ - PanelLayer.h \ - PanelPointSet.h \ - PanelROI.h \ - PanelSurface.h \ - PanelVolume.h \ - qtcolorpicker.h \ - Region2D.h \ - Region2DLine.h \ - Region2DPolyline.h \ - Region2DRectangle.h \ - RenderView.h \ - RenderView2D.h \ - RenderView3D.h \ - SurfaceLabel.h \ - SurfaceAnnotation.h \ - SurfaceOverlay.h \ - SurfaceOverlayProperty.h \ - SurfaceRegion.h \ - SurfaceRegionGroups.h \ - TermWidget.h \ - ThreadBuildContour.h \ - ThreadIOWorker.h \ - ToolWindowEdit.h \ - ToolWindowMeasure.h \ - ToolWindowROIEdit.h \ - UIUpdateHelper.h \ - VolumeCropper.h \ - VolumeFilter.h \ - VolumeFilterSobel.h \ - vtkSimpleLabelEdgeFilter.h \ - WidgetHistogram.h \ - WindowConfigureOverlay.h \ - WindowQuickReference.h \ - FSTrack.h \ - TrackData.h \ - LayerTrack.h \ - TrackGroup.h \ - PanelTrack.h \ - LayerPropertyTrack.h \ - DialogSaveVolume.h \ - DialogReplaceLabel.cpp \ - DialogReplaceLabel.h \ - LayerVolumeTrack.cpp \ - LayerVolumeTrack.h \ - LayerLandmarks.cpp \ - LayerLandmarks.h \ - SurfaceROI.cpp \ - SurfaceROI.h \ - SurfacePath.cpp \ - SurfacePath.h \ - MainApplication.cpp \ - MainApplication.h \ - ProgressCallback.cpp \ - ProgressCallback.h \ - DialogRepositionSurface.cpp \ - DialogRepositionSurface.h \ - WindowTimeCourse.cpp \ - WindowTimeCourse.h \ - WidgetTimeCoursePlot.cpp \ - WidgetTimeCoursePlot.h \ - LayerMRIWorkerThread.cpp \ - LayerMRIWorkerThread.h \ - DialogLabelStats.cpp \ - DialogLabelStats.h \ - VolumeFilterWorkerThread.cpp \ - VolumeFilterWorkerThread.h \ - FSGroupDescriptor.cpp \ - FSGroupDescriptor.h \ - WindowGroupPlot.cpp \ - WindowGroupPlot.h \ - WidgetGroupPlot.cpp \ - WidgetGroupPlot.h \ - SurfaceSpline.cpp \ - SurfaceSpline.h \ - DialogLoadSurfaceOverlay.cpp \ - DialogLoadSurfaceOverlay.h \ - DialogReloadLayer.cpp \ - DialogReloadLayer.h \ - DialogSmoothSurface.cpp \ - DialogSmoothSurface.h \ - LayerLineProfile.cpp \ - LayerLineProfile.h \ - DialogLineProfile.cpp \ - DialogLineProfile.h \ - LayerPropertyLineProfile.cpp \ - LayerPropertyLineProfile.h \ - LayerConnectomeMatrix.cpp \ - LayerConnectomeMatrix.h \ - LayerPropertyConnectomeMatrix.cpp \ - LayerPropertyConnectomeMatrix.h \ - PanelConnectomeMatrix.cpp \ - PanelConnectomeMatrix.h \ - DialogLoadConnectome.cpp \ - DialogLoadConnectome.h \ - PanelAllLayers.cpp \ - PanelAllLayers.h \ - DialogLoadSurface.cpp \ - DialogLoadSurface.h \ - LayerFCD.cpp \ - LayerFCD.h \ - LayerPropertyFCD.cpp \ - LayerPropertyFCD.h \ - PanelFCD.cpp \ - PanelFCD.h \ - DialogLoadFCD.cpp \ - DialogLoadFCD.h \ - LayerFCDWorkerThread.cpp \ - LayerFCDWorkerThread.h \ - DialogSetCamera.cpp \ - DialogSetCamera.h \ - DialogThresholdVolume.cpp \ - DialogThresholdVolume.h \ - DialogVolumeSegmentation.cpp \ - DialogVolumeSegmentation.h \ - DialogLoadTransform.cpp \ - DialogLoadTransform.h \ - DialogAddPointSetStat.cpp \ - DialogAddPointSetStat.h \ - BinaryTreeEdge.cpp \ - BinaryTreeEdge.h \ - BinaryTreeNode.cpp \ - BinaryTreeNode.h \ - BinaryTreeView.cpp \ - BinaryTreeView.h \ - DialogSelectSplines.cpp \ - DialogSelectSplines.h \ - DialogCustomFill.cpp \ - DialogCustomFill.h \ - freeview.qrc - -qrc_freeview.cpp: freeview.qrc - cp -v $(top_srcdir)/distribution/FreeSurferColorLUT.txt resource/ - $(RCC) $< -o $@ - -if HAVE_MAC_OSX -AM_CXXFLAGS=\ - -fno-strict-aliasing \ - -Wno-deprecated \ - -Wno-unused \ - -Wno-uninitialized \ - -Wno-return-type \ - -Wno-reorder \ - -Wno-sign-compare \ - -I$(top_srcdir)/include \ - $(GL_CFLAGS) \ - $(VTK_COCOA_CXXFLAGS) \ - -I$(top_srcdir)/vtkfsio \ - -I$(top_srcdir)/vtkutils \ - $(ITK_CFLAGS) -DHAVE_ITK_LIBS \ - $(VXL_CFLAGS) \ - -I$(top_srcdir)/lineprof \ - -Wno-error - -freeview_CXXFLAGS = $(QT_CXXFLAGS) $(AM_CXXFLAGS) $(JSON_INCLUDE) -freeview_CPPFLAGS = $(QT_CPPFLAGS) $(AM_CPPFLAGS) -freeview_LDFLAGS = $(QT_LDFLAGS) $(OS_LDFLAGS) \ - -framework Cocoa -framework IOKit -framework Accelerate -freeview_LDADD = $(QT_LIBS) \ - $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(top_builddir)/vtkfsio/libvtkfsio.a \ - $(top_builddir)/vtkutils/libvtkutils.a \ - $(top_builddir)/lineprof/liblineprof.a \ - $(VTK_COCOA_LIBS) $(VTK_VERDICT_LIB) -lvtkGraphics \ - $(VTK_EXPAT_LIB) $(VTK_FREETYPE_LIB) \ - $(VTK_TIFF_LIB) $(VTK_JPEG_LIB) \ - $(VTK_METAIO_LIB) $(VTK_PNG_LIB) $(VTK_Z_LIB) \ - $(VTK_SQLITE_LIB) \ - -lvtkImaging -lvtkFiltering \ - -lvtkCommon -lvtksys -lvtkGenericFiltering \ - -lvtkexoIIc -lvtkNetCDF $(VTK_NETCDFCXX_LIB) \ - -lvtkVolumeRendering -lvtkRendering -lvtkftgl \ - -lvtkWidgets -lvtkHybrid $(VTK_HDF5_LIB) \ - -lvtkIO $(VTK_LSDYNA_LIB) -lvtkDICOMParser $(VTK_MPEG2ENCODE_LIB) \ - $(PETSC_LIBS) -lpetscts -lpetscsnes -lpetscksp -lpetscdm -lpetscmat \ - -lpetscvec -lpetsc -lmpich -lpmpich - -# need to create a bundle for Macs -install-exec-hook:freeview - rm -Rf $(DESTDIR)$(bindir)/../Freeview.app - mkdir -p $(DESTDIR)$(bindir)/../Freeview.app - mkdir -p $(DESTDIR)$(bindir)/../Freeview.app/Contents - mkdir -p $(DESTDIR)$(bindir)/../Freeview.app/Contents/MacOS - mkdir -p $(DESTDIR)$(bindir)/../Freeview.app/Contents/Resources - mkdir -p $(DESTDIR)$(bindir)/../Freeview.app/Contents/Resources/English.lproj - mkdir -p $(DESTDIR)$(bindir)/../Freeview.app/Contents/Frameworks - echo -n 'APPL????' > $(DESTDIR)$(bindir)/../Freeview.app/Contents/PkgInfo - cp $(top_builddir)/freeview/freeview $(DESTDIR)$(bindir)/../Freeview.app/Contents/MacOS/Freeview - cp $(top_builddir)/freeview/Info.plist $(DESTDIR)$(bindir)/../Freeview.app/Contents/ - cp $(top_builddir)/freeview/resource/icons/freeview.icns $(DESTDIR)$(bindir)/../Freeview.app/Contents/Resources/freeview.icns - echo "#!/bin/tcsh -f" > $(DESTDIR)$(bindir)/freeview - echo "if(\$$#argv > 0) then" \ - >> $(DESTDIR)$(bindir)/freeview - echo " if(\"\$$argv[1]\" == \"-tkmedit\") then" \ - >> $(DESTDIR)$(bindir)/freeview - echo " tkmeditfv \$$argv[2-\$$#argv]" \ - >> $(DESTDIR)$(bindir)/freeview - echo " exit 0" >> $(DESTDIR)$(bindir)/freeview - echo " endif" >> $(DESTDIR)$(bindir)/freeview - echo "endif" >> $(DESTDIR)$(bindir)/freeview - echo "source \$$FREESURFER_HOME/sources.csh" >> $(DESTDIR)$(bindir)/freeview - echo "\$$FREESURFER_HOME/Freeview.app/Contents/MacOS/Freeview \$$*" >> $(DESTDIR)$(bindir)/freeview - chmod a+x $(DESTDIR)$(bindir)/freeview - chgrp -R admin $(DESTDIR)$(bindir)/../Freeview.app/ - chmod -R a+rx $(DESTDIR)$(bindir)/../Freeview.app - chmod -R g+w $(DESTDIR)$(bindir)/../Freeview.app - $(QT_PATH)/macdeployqt $(DESTDIR)$(bindir)/../Freeview.app - -uninstall-hook: - rm -f $(DESTDIR)$(bindir)/freeview - rm -rf $(DESTDIR)$(bindir)/../Freeview.app - -else - -AM_CXXFLAGS=\ - -fno-strict-aliasing \ - -Wno-deprecated \ - -Wno-unused \ - -Wno-uninitialized \ - -Wno-return-type \ - -Wno-reorder \ - -Wno-sign-compare \ - -I$(top_srcdir)/include \ - $(GL_CFLAGS) \ - $(VTK_CXXFLAGS) \ - -I$(top_srcdir)/vtkfsio \ - -I$(top_srcdir)/vtkutils \ - $(ITK_CFLAGS) -DHAVE_ITK_LIBS \ - $(VXL_CFLAGS) \ - -I$(top_srcdir)/lineprof \ - -DVCL_CAN_STATIC_CONST_INIT_FLOAT=0 \ - -Wno-error - -freeview_CXXFLAGS = $(QT_CXXFLAGS) $(AM_CXXFLAGS) $(JSON_INCLUDE) -freeview_CPPFLAGS = $(QT_CPPFLAGS) $(AM_CPPFLAGS) -freeview_LDFLAGS = $(QT_LDFLAGS) $(OS_LDFLAGS) \ - -Wl,--allow-multiple-definition -freeview_LDADD = $(QT_LIBS) \ - $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(top_builddir)/vtkfsio/libvtkfsio.a \ - $(top_builddir)/vtkutils/libvtkutils.a \ - $(top_builddir)/lineprof/liblineprof.a \ - $(VTK_LIBS) $(VTK_VERDICT_LIB) -lvtkGraphics \ - $(VTK_EXPAT_LIB) $(VTK_FREETYPE_LIB) \ - $(VTK_TIFF_LIB) $(VTK_JPEG_LIB) \ - $(VTK_METAIO_LIB) $(VTK_PNG_LIB) $(VTK_Z_LIB) \ - $(VTK_SQLITE_LIB) \ - -lvtkImaging -lvtkFiltering \ - -lvtkCommon -lvtksys -lvtkGenericFiltering \ - -lvtkexoIIc -lvtkNetCDF $(VTK_NETCDFCXX_LIB) \ - -lvtkVolumeRendering -lvtkRendering -lvtkftgl \ - -lvtkWidgets -lvtkHybrid $(VTK_HDF5_LIB) \ - -lvtkIO $(VTK_LSDYNA_LIB) -lvtkDICOMParser $(VTK_MPEG2ENCODE_LIB) \ - $(ITK_LIBS) -lX11 \ - $(PETSC_LIBS) -lpetscts -lpetscsnes -lpetscksp \ - -lpetscdm -lpetscmat -lpetscvec -lpetsc -lmpich -lfmpich \ - $(LIB_GFORTRAN) $(LIB_LAPACK) $(LIB_BLAS) $(LIB_G2C_A) $(LIB_GFORTRAN) - -# put a wrapper around the bin, used to setup tcltktixblt,vtk enviro vars -# and if the OS is MACOSX have a different install-hook to create a bundle -install-exec-hook:freeview - cp $(top_builddir)/freeview/freeview $(DESTDIR)$(bindir)/freeview.bin - echo "#!/bin/tcsh -ef" > $(DESTDIR)$(bindir)/freeview - echo "source \$$FREESURFER_HOME/bin/tcl_setup" \ - >> $(DESTDIR)$(bindir)/freeview - echo "source \$$FREESURFER_HOME/bin/vtk_setup" \ - >> $(DESTDIR)$(bindir)/freeview - echo "source \$$FREESURFER_HOME/bin/qt_setup" \ - >> $(DESTDIR)$(bindir)/freeview - echo "if(\$$#argv > 0) then" \ - >> $(DESTDIR)$(bindir)/freeview - echo " if(\"\$$argv[1]\" == \"-tkmedit\") then" \ - >> $(DESTDIR)$(bindir)/freeview - echo " tkmeditfv \$$argv[2-\$$#argv]" \ - >> $(DESTDIR)$(bindir)/freeview - echo " exit 0" >> $(DESTDIR)$(bindir)/freeview - echo " endif" >> $(DESTDIR)$(bindir)/freeview - echo "endif" >> $(DESTDIR)$(bindir)/freeview - echo "freeview.bin \$$argv:q" >> $(DESTDIR)$(bindir)/freeview - chmod a+x $(DESTDIR)$(bindir)/freeview - if [[ -f /usr/pubsw/bin/chrpath ]]; then \ - /usr/pubsw/bin/chrpath -d $(DESTDIR)$(bindir)/freeview.bin; fi - -uninstall-hook: - rm -f $(DESTDIR)$(bindir)/freeview.bin -endif - -clean-local: - rm -f $(BUILT_SOURCES) - rm -f resource/FreeSurferColorLUT.txt -endif - -EXTRA_DIST=$(freeview_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - diff --git a/fsfast/Makefile.am b/fsfast/Makefile.am deleted file mode 100644 index fdd74e8b2b3..00000000000 --- a/fsfast/Makefile.am +++ /dev/null @@ -1,11 +0,0 @@ -# -# Makefile.am for fsfast -# -SUBDIRS=bin toolbox docs - - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/fsfast/bin/Makefile.am b/fsfast/bin/Makefile.am deleted file mode 100644 index 678b2b57187..00000000000 --- a/fsfast/bin/Makefile.am +++ /dev/null @@ -1,223 +0,0 @@ -# -# Makefile.am for fsfast/bin -# - -foodir=$(prefix)/fsfast/bin - -TDR_FILES=\ - tdr-avgechoes \ - tdr-fidmat \ - tdr-ghostcomp \ - tdr-rcolmat \ - tdr-recon - -FSF_FILES=\ - acfseg-sess \ - acorfunc-sess \ - addmcparams \ - aseg2funcmask-sess \ - autoreg-fsl \ - autoreg-sess \ - avgraw \ - bfileconvert \ - bfvcheck \ - bgmask-sess \ - cat-bvolume \ - checkmincdir \ - check-sliceres-sess \ - clusterspec2mask \ - cluster-sess \ - cmpanalyses-sess \ - cmpsesssnr-sess \ - cmpsnr-sess \ - compress-sess \ - concat-bvolumes \ - conmask-sess \ - cordiff \ - countncond \ - cp-bvolume \ - crossrun.ffx.fsf \ - df-sess \ - diag-fmri \ - diag-optseq \ - difffsfast \ - du-sess \ - evfunc \ - evfunc-sess \ - evpve-sess \ - evspatfil \ - evspatfil-sess \ - fast_getext \ - fast-log-preamble.csh \ - fcseed-config \ - fcseedcor \ - fcseed-sess \ - fcreg-sess \ - feat.fsfast-patch \ - feat.fsfast-patch.tcl \ - fieldsign-sess \ - fixseqinfo-sess \ - flacproc-sess \ - fsfast-version \ - fsfast-gui-bug \ - fsfeat \ - fsfeatffx \ - fsfeat-sess \ - fsf-glmfit \ - fsf-kmnacf \ - fsf-kmracf \ - fslregister-sess \ - fsl2par \ - func2acf \ - func2label \ - funcroi-config \ - funcroi-sess \ - funcroi-table-sess \ - functcvm \ - functcvm-sess \ - functwf-sess \ - fwhmest \ - fwhmest-sess \ - getana \ - getbext \ - getbfvdim \ - getendian \ - getfirstrundir-sess \ - getfirstsliceno \ - getformat_from_stem \ - getfullpath \ - geticoorder \ - getlastsliceno \ - getmatlab \ - getncols \ - getnconds \ - getnframes \ - getnrows \ - getnslices \ - getpwdcmd \ - getrunlist \ - getsesspath \ - getsliceno \ - getslicestr \ - getspacetype \ - getstem \ - gettalres \ - ghostdet \ - ghostdet-sess \ - glmest \ - glmfourier \ - glmfourier-sess \ - glmstats \ - groupreg-sess \ - ipfsl \ - isargflag \ - isroiavg \ - isxavg-fe \ - isxavg-fe-abb-sess \ - isxavg-fe-sess \ - isxavg-fe-sess-1.3 \ - isxavg-re \ - isxavg-re-abb-sess \ - isxavg-re-sess \ - isxconcat0-sess \ - isxconcat-sess \ - kmacfcond-sess \ - kmacf-sess \ - kmacfwht-sess \ - lrst-blk \ - lrst-blk-sess \ - mc-afni \ - mc-afni2 \ - mcdat2mcextreg \ - mcparams2extreg \ - mc-sess \ - meanimg \ - mkanalysis-sess \ - mkblockpar \ - mkbrainmask \ - mkbrainmask-sess \ - mkcmanova-sess \ - mkcontrast \ - mkcontrast2 \ - mkcontrast-sess \ - mkdesignmtx \ - mkdesmtx-sess \ - mkfeat-sess \ - mkfieldsign \ - mkmosaic \ - mkprestimcon \ - mktalreg \ - mktalxfm-sess \ - mktemplate-sess \ - mkvoxshiftmap \ - mris_glm-sess \ - optseq \ - optseq.matlab \ - par2fsl \ - par2fsl3 \ - par2kspar \ - par2schedule \ - par2stf \ - parse-measasc \ - plot-pve \ - plot-twf-sess \ - preproc-sess \ - prmerge-sess \ - qmedit \ - qsurfer \ - rawavg-sess \ - rawfunc2surf-sess \ - rawfunc2tal \ - rawfunc2tal-sess \ - reg2subj \ - register-sess \ - rocview \ - roiavg \ - roiavgraw \ - roitxt2tbl \ - roixrunsum-sess \ - selxavg2 \ - selxavg3-sess \ - selxavg-jk-sess \ - selxavg-sess \ - selxavg-sess-perrun \ - seqefficiency \ - sliceview-sess \ - spatialsmooth-sess \ - spikedet \ - spikedet-sess \ - splitstr \ - spmimg2bvolume \ - spmregister-sess \ - stc.fsl \ - stc-sess \ - stem2fmt \ - stripsessargs \ - subject-sess \ - surf-sess \ - surfsmooth-sess \ - sxacfg-get \ - synthrawroi \ - synth-sess \ - synthstudy \ - tar-sess \ - tkmedit-sess \ - tkregister-sess \ - tksurfer-sess \ - vlrmerge - -foo_SCRIPTS=$(FSF_FILES) - -foo_datafiles=fast_selxavg3b.glnxa64 mkcontrast2m.glnxa64 - -install-data-local: - test -z $(DESTDIR)$(bindir) || $(mkdir_p) $(DESTDIR)$(bindir) - $(INSTALL_SCRIPT) $(foo_datafiles) $(DESTDIR)$(bindir) - -EXTRA_DIST=$(FSF_FILES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES=$(TDR_FILES) CVS func2roi-sess -include $(top_srcdir)/Makefile.extra diff --git a/fsfast/docs/Makefile.am b/fsfast/docs/Makefile.am deleted file mode 100644 index d234d052f0c..00000000000 --- a/fsfast/docs/Makefile.am +++ /dev/null @@ -1,59 +0,0 @@ -# -# Makefile.am for docs -# - -# Note: the pdf files should be committed to CVS, so as not to require a -# latex installation on all build systems. - -# NJS: notice the .pdf files are not removed during clean or distclean. -# this is done so as not to play havoc with cvs updates since the pdf -# files are committed. so this means that if the tex files change, -# someone must manually delete the pdfs then run make. - -foodir=$(prefix)/fsfast/docs -# cannot specify *, since Makefile etc will be copied -TEXFILES=\ - bert-functional.howto.tex\ - bfile.tex\ - condfit.tex\ - fmri-analysis-theory.tex\ - func2roi-sess.tex\ - inorm.tex\ - INSTALL.tex\ - intergroup-sess.tex\ - isxavg-fe.tex\ - isxavg-re.tex\ - mc-afni.tex\ - mkcontrast.tex\ - mkmosaic16.tex\ - mkmosaic.tex\ - mtp-repack.tex\ - optseq.tex\ - overview.tex\ - paint.tex\ - paradigm.tex\ - selfreq.tex\ - selxavg.tex\ - seqefficiency.tex\ - stxgrinder.tex\ - univar-analysis.tex\ - vol2roi.tex\ - yakview.tex - -foo_datafiles = $(TEXFILES:%.tex=%.pdf) - -clean-local: - rm -f *.aux *.log *.ps - -distclean-local: - rm -f Makefile - -install-data-local: - test -z $(DESTDIR)$(foodir) || $(mkdir_p) $(DESTDIR)$(foodir) - $(INSTALL_DATA) $(foo_datafiles) $(DESTDIR)$(foodir) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/fsfast/toolbox/Makefile.am b/fsfast/toolbox/Makefile.am deleted file mode 100644 index 3697d625107..00000000000 --- a/fsfast/toolbox/Makefile.am +++ /dev/null @@ -1,621 +0,0 @@ -# -# Makefile.am for fsfast/toolbox -# - -foodir=$(prefix)/fsfast/toolbox - -MFILES=\ - afni2bvol.m \ - arCorrFun.m \ - avgrandeff.m \ - basename.m \ - binomialcdf.m \ - binomialconf.m \ - binomialpdf.m \ - bliweights.m \ - boldview.m \ - bvbinomialpdf.m \ - ComputeFPR.m \ - ComputePDF.m \ - cor2bshort.m \ - corbfile2register.m \ - defmossize.m \ - direxists.m \ - dirname.m \ - drclip.m \ - drsqueeze.m \ - dumphdrest.m \ - editmask.m \ - erlang.m \ - fast_aareg.m \ - fast_aaz.m \ - fast_acf_3dgsm.m \ - fast_acfcond.m \ - fast_acf_err.m \ - fast_acfseg.m \ - fast_acf_svdreg.m \ - fast_acorr.m \ - fast_anovamtx.m \ - fast_ar12fwhm.m \ - fast_ar1err.m \ - fast_ar1_fiterr.m \ - fast_ar1mtx.m \ - fast_ar1w_acf.m \ - fast_ar1w_fiterr.m \ - fast_ar1w_fit.m \ - fast_ar1w_mse.m \ - fast_ar1w_opt.m \ - fast_ar2acf.m \ - fast_arnw_acf.m \ - fast_arnw_fiterr.m \ - fast_baselinemtx.m \ - fast_beta2sxa.m \ - fast_bfileconvert.m \ - fast_bgmask.m \ - fast_binmean.m \ - fast_blockdiag2.m \ - fast_blockdiag.m \ - fast_blockident.m \ - fast_boxcarmat.m \ - fast_cbm2.m \ - fast_cbm.m \ - fast_clip.m \ - fast_cmpdesign_nsd.m \ - fast_compute_cvm.m \ - fast_condctrstmtx.m \ - fast_condfit.m \ - fast_contrastmtx.m \ - fast_conv_invirf.m \ - fast_corrcoef.m \ - fast_corsort.m \ - fast_crs_scnfilter.m \ - fast_cvm2acor.m \ - fast_cvm2corm.m \ - fast_cvm2whtn.m \ - fast_cvm_condrgl.m \ - fast_cvm_normalize.m \ - fast_cvm_normposdef.m \ - fast_cvm_normrgl.m \ - fast_cvm_pvergl.m \ - fast_cvm_regularize.m \ - fast_dftmtx.m \ - fast_dilate.m \ - fast_dirname.m \ - fast_dlh.m \ - fast_ecm2invlambda.m \ - fast_ecvm2wmtx.m \ - fast_erm2Xtask.m \ - fast_estdimsvd.m \ - fast_esttrans.m \ - fast_evfunc.m \ - fast_evspatfil.m \ - fast_exptrendmtx.m \ - fast_fcreg.m \ - fast_fcseedcor.m \ - fast_fdrthresh.m \ - fast_fftaxis.m \ - fast_ffx.m \ - fast_ffx_osgm.m \ - fast_fgnoise.m \ - fast_fildecomp.m \ - fast_fileexists.m \ - fast_flacfg_load.m \ - fast_flacfg_struct.m \ - fast_flacfg_write.m \ - fast_flacproc_sess.m \ - fast_fla_desmat.m \ - fast_flafit0.m \ - fast_fla_irf.m \ - fast_flip2wvar.m \ - fast_fmri2tcvm.m \ - fast_fmrimovie.m \ - fast_fmriqa.m \ - fast_fnorm.m \ - fast_fourier_reg.m \ - fast_fratio.m \ - fast_fratiow.m \ - fast_fread3.m \ - fast_fslgamma.m \ - fast_func2acor.m \ - fast_func2roi.m \ - fast_functwf.m \ - fast_fwhm2std.m \ - fast_fwrite3.m \ - fast_fxcfg_extreg.m \ - fast_fxcfg_fir.m \ - fast_fxcfg_fourier.m \ - fast_fxcfg_gamma.m \ - fast_fxcfg.m \ - fast_fxcfg_poly.m \ - fast_fxcfg_spmhrf.m \ - fast_fxcfg_struct.m \ - fast_gammaderiv.m \ - fast_gamma.m \ - fast_gaussian.m \ - fast_gui_bug.m \ - fast_getvolformat.m \ - fast_ghostdet.m \ - fast_ghostmask.m \ - fast_glm2anova_mtx.m \ - fast_glmfit.m \ - fast_glm_pcc.m \ - fast_glmfitw.m \ - fast_glmpower.m \ - fast_group_glm.m \ - fast_hann.m \ - fast_histeq.m \ - fast_hlist.m \ - fast_hrf_halfcos.m \ - fast_hypospec2cmtx.m \ - fast_idealXtX.m \ - fast_igxavg2.m \ - fast_igxavg.m \ - fast_indfreq.m \ - fast_inorm.m \ - fast_intergroupavg.m \ - fast_invlambda.m \ - fast_isbvol.m \ - fast_isminc.m \ - fast_ismincvol.m \ - fast_isxavg_fe.m \ - fast_isxavg_re_abb_sess.m \ - fast_isxavg_re.m \ - fast_jkz.m \ - fast_kjw_mtx.m \ - fast_kmacf.m \ - fast_kmeans.m \ - fast_ldanacfg.m \ - fast_ldanaflac.m \ - fast_ldanalyze.m \ - fast_lpfmtx.m \ - fast_ldbfile.m \ - fast_ldbfiletp.m \ - fast_ldbhdr.m \ - fast_ldbslice.m \ - fast_ldbvoxel.m \ - fast_ldcorslice.m \ - fast_ldflac.m \ - fast_ldfslabel.m \ - fast_ldlabel.m \ - fast_ldmri.m \ - fast_ldpar4.m \ - fast_ldretpar.m \ - fast_ldroisum.m \ - fast_ldslice.m \ - fast_ldstf.m \ - fast_ldsurfglmmat.m \ - fast_ldsxabfile.m \ - fast_ldsxabvolume.m \ - fast_ldsxavol.m \ - fast_ldtable.m \ - fast_ldtpexcl.m \ - fast_ldwfile.m \ - fast_lmfit.m \ - fast_log10p.m \ - fast_lsc.m \ - fast_maskvol.m \ - fast_mat2vol.m \ - fast_mergesxa.m \ - fast_mkdesignmtx.m \ - fast_mkgausmtx.m \ - fast_mkoverlay.m \ - fast_monotonize.m \ - fast_mri_struct.m \ - fast_mrivolstruct.m \ - fast_mshift.m \ - fast_nirs2oxy.m \ - fast_normcovmtx.m \ - fast_norm_con.m \ - fast_npernull.m \ - fast_nswfflac_sess.m \ - fast_omnibusmtx.m \ - fast_outliermtx.m \ - fast_overlay.m \ - fast_p2z.m \ - fast_par2nconds.m \ - fast_par2st.m \ - fast_par2Xfir.m \ - fast_par2Xtask.m \ - fast_parabfit.m \ - fast_pixrep.m \ - fast_polyorder.m \ - fast_polytrendmtx.m \ - fast_polyzacf_fit.m \ - fast_prayleigh.m \ - fast_psc2t2s.m \ - fast_psdwin.m \ - fast_pvs.m \ - fast_quadtrendmtx.m \ - fast_racf_exp.m \ - fast_randrundist.m \ - fast_randschedule.m \ - fast_raygauscost.m \ - fast_raygausinit.m \ - fast_raygaus.m \ - fast_raygausthresh.m \ - fast_read_curv.m \ - fast_read_wfile.m \ - fast_rescalefactor.m \ - fast_retroicor.m \ - fast_rfm2nrho1.m \ - fast_rmzerocols.m \ - fast_rphacf.m \ - fast_rphacfrmse.m \ - fast_runlistfile.m \ - fast_runlist.m \ - fast_sched2Xerm.m \ - fast_sched2Xfir.m \ - fast_sched2Xgammaderiv.m \ - fast_sched2Xgamma.m \ - fast_schedseq.m \ - fast_selfreqavg.m \ - fast_selxavg2.m \ - fast_selxavg3.m \ - fast_selxavg3b.m \ - fast_selxavg.m \ - fast_sesscfg_struct.m \ - fast_sigmoid.m \ - fast_sim_acfsvd.m \ - fast_sincmtx.m \ - fast_slicedelay.m \ - fast_smooth1d.m \ - fast_smooth2d.m \ - fast_smooth3d.m \ - fast_spatcornoise.m \ - fast_spatevfilter.m \ - fast_spatev.m \ - fast_spatialacf.m \ - fast_spmhrf.m \ - fast_spmhrf_sampled.m \ - fast_st2fir.m \ - fast_stxgrinder2_sess.m \ - fast_stxgrinder3_sess.m \ - fast_svanalyze.m \ - fast_svana.m \ - fast_svbhdr.m \ - fast_svbslice.m \ - fast_svcor.m \ - fast_svcorslice.m \ - fast_svdfilter.m \ - fast_svdfunctcvm.m \ - fast_svd.m \ - fast_svdregpct.m \ - fast_svextreg.m \ - fast_svlabel.m \ - fast_svtable.m \ - fast_swfflac_nbhd_sess.m \ - fast_swfflac_sess.m \ - fast_synthnoise.m \ - fast_tcvm_rmrun.m \ - fast_tnorm.m \ - fast_trendmtx.m \ - fast_trf_sup_surf.m \ - fast_tspvsrank.m \ - fast_unmask.m \ - fast_uvffx.m \ - fast_viewvol.m \ - fast_vol2mat.m \ - fast_volstruct.m \ - fast_volview.m \ - fast_voxthresh.m \ - fast_vvglm.m \ - fast_weiskopf.m \ - fast_weiskopf_perm.m \ - fast_wopt2x2.m \ - fast_wopt.m \ - fast_wparnonlin.m \ - fast_write_curv.m \ - fast_write_wfile.m \ - fast_xmat2xtxt.m \ - fast_yacf_kjw.m \ - fast_z2p.m \ - fbirn_mktable.m \ - fbirn_sitelist.m \ - fbirn_sitename.m \ - fbirn_siteno.m \ - fidinterp.m \ - flac_conindex.m \ - flac_conmat.m \ - flac_customize.m \ - flac_desmat.m \ - flac_ev2irf.m \ - flac_evconw.m \ - flac_evindex.m \ - flac_ev_parse.m \ - flac_evregind.m \ - flac_evtaskind.m \ - flac_funcstem.m \ - flacffx.m \ - flac_nuisregind.m \ - flac_resynth.m \ - flacrfx.m \ - flac_taskregind.m \ - flac_tfilter.m \ - flac_tfilter_parse.m \ - flacview.m \ - fmri_abjackknife.m \ - fmri_accrandeff.m \ - fmri_acorr2covmtx.m \ - fmri_acorrfit.m \ - fmri_acorr.m \ - fmri_acorrsig.m \ - fmri_acorrsynth.m \ - fmri_avgmtx_is.m \ - fmri_avgrandeff.m \ - fmri_avgxavg.m \ - fmri_axaslice.m \ - fmri_bfiledim.m \ - fmri_boxcar.m \ - fmri_bvoldim.m \ - fmri_cvmstruct.m \ - fmri_detrend.m \ - fmri_dof.m \ - fmri_ecovar.m \ - fmri_estsignal.m \ - fmri_fstem.m \ - fmri_getstem.m \ - fmri_hankernel.m \ - fmri_havg_is.m \ - fmri_hcovar.m \ - fmri_hdrdatstruct.m \ - fmri_hemodyn.m \ - fmri_idealcbpm.m \ - fmri_idealxtx.m \ - fmri_imresize.m \ - fmri_indfreqfft.m \ - fmri_isavgstg.m \ - fmri_isavgstruct.m \ - fmri_isconsec.m \ - fmri_isroiavg.m \ - fmri_isxavg_fe.m \ - fmri_isxgrinder.m \ - fmri_isxgslice.m \ - fmri_jackknife.m \ - fmri_ldbfile.m \ - fmri_ldbheader.m \ - fmri_ldbvolume.m \ - fmri_ldcor.m \ - fmri_ldcvm.m \ - fmri_lddat2.m \ - fmri_lddat3.m \ - fmri_lddat.m \ - fmri_lddof.m \ - fmri_lddot.m \ - fmri_ldpar.m \ - fmri_ldsadof.m \ - fmri_ldsfa.m \ - fmri_ldslicedelay.m \ - fmri_ldsynch.m \ - fmri_ldtpexcl.m \ - fmri_lmsfit.m \ - fmri_mcorrrestriction.m \ - fmri_minseqcbe.m \ - fmri_minseqtr.m \ - fmri_minsig.m \ - fmri_mrestriction2.m \ - fmri_mrestriction.m \ - fmri_nmjackknife.m \ - fmri_normcovar.m \ - fmri_norm.m \ - fmri_optseq.m \ - fmri_optseqstruct.m \ - fmri_par2sam.m \ - fmri_par2scm0.m \ - fmri_par2scm2.m \ - fmri_par2scm.m \ - fmri_parsebfilename.m \ - fmri_pcacovmtx.m \ - fmri_pmax.m \ - fmri_pmin.m \ - fmri_pscavg.m \ - fmri_qrplusc.m \ - fmri_qsvd.m \ - fmri_qweiner.m \ - fmri_randc.m \ - fmri_randeff.m \ - fmri_readreg.m \ - fmri_rescale.m \ - fmri_residual.m \ - fmri_rhaslice.m \ - fmri_roiavg.m \ - fmri_sa2sxa.m \ - fmri_saxslice.m \ - fmri_scm2gcm.m \ - fmri_segment.m \ - fmri_selsum.m \ - fmri_seq2scm.m \ - fmri_seqbase.m \ - fmri_seqmutate.m \ - fmri_sfastruct.m \ - fmri_sfaunpack.m \ - fmri_shiftcol.m \ - fmri_sigmin.m \ - fmri_sobel.m \ - fmri_spatfilter.m \ - fmri_srchseq.m \ - fmri_stxgrinder.m \ - fmri_stxgslice.m \ - fmri_subsampmat.m \ - fmri_svbfile.m \ - fmri_svbvolume.m \ - fmri_svcvm.m \ - fmri_svdat2.m \ - fmri_svdat3.m \ - fmri_svpar.m \ - fmri_svsfa.m \ - fmri_sxa2sa.m \ - fmri_sxaslice.m \ - fmri_sxavol.m \ - fmri_synthpar2.m \ - fmri_synthpar3.m \ - fmri_synthpar.m \ - fmri_synth_phenc_sig.m \ - fmri_synthrun.m \ - fmri_synthrunstruct.m \ - fmri_tavgslice.m \ - fmri_touch.m \ - fmri_untangle2.m \ - fmri_untangle.m \ - fmri_voxvar.m \ - fmri_vrestriction.m \ - fmri_wisxavg_fe.m \ - fmri_xtx2cbp.m \ - fslmat2register.m \ - FTest.m \ - gammadist.m \ - gaussian.m \ - gensynthdata.m \ - gr1dmin_update.m \ - hdrviewlite.m \ - hdrview.m \ - hsa_convert.m \ - hview.m \ - imagesc1d.m \ - imgoverlay.m \ - imgoverlaytc2.m \ - imgoverlaytc.m \ - imgto1d.m \ - indbrain2ghost.m \ - invillcond.m \ - kimgfunc.m \ - krfunc_lsqr.m \ - kspacevector2.m \ - ldstruct.m \ - linfit.m \ - load_corinfo.m \ - mar.m \ - maxmd.m \ - mkanalysis_gui.m \ - mkcontrast_gui.m \ - mkcontrast2m.m \ - mkdirp.m \ - mkmosaic.m \ - mkprestimcon.m \ - mos2vol.m \ - mosind2volind.m \ - mossub2volsub.m \ - mrsignalsample.m \ - mstk2mos.m \ - nmrcolormap.m \ - ovstruct.m \ - pairedtx.m \ - par2condidmap.m \ - parboxcar.m \ - par_recode.m \ - pdf_gamma.m \ - pdf_rayleigh.m \ - pedmatrix.m \ - permutation.m \ - pertrapezoid.m \ - pkpulse.m \ - plot_detrend5.m \ - plthankernels.m \ - pulsespectrum.m \ - pvecovmtx.m \ - qoe.m \ - rande.m \ - randnorm.m \ - randr.m \ - rawplot.m \ - ReadAFNIHead2.m \ - ReadBRIK2.m \ - readln.m \ - register2fslmat.m \ - remap_par.m \ - reshape1d.m \ - reshape2d.m \ - rft_zcluster_cdf.m \ - rimgfunc.m \ - roi2ind.m \ - samp2pdf.m \ - samplecdf.m \ - showfigxy.m \ - silverstein.m \ - splitstring.m \ - spmhrf.m \ - spm_to_bfloat.m \ - spm_to_bshort.m \ - spm_to_sagbshort.m \ - sscanfitem.m \ - stxgpredict.m \ - sub2indmask.m \ - subbrain2ghost.m \ - svdfunctcvm.m \ - svstruct.m \ - swapview.m \ - synthcornoise.m \ - tal_csr2xyz.m \ - tal_xyz2csr.m \ - tliweights.m \ - trapezoid.m \ - tTest.m \ - tukeytaper.m \ - uliweights.m \ - univarlab.m \ - vol2mos.m \ - volind2mosind.m \ - volsub2mossub.m \ - vqm.m \ - yak2.m \ - yak.m \ - yakview.m \ - yvplt_acffit.m \ - yvpltraw.m - -TDRMFILES=\ - tdr_b1map2d.m \ - tdr_deghost.m \ - tdr_dftmtx2d.m \ - tdr_epi_phtraj.m \ - tdr_epirecon.m \ - tdr_fftshift2d.m \ - tdr_fidb0.m \ - tdr_fidmat2.m \ - tdr_fidmat.m \ - tdr_fidt2star.m \ - tdr_ghostcomp.m \ - tdr_graddumpinterp.m \ - tdr_gradmtx.m \ - tdr_ifftslice.m \ - tdr_intpertrap.m \ - tdr_kshift.m \ - tdr_ldgraddump.m \ - tdr_lininterp.m \ - tdr_measasc.m \ - tdr_pedmatrix.m \ - tdr_peshift.m \ - tdr_phdist_est.m \ - tdr_rcolmat.m \ - tdr_recon_cols.m \ - tdr_recon.m \ - tdr_recon_rows.m \ - tdr_recon_sim.m \ - tdr_regrid.m \ - tdr_rledecode.m \ - tdr_rotate_ktraj.m \ - tdr_rtraj.m \ - tdr_sliceorder.m \ - tdr_smooth2d.m \ - tdr_trapspect2d.m \ - tdr_uniform_dft1d.m \ - tdr_uniform_idft2d.m \ - tdr_uniform_phtraj.m - -FIGFILES=\ - mkanalysis_gui.fig \ - univarlab.fig \ - rawplot.fig - -if NMR_INSTALL -foo_DATA=$(MFILES) $(TDRMFILES) $(FIGFILES) -else -foo_DATA=$(MFILES) $(FIGFILES) -endif - -EXTRA_DIST=$(foo_DATA) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES=$(TDRMFILES) -include $(top_srcdir)/Makefile.extra diff --git a/fsgdf/Makefile.am b/fsgdf/Makefile.am deleted file mode 100644 index 542bd39c320..00000000000 --- a/fsgdf/Makefile.am +++ /dev/null @@ -1,51 +0,0 @@ -# -# Makefile for fsgdf -# - -# -# Note: fsgdf_wrap.c is created using swig: -# swig -tcl fsgdf.i -# and then all the unused routines, as indicated by the compiler errors, -# are removed. the callocs were also increased to size 2048 for safety. -# fsgdf_wrap.c is built by tksurfer and qdec. -# - -if ENABLE_TCLTK_APPS -AM_CPPFLAGS=-I$(top_srcdir)/include $(TCL_CFLAGS) -else -AM_CPPFLAGS=-I$(top_srcdir)/include $(TCL_CFLAGS) -endif -AM_LDFLAGS= - -noinst_LIBRARIES= libfsgdf.a -if ENABLE_TCLTK_APPS -libfsgdf_a_SOURCES = fsgdf.c fsgdf_wrap.c FsgdfPlot.cxx -else -libfsgdf_a_SOURCES = fsgdf.c -endif - -if ENABLE_TCLTK_APPS -# trick to get test data into the build directory -foo_SOURCES= -foo: - if ! test -f "$(top_builddir)/fsgdf/test_data.tar.gz"; then \ - cp -v $(top_srcdir)/fsgdf/test_data.tar.gz \ - $(top_builddir)/fsgdf/; fi; - if ! test -f "$(top_builddir)/fsgdf/test.tcl"; then \ - cp -v $(top_srcdir)/fsgdf/test.tcl \ - $(top_builddir)/fsgdf/; fi; - -check_PROGRAMS=foo test -test_SOURCES=test.c fsgdf_wrap.c -test_LDFLAGS=$(LDFLAGS_TCL) -test_LDADD=libfsgdf.a $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(LIBS_TCL) -TESTS=setup_test_data test -endif - -EXTRA_DIST=setup_test_data test_data.tar.gz fsgdf.i test.tcl FsgdfPlot.cxx - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/fslutils/Makefile.am b/fslutils/Makefile.am deleted file mode 100644 index aeeb97b6ad9..00000000000 --- a/fslutils/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = fsl_label2voxel -fsl_label2voxel_SOURCES=fsl_label2voxel.cpp -fsl_label2voxel_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -fsl_label2voxel_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/gpu_utils/Makefile.am b/gpu_utils/Makefile.am deleted file mode 100644 index 75001b53414..00000000000 --- a/gpu_utils/Makefile.am +++ /dev/null @@ -1,40 +0,0 @@ -## -## Makefile.am -## - -# BUILDCUDA is defined if configure.in finds CUDA -if BUILDCUDA - -bin_PROGRAMS=cudadetect - -cudadetect_SOURCES=cudadetect.cpp - - -if HAVE_MAC_OSX -cudadetect_LDFLAGS=-rdynamic -ldl -F/Library/Frameworks -framework CUDA -else -cudadetect_LDFLAGS=-rdynamic -ldl -endif - -cudadetect_CXXFLAGS=$(CUDA_CFLAGS) -DFS_CUDA -cudadetect_LDADD=$(CUDA_LIBS) - -# put a wrapper around the bin, to set LD_LIBRARY_PATH to /usr/local/cuda -install-exec-hook:cudadetect - cp $(top_builddir)/gpu_utils/cudadetect $(DESTDIR)$(bindir)/cudadetect.bin - echo "#!/bin/tcsh -ef" > $(DESTDIR)$(bindir)/cudadetect - echo "source \$$FREESURFER_HOME/bin/cuda_setup" \ - >> $(DESTDIR)$(bindir)/cudadetect - echo "cudadetect.bin \$$argv" >> $(DESTDIR)$(bindir)/cudadetect - chmod a+x $(DESTDIR)$(bindir)/cudadetect - if [[ -f /usr/pubsw/bin/chrpath ]]; then \ - /usr/pubsw/bin/chrpath -d $(DESTDIR)$(bindir)/cudadetect.bin; fi - -uninstall-hook: - rm -f $(DESTDIR)$(bindir)/cudadetect.bin - -endif - - -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/hiam_make_surfaces/Makefile.am b/hiam_make_surfaces/Makefile.am deleted file mode 100644 index 0e2fa8a9cb4..00000000000 --- a/hiam_make_surfaces/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = hiam_make_surfaces -hiam_make_surfaces_SOURCES=hiam_make_surfaces.c -hiam_make_surfaces_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -hiam_make_surfaces_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/hiam_make_template/Makefile.am b/hiam_make_template/Makefile.am deleted file mode 100644 index 8d9e77a7e7e..00000000000 --- a/hiam_make_template/Makefile.am +++ /dev/null @@ -1,18 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = hiam_make_template -hiam_make_template_SOURCES=hiam_make_template.c -hiam_make_template_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -hiam_make_template_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - diff --git a/hiam_register/Makefile.am b/hiam_register/Makefile.am deleted file mode 100644 index 21b40413703..00000000000 --- a/hiam_register/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = hiam_register -hiam_register_SOURCES=hiam_register.c -hiam_register_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -hiam_register_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/hipsstubs/Makefile.am b/hipsstubs/Makefile.am deleted file mode 100644 index 9c51928303c..00000000000 --- a/hipsstubs/Makefile.am +++ /dev/null @@ -1,15 +0,0 @@ -# -# Makefile.am -# - -AM_CPPFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -noinst_LIBRARIES= libhipsstubs.a -libhipsstubs_a_SOURCES = hipsrepl.c hipsstubs.c - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/histo_compute_joint_density/Makefile.am b/histo_compute_joint_density/Makefile.am deleted file mode 100644 index 474ab26234b..00000000000 --- a/histo_compute_joint_density/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS=histo_compute_joint_density -histo_compute_joint_density_SOURCES=histo_compute_joint_density.c -histo_compute_joint_density_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -histo_compute_joint_density_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/histo_fix_topology/Makefile.am b/histo_fix_topology/Makefile.am deleted file mode 100644 index 007910fc8f7..00000000000 --- a/histo_fix_topology/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = histo_fix_topology -histo_fix_topology_SOURCES=histo_fix_topology.c -histo_fix_topology_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -histo_fix_topology_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/histo_register/Makefile.am b/histo_register/Makefile.am deleted file mode 100644 index 84094b97349..00000000000 --- a/histo_register/Makefile.am +++ /dev/null @@ -1,78 +0,0 @@ -# -# Makefile.am -# - -if BUILDOPENCV -SBL=$(top_srcdir)/histo_register/SimpleBaseLib -PVL=$(top_srcdir)/histo_register/ParticleVideoLib -SBL_BUILD=$(top_builddir)/histo_register/SimpleBaseLib -PVL_BUILD=$(top_builddir)/histo_register/ParticleVideoLib -SUBDIRS=./SimpleBaseLib ./ParticleVideoLib - -bin_PROGRAMS = histo_register -histo_register_SOURCES=\ - prep/BlockPrep.cc \ - prep/HistoPrep.cc \ - prep/HistoStats.cc \ - prep/HistoStitch.cc \ - prep/MPrep.cc \ - prep/Polarization.cc \ - prep/Prediction.cc \ - prep/StitchNode.cc \ - prep/VolumeFile.cc \ - prep/VolumeUtil.cc \ - registration/BlockRegister.cc \ - registration/CorresField3D.cc \ - registration/HistoRegister.cc \ - registration/HistoTransform.cc \ - registration/ImageSetSeq.cc \ - registration/Normalization.cc \ - registration/TestCorres3D.cc \ - registration/VarCorres3D.cc \ - registration/VarCorres3DUtil.cc \ - prep/BlockPrep.h \ - prep/MPrep.h \ - prep/Polarization.h \ - prep/VolumeFile.h \ - prep/HistoStats.h \ - prep/Prediction.h \ - prep/VolumeUtil.h \ - prep/HistoStitch.h \ - prep/HistoPrep.h \ - prep/StitchNode.h \ - registration/HistoTransform.h \ - registration/HistoRegister.h \ - registration/VarCorres3DUtil.h \ - registration/TestCorres3D.h \ - registration/VarCorres3D.h \ - registration/Normalization.h \ - registration/CorresField3D.h \ - registration/BlockRegister.h \ - registration/ImageSetSeq.h \ - Main.cc - -histo_register_CXXFLAGS=-I. -I$(SBL)/include -I$(SBL)/external -I$(PVL)/include $(OPENCV_CXXFLAGS) -histo_register_CPPFLAGS=-DUSE_OPENCV -DUSE_CDT -LOCALLIBS=-L$(SBL_BUILD) -L$(PVL_BUILD) -lpvl -lsbl -histo_register_LDADD=$(OPENCV_LIBS) $(LOCALLIBS) - - -install-exec-hook: - cp $(top_builddir)/histo_register/histo_register \ - $(DESTDIR)$(bindir)/histo_register.bin - echo "#!/bin/tcsh -ef" > $(DESTDIR)$(bindir)/histo_register - echo "setenv LD_LIBRARY_PATH $(OPENCV_DIR)/lib" \ - >> $(DESTDIR)$(bindir)/histo_register - echo "histo_register.bin \$$argv" >> $(DESTDIR)$(bindir)/histo_register - chmod a+x $(DESTDIR)$(bindir)/histo_register - -uninstall-hook: - rm -f $(DESTDIR)$(bindir)/histo_register.bin - -endif - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/histo_register/ParticleVideoLib/Makefile.am b/histo_register/ParticleVideoLib/Makefile.am deleted file mode 100644 index 68fa65f9e63..00000000000 --- a/histo_register/ParticleVideoLib/Makefile.am +++ /dev/null @@ -1,34 +0,0 @@ -# -# Makefile.am -# - -noinst_LIBRARIES=libpvl.a - -libpvl_a_CXXFLAGS=-I$(top_srcdir)/histo_register/ParticleVideoLib/include \ - $(OPENCV_CXXFLAGS) -I$(top_srcdir)/histo_register/SimpleBaseLib/include -libpvl_a_CPPFLAGS=-DUSE_CDT -DUSE_OPENCV -libpvl_a_SOURCES=\ - src/Occlusion.cc \ - src/SimpleParticleBuild.cc \ - src/SimpleParticleData.cc \ - src/SimpleParticleOptimize.cc \ - src/SparseSystem.cc \ - src/VarMotion.cc \ - src/VarMotionMultiRes.cc \ - src/VarMotionUtil.cc \ - include/pvl/Occlusion.h \ - include/pvl/SimpleParticleBuild.h \ - include/pvl/SimpleParticleData.h \ - include/pvl/SimpleParticleOptimize.h \ - include/pvl/SparseSystem.h \ - include/pvl/VarMotionUtil.h \ - include/pvl/VarMotionMultiRes.h \ - include/pvl/VarMotion.h - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - - diff --git a/histo_register/SimpleBaseLib/Makefile.am b/histo_register/SimpleBaseLib/Makefile.am deleted file mode 100644 index 1cf56e4b70b..00000000000 --- a/histo_register/SimpleBaseLib/Makefile.am +++ /dev/null @@ -1,130 +0,0 @@ -# -# Makefile.am -# - -noinst_LIBRARIES=libsbl.a - -libsbl_a_CXXFLAGS=-I$(top_srcdir)/histo_register/SimpleBaseLib/include/ \ - $(OPENCV_CXXFLAGS) -libsbl_a_CPPFLAGS=-DUSE_OPENCV -DUSE_ZLIB -DUSE_CDT -libsbl_a_SOURCES=\ - src/system/Timer.cc \ - src/system/FileSystem.cc \ - src/system/SerialPort.cc \ - src/system/TimeUtil.cc \ - src/system/Microcontroller.cc \ - src/system/Signal.cc \ - src/system/Socket.cc \ - src/core/StringUtil.cc \ - src/core/String.cc \ - src/core/Init.cc \ - src/core/Table.cc \ - src/core/Command.cc \ - src/core/Config.cc \ - src/core/UnitTest.cc \ - src/core/File.cc \ - src/core/Display.cc \ - src/core/PathConfig.cc \ - src/other/DrawingLayer.cc \ - src/other/ImageDrawingLayer.cc \ - src/other/SVG.cc \ - src/other/Plot.cc \ - src/other/CodeCheck.cc \ - src/other/Scripting.cc \ - src/other/TaggedFile.cc \ - src/math/ConfigOptimizer.cc \ - src/math/VectorUtil.cc \ - src/math/TensorUtil.cc \ - src/math/Optimizer.cc \ - src/math/MathUtil.cc \ - src/math/Triangulation.cc \ - src/math/KMeans.cc \ - src/math/Geometry.cc \ - src/math/MatrixUtil.cc \ - src/math/TimeSeries.cc \ - src/math/OptimizerUtil.cc \ - src/image/Video.cc \ - src/image/MotionFieldSeq.cc \ - src/image/Track.cc \ - src/image/ImageDraw.cc \ - src/image/ImageRegister.cc \ - src/image/MotionField.cc \ - src/image/Filter.cc \ - src/image/MotionFieldUtil.cc \ - src/image/ImageTransform.cc \ - src/image/Image.cc \ - src/image/ImageSeqUtil.cc \ - src/image/ImageUtil.cc \ - external/CDT/CDT.cc - -EXTRA_DIST=\ - external/CDT/CDT.h \ - external/win_dirent.h \ - external/win_timegm.h \ - include/sbl/gui/ConfigEditor.h \ - include/sbl/gui/ImageViewer.h \ - include/sbl/gui/MiscWidgets.h \ - include/sbl/gui/GraphicViewer.h \ - include/sbl/gui/ImageSeqViewer.h \ - include/sbl/gui/MainWindow.h \ - include/sbl/gui/ConfigViewer.h \ - include/sbl/core/Config.h \ - include/sbl/core/StringUtil.h \ - include/sbl/core/Table.h \ - include/sbl/core/Pointer.h \ - include/sbl/core/Init.h \ - include/sbl/core/File.h \ - include/sbl/core/PathConfig.h \ - include/sbl/core/Command.h \ - include/sbl/core/Display.h \ - include/sbl/core/Array.h \ - include/sbl/core/String.h \ - include/sbl/core/Dict.h \ - include/sbl/core/UnitTest.h \ - include/sbl/system/SerialPort.h \ - include/sbl/system/TimeUtil.h \ - include/sbl/system/FileSystem.h \ - include/sbl/system/Signal.h \ - include/sbl/system/Socket.h \ - include/sbl/system/Timer.h \ - include/sbl/system/Microcontroller.h \ - include/sbl/other/CodeCheck.h \ - include/sbl/other/SVG.h \ - include/sbl/other/Scripting.h \ - include/sbl/other/ImageDrawingLayer.h \ - include/sbl/other/TaggedFile.h \ - include/sbl/other/Plot.h \ - include/sbl/other/DrawingLayer.h \ - include/sbl/math/KMeans.h \ - include/sbl/math/Optimizer.h \ - include/sbl/math/Vector.h \ - include/sbl/math/MatrixUtil.h \ - include/sbl/math/Matrix.h \ - include/sbl/math/MathUtil.h \ - include/sbl/math/OptimizerUtil.h \ - include/sbl/math/Tensor.h \ - include/sbl/math/Triangulation.h \ - include/sbl/math/VectorUtil.h \ - include/sbl/math/TimeSeries.h \ - include/sbl/math/TensorUtil.h \ - include/sbl/math/ConfigOptimizer.h \ - include/sbl/math/Geometry.h \ - include/sbl/image/ImageDraw.h \ - include/sbl/image/Video.h \ - include/sbl/image/MotionFieldSeq.h \ - include/sbl/image/Image.h \ - include/sbl/image/Filter.h \ - include/sbl/image/ImageTransform.h \ - include/sbl/image/ImageSeqUtil.h \ - include/sbl/image/MotionField.h \ - include/sbl/image/ImageUtil.h \ - include/sbl/image/MotionFieldUtil.h \ - include/sbl/image/ImageRegister.h \ - include/sbl/image/Track.h - - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/histo_register_block/Makefile.am b/histo_register_block/Makefile.am deleted file mode 100644 index 0d19aef1f4d..00000000000 --- a/histo_register_block/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = histo_register_block -histo_register_block_SOURCES=histo_register_block.c -histo_register_block_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -histo_register_block_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/histo_segment/Makefile.am b/histo_segment/Makefile.am deleted file mode 100644 index 52fc286bb21..00000000000 --- a/histo_segment/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = histo_segment -histo_segment_SOURCES=histo_segment.c -histo_segment_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -histo_segment_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/histo_synthesize/Makefile.am b/histo_synthesize/Makefile.am deleted file mode 100644 index 543a4a8c952..00000000000 --- a/histo_synthesize/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = histo_synthesize -histo_synthesize_SOURCES=histo_synthesize.c -histo_synthesize_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -histo_synthesize_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/images/Makefile.am b/images/Makefile.am deleted file mode 100644 index 8c5d5adc3eb..00000000000 --- a/images/Makefile.am +++ /dev/null @@ -1,157 +0,0 @@ -# -# Makefile.am -# - -foodir=$(prefix)/lib/images - -GIF=\ - icon_analysis_open.gif \ - icon_arrow_ccw.gif \ - icon_arrow_cw.gif \ - icon_arrow_down.gif \ - icon_arrow_expand_x.gif \ - icon_arrow_expand_y.gif \ - icon_arrow_left.gif \ - icon_arrow_right.gif \ - icon_arrow_rot_x_neg.gif \ - icon_arrow_rot_x_pos.gif \ - icon_arrow_rot_y_neg.gif \ - icon_arrow_rot_y_pos.gif \ - icon_arrow_rot_z_neg.gif \ - icon_arrow_rot_z_pos.gif \ - icon_arrow_shrink_x.gif \ - icon_arrow_shrink_y.gif \ - icon_arrow_up.gif \ - icon_aux_volume.gif \ - icon_brush_3d.gif \ - icon_brush_circle.gif \ - icon_brush_square.gif \ - icon_camera.gif \ - icon_color_label.gif \ - icon_colormap_grayscale.gif \ - icon_colormap_lut.gif \ - icon_color_picker.gif \ - icon_color_scalebar.gif \ - icon_control_point.gif \ - icon_cursor_goto.gif \ - icon_cursor_save.gif \ - icon_curv.gif \ - icon_curv_bw.gif \ - icon_cut_area.gif \ - icon_cut_clear.gif \ - icon_cut_closed_line.gif \ - icon_cut_line.gif \ - icon_cut_plane.gif \ - icon_disk.gif \ - icon_disk_multiview.gif \ - icon_disk_new_name.gif \ - icon_draw_line_closed.gif \ - icon_draw_line.gif \ - icon_edit_ctrlpts.gif \ - icon_edit_custom.gif \ - icon_edit_label.gif \ - icon_edit_parc.gif \ - icon_edit_volume.gif \ - icon_erase_label.gif \ - icon_erase_line.gif \ - icon_fill.gif \ - icon_fill_label.gif \ - icon_fill_roi.gif \ - icon_fill_volume.gif \ - icon_folder.gif \ - icon_home.gif \ - icon_label_filled.gif \ - icon_label_list.gif \ - icon_label_off.gif \ - icon_label_open.gif \ - icon_label_outline.gif \ - icon_label_save.gif \ - icon_label_table.gif \ - icon_label_to_marked.gif \ - icon_line_tool.gif \ - icon_linked_cursors.gif \ - icon_main_volume.gif \ - icon_marked_to_label.gif \ - icon_marker_crosshair.gif \ - icon_marker_diamond.gif \ - icon_matrix_erase.gif \ - icon_matrix_write.gif \ - icon_navigate.gif \ - icon_orientation_coronal.gif \ - icon_orientation_coronal_pdm.gif \ - icon_orientation_horizontal.gif \ - icon_orientation_horizontal_pdm.gif \ - icon_orientation_sagittal.gif \ - icon_orientation_sagittal_pdm.gif \ - icon_orientation_x.gif \ - icon_orientation_y.gif \ - icon_orientation_z.gif \ - icon_overlay.gif \ - icon_redraw.gif \ - icon_rotate_plane.gif \ - icon_seg_volume.gif \ - icon_selection_add.gif \ - icon_selection_subtract.gif \ - icon_snapshot_load.gif \ - icon_snapshot_save.gif \ - icon_stopwatch.gif \ - icon_surface_inflated.gif \ - icon_surface_main.gif \ - icon_surface_original.gif \ - icon_surface_pial.gif \ - icon_surface_white.gif \ - icon_table_open.gif \ - icon_view_31.gif \ - icon_view_mosaic.gif \ - icon_view_mosaic_pdm.gif \ - icon_view_multiple.gif \ - icon_view_multiple_pdm.gif \ - icon_view_single.gif \ - icon_view_single_pdm.gif \ - icon_zoom_in.gif \ - icon_zoom_out.gif - -TIF=\ - icon_analysis_open.tif \ - icon_arrow_rot_x_neg.tif \ - icon_arrow_rot_x_pos.tif \ - icon_arrow_rot_y_neg.tif \ - icon_arrow_rot_y_pos.tif \ - icon_arrow_rot_z_neg.tif \ - icon_arrow_rot_z_pos.tif \ - icon_camera.tif \ - icon_colormap_grayscale.tif \ - icon_colormap_lut.tif \ - icon_curv_bw.tif \ - icon_disk_new_name.tif \ - icon_disk.tif \ - icon_disk_multiview.tif \ - icon_folder.tif \ - icon_home.tif \ - icon_label_open.tif \ - icon_label_save.tif \ - icon_marker_crosshair.tif \ - icon_matrix_erase.tif \ - icon_matrix_write.tif \ - icon_redraw.tif \ - icon_selection_add.tif \ - icon_selection_subtract.tif \ - icon_table_open.tif \ - icon_view_multiple.tif \ - icon_view_single.tif \ - icon_zoom_in.tif \ - icon_zoom_out.tif - -foo_datafiles= $(GIF) $(TIF) \ - icon_zoom_out.png icon_label_list.xpm icon_fill_roi.png \ - icon_fill_volume.png icon_label_table.xpm - -install-data-local: - test -z $(DESTDIR)$(foodir) || $(mkdir_p) $(DESTDIR)$(foodir) - $(INSTALL_DATA) $(foo_datafiles) $(DESTDIR)$(foodir) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/include/Makefile.am b/include/Makefile.am deleted file mode 100644 index 4a48726718f..00000000000 --- a/include/Makefile.am +++ /dev/null @@ -1,763 +0,0 @@ -SUBDIRS=dicom xview pixrect sys NrrdIO topology fs_vnl - -EXTRA_DIST=\ - affine.h \ - affine.hpp \ - affinegpu.hpp \ - AFNI.h \ - analyze.h \ - annotation.h \ - argparse.hpp \ - art1.h \ - artmap.h \ - autoencoder.h \ - aseg_edit_svm.h \ - backprop.h \ - bfileio.h \ - box.h \ - Bruker.h \ - canny.h \ - cdflib.h \ - cephes.h \ - chklc.h \ - chronometer.h \ - chronometer.hpp \ - classify.h \ - class_array.h \ - cluster.h \ - cma.h \ - cmat.h \ - cmdargs.h \ - colortab.h \ - congraph.h \ - connect.h \ - const.h \ - corio.h \ - cpputils.h \ - ctrpoints.h \ - cvector.h \ - dct.h \ - density.h \ - diag.h \ - DICOMRead.h \ - dti.h \ - dtk.fs.h \ - error.h \ - evschutils.h \ - fastmarching.h \ - fcd.h \ - fexterns.h \ - fftutils.h \ - fgutil.h \ - field_code.h \ - filecode.h \ - filter.h \ - fio.h \ - flash.h \ - fmarchmesh.h \ - fmriutils.h \ - fsenv.h \ - fsgdf.h \ - fsinit.h \ - FsgdfPlot.h \ - fsgdf_wrap.h \ - fsglm.h \ - fixedmap.hpp \ - gcaboundary.h \ - gca.h \ - gcalinearnode.hpp \ - gcalinearprior.hpp \ - gcamcomputegradient_cuda.hpp \ - gcamfots_cuda.hpp \ - gcamorphcpu.hpp \ - gcamorphenergy.hpp \ - gcamorphgpu.hpp\ - gcamorphtermgpu.hpp\ - gcamorphtestutils.hpp\ - gcamregisterlevel_cuda.hpp \ - gcanodegpu.hpp \ - gcapriorgpu.hpp \ - gcasgpu.hpp \ - gcautils.hpp \ - gcamorph.h \ - gcamorphtestutils.h \ - gcamfots_cuda.h \ - gcanodegpu.hpp \ - gcarray.h \ - gclass.h \ - gcsa.h \ - general.h \ - generators.hpp \ - geos.h \ - getdelim.h \ - getline.h \ - gifti_io.h \ - gifti_local.h \ - gifti_xml.h \ - gw_utils.h \ - handle.h \ - heap.h \ - hip_brf.h \ - hipl_for.h \ - hipl_format.h \ - hippo.h \ - hips_basic.h \ - hips_error.h \ - hipsext.h \ - hips.h \ - hips_header.h \ - hipsh.h \ - hips_parser.h \ - hipspub.h \ - hipsu.h \ - histo.h \ - h_logz.h \ - hmem.h \ - icosahedron.h \ - image.h \ - imautils.h \ - intensity_eig.h \ - inverse.h \ - iutils.h \ - kernel.h \ - kinput.h \ - label.h \ - ldtmplt.h \ - log.hpp \ - lpafile.h \ - machine.h \ - macros.h \ - mailbox.h \ - map.h \ - MARS_DT_Boundary.h \ - matfile.h \ - matrix.h \ - MC.h \ - mconf.h \ - mghendian.h \ - mgh_filter.h \ - mgh_matrix.h \ - min_heap.h \ - mincutils.h \ - minc_volume_io.h \ - minmaxrc.h \ - minmax.hpp \ - mosaic.h \ - mri2.h \ - mriBSpline.h \ - mri_ca_configFile.h \ - mri_ca_gausDist.h \ - mri_ca_labelingParameters.h \ - mri_ca_labelLUT.h \ - mri_ca_labelMapper.h \ - mri_ca_measMapper.h \ - mri_ca_measure.h \ - mri_ca_measureVolume.h \ - mri_ca_sparse2DGausDistMatrix.h \ - mri_ca_sparse2DMatrix.h \ - mri_ca_sparse3DMatrix.h \ - mri_ca_statisticsVolumeHeader.h \ - mri_ca_trainingParameters.h \ - mri_ca_util.h \ - mri_circulars.h \ - mriclass.h \ - mri_conform.h \ - mricurv.h \ - mriFunctionalDataAccess.h \ - mri.h \ - mriHeadPointList.h \ - mri_identify.h \ - MRIio_old.h \ - mrimorph.h \ - mrinorm.h \ - mriROI.h \ - mrisbiorthogonalwavelets.h \ - mrisegment.h \ - mris_expand.h \ - mrishash.h \ - mris_topology.h \ - mriSurface.h \ - mrisurf.h \ - mrisutils.h \ - mri_tess.h \ - mri_topology.h \ - mri_transform.h \ - mriTransform.h \ - mriTypes.h \ - mriVolume.h \ - mrivol2vol_cuda.h \ - mriconvolve_cuda.h \ - mrimean_cuda.h \ - mrivol2vol_cuda.hpp \ - mriconvolve_cuda.hpp \ - mrimean_cuda.hpp \ - mrilabels_cuda.hpp \ - mrisurf_cuda.h \ - mriframegpu.hpp \ - volumegpu.hpp \ - volumegpu_impl.hpp \ - cudatypeutils.hpp \ - cudacheck.h \ - devicemanagement.h \ - MRISOBBTree.h \ - MRISdistancefield.h \ - mris_compVolFrac.h \ - mthread.h \ - nifti1.h \ - nifti1_io.h \ - numerics.h \ - path.h \ - pbm.h \ - pbmplus.h \ - pdf.h \ - pgm.h \ - pnm.h \ - ppm.h \ - prime.h \ - proto.h \ - qdecutils.h \ - queue.h \ - randomfields.h \ - rbf.h \ - rbm.h \ - rec.h \ - region.h \ - registerio.h \ - resample.h \ - rescale.h \ - retinotopy.h \ - rfa.h \ - rfutils.h \ - rforest.h \ - rfutils.h \ - rgb_image.h \ - rgb_utils.h \ - runfuncs.h \ - selxavgio.h \ - sig.h \ - signa.h \ - sse_mathfun.h \ - stats.h \ - stc.h \ - struct.h \ - connectcomp.h \ - surfcluster.h \ - svm.h \ - tags.h \ - talairachex.h \ - testgpu.h \ - TexFont.h \ - thread.h \ - timer.h \ - transform.h \ - trig512.h \ - tritri.h \ - tukey.h \ - typedefs.h \ - utils.h \ - utilsmath.h \ - version.h \ - vlabels.h \ - volcluster.h \ - volumegpucompare.hpp \ - volumecpu.hpp \ - voxlist.h \ - windiag.h \ - x3DList.h \ - xDebug.h \ - xGLutWindow.h \ - xGrowableArray.h \ - xList.h \ - xSparseVolume.h \ - xTypes.h \ - xUndoList.h \ - xUtilities.h \ - xVoxel.h \ - znzlib.h \ - thrust/CHANGELOG \ - thrust/set_intersection.h \ - thrust/binary_search.h \ - thrust/generate.h \ - thrust/iterator/iterator_traits.h \ - thrust/iterator/iterator_adaptor.h \ - thrust/iterator/reverse_iterator.h \ - thrust/iterator/constant_iterator.h \ - thrust/iterator/iterator_facade.h \ - thrust/iterator/zip_iterator.h \ - thrust/iterator/permutation_iterator.h \ - thrust/iterator/iterator_categories.h \ - thrust/iterator/transform_iterator.h \ - thrust/iterator/counting_iterator.h \ - thrust/iterator/detail/universal_categories.h \ - thrust/iterator/detail/reverse_iterator_base.h \ - thrust/iterator/detail/iterator_category_to_space.h \ - thrust/iterator/detail/minimum_category.h \ - thrust/iterator/detail/backend_iterator_categories.h \ - thrust/iterator/detail/is_iterator_category.h \ - thrust/iterator/detail/iterator_category_to_traversal.h \ - thrust/iterator/detail/placement/is_placed.h \ - thrust/iterator/detail/constant_iterator_base.h \ - thrust/iterator/detail/backend_iterator_spaces.h \ - thrust/iterator/detail/forced_iterator.h \ - thrust/iterator/detail/minimum_space.h \ - thrust/iterator/detail/any_space_tag.h \ - thrust/iterator/detail/device_iterator_category_to_backend_space.h \ - thrust/iterator/detail/zip_iterator_base.h \ - thrust/iterator/detail/distance_from_result.h \ - thrust/iterator/detail/normal_iterator.h \ - thrust/iterator/detail/permutation_iterator_base.h \ - thrust/for_each.h \ - thrust/random/uniform_int_distribution.h \ - thrust/random/subtract_with_carry_engine.h \ - thrust/random/linear_congruential_engine.h \ - thrust/random/discard_block_engine.h \ - thrust/random/xor_combine_engine.h \ - thrust/random/normal_distribution.h \ - thrust/random/uniform_real_distribution.h \ - thrust/random/linear_feedback_shift_engine.h \ - thrust/random/detail/xor_combine_engine_max.h \ - thrust/random/detail/linear_feedback_shift_engine_wordmask.h \ - thrust/random/detail/mod.h \ - thrust/random/detail/random_core_access.h \ - thrust/random/detail/linear_congruential_engine_discard.h \ - thrust/adjacent_difference.h \ - thrust/unique.h \ - thrust/distance.h \ - thrust/tuple.h \ - thrust/gather.h \ - thrust/count.h \ - thrust/device_new.h \ - thrust/partition.h \ - thrust/experimental/cuda/pinned_allocator.h \ - thrust/experimental/cuda/ogl_interop_allocator.h \ - thrust/device_vector.h \ - thrust/functional.h \ - thrust/sort.h \ - thrust/utility.h \ - thrust/uninitialized_fill.h \ - thrust/random.h \ - thrust/system/error_code.h \ - thrust/system/cuda_error.h \ - thrust/system/system_error.h \ - thrust/system/detail/errno.h \ - thrust/host_vector.h \ - thrust/find.h \ - thrust/transform_scan.h \ - thrust/device_malloc_allocator.h \ - thrust/system_error.h \ - thrust/inner_product.h \ - thrust/remove.h \ - thrust/device_new_allocator.h \ - thrust/scan.h \ - thrust/version.h \ - thrust/device_malloc.h \ - thrust/transform.h \ - thrust/sequence.h \ - thrust/replace.h \ - thrust/fill.h \ - thrust/pair.h \ - thrust/is_sorted.h \ - thrust/swap.h \ - thrust/equal.h \ - thrust/advance.h \ - thrust/reduce.h \ - thrust/device_delete.h \ - thrust/set_operations.h \ - thrust/uninitialized_copy.h \ - thrust/copy.h \ - thrust/scatter.h \ - thrust/transform_reduce.h \ - thrust/device_allocator.h \ - thrust/reverse.h \ - thrust/mismatch.h \ - thrust/logical.h \ - thrust/extrema.h \ - thrust/detail/util/align.h \ - thrust/detail/util/blocking.h \ - thrust/detail/device_ptr_traits.h \ - thrust/detail/diagnostic.h \ - thrust/detail/mpl/math.h \ - thrust/detail/destroy.h \ - thrust/detail/trivial_sequence.h \ - thrust/detail/numeric_traits.h \ - thrust/detail/integer_traits.h \ - thrust/detail/tuple_meta_transform.h \ - thrust/detail/static_assert.h \ - thrust/detail/dispatch/binary_search.h \ - thrust/detail/dispatch/for_each.h \ - thrust/detail/dispatch/adjacent_difference.h \ - thrust/detail/dispatch/unique.h \ - thrust/detail/dispatch/distance.h \ - thrust/detail/dispatch/destroy.h \ - thrust/detail/dispatch/partition.h \ - thrust/detail/dispatch/sort.h \ - thrust/detail/dispatch/uninitialized_fill.h \ - thrust/detail/dispatch/is_trivial_copy.h \ - thrust/detail/dispatch/find.h \ - thrust/detail/dispatch/remove.h \ - thrust/detail/dispatch/scan.h \ - thrust/detail/dispatch/fill.h \ - thrust/detail/dispatch/advance.h \ - thrust/detail/dispatch/reduce.h \ - thrust/detail/dispatch/set_operations.h \ - thrust/detail/dispatch/uninitialized_copy.h \ - thrust/detail/dispatch/copy.h \ - thrust/detail/dispatch/extrema.h \ - thrust/detail/move.h \ - thrust/detail/host/binary_search.h \ - thrust/detail/host/for_each.h \ - thrust/detail/host/adjacent_difference.h \ - thrust/detail/host/unique.h \ - thrust/detail/host/partition.h \ - thrust/detail/host/sort.h \ - thrust/detail/host/find.h \ - thrust/detail/host/dispatch/copy.h \ - thrust/detail/host/remove.h \ - thrust/detail/host/scan.h \ - thrust/detail/host/fill.h \ - thrust/detail/host/reduce.h \ - thrust/detail/host/set_operations.h \ - thrust/detail/host/copy.h \ - thrust/detail/host/extrema.h \ - thrust/detail/host/detail/trivial_copy.h \ - thrust/detail/host/detail/insertion_sort.h \ - thrust/detail/host/detail/general_copy.h \ - thrust/detail/host/detail/stable_merge_sort.h \ - thrust/detail/host/detail/merge.h \ - thrust/detail/host/detail/copy_backward.h \ - thrust/detail/type_traits.h \ - thrust/detail/tuple_transform.h \ - thrust/detail/config/compiler.h \ - thrust/detail/config/debug.h \ - thrust/detail/config/device_backend.h \ - thrust/detail/config/host_device.h \ - thrust/detail/config/simple_defines.h \ - thrust/detail/config/config.h \ - thrust/detail/internal_functional.h \ - thrust/detail/contiguous_storage.h \ - thrust/detail/device/binary_search.h \ - thrust/detail/device/for_each.h \ - thrust/detail/device/dereference.h \ - thrust/detail/device/adjacent_difference.h \ - thrust/detail/device/unique.h \ - thrust/detail/device/generic/binary_search.h \ - thrust/detail/device/generic/malloc.h \ - thrust/detail/device/generic/adjacent_difference.h \ - thrust/detail/device/generic/unique.h \ - thrust/detail/device/generic/partition.h \ - thrust/detail/device/generic/copy_if.h \ - thrust/detail/device/generic/no_throw_free.h \ - thrust/detail/device/generic/find.h \ - thrust/detail/device/generic/remove.h \ - thrust/detail/device/generic/free.h \ - thrust/detail/device/generic/scan_by_key.h \ - thrust/detail/device/generic/fill.h \ - thrust/detail/device/generic/reduce_by_key.h \ - thrust/detail/device/generic/reduce.h \ - thrust/detail/device/generic/set_operations.h \ - thrust/detail/device/generic/copy.h \ - thrust/detail/device/generic/extrema.h \ - thrust/detail/device/partition.h \ - thrust/detail/device/sort.h \ - thrust/detail/device/no_throw_free.h \ - thrust/detail/device/find.h \ - thrust/detail/device/dispatch/for_each.h \ - thrust/detail/device/dispatch/malloc.h \ - thrust/detail/device/dispatch/sort.h \ - thrust/detail/device/dispatch/no_throw_free.h \ - thrust/detail/device/dispatch/free.h \ - thrust/detail/device/dispatch/scan.h \ - thrust/detail/device/dispatch/fill.h \ - thrust/detail/device/dispatch/reduce.h \ - thrust/detail/device/dispatch/set_operations.h \ - thrust/detail/device/dispatch/uninitialized_copy.h \ - thrust/detail/device/dispatch/copy.h \ - thrust/detail/device/omp/for_each.h \ - thrust/detail/device/omp/copy_host_or_any_to_device.h \ - thrust/detail/device/omp/sort.h \ - thrust/detail/device/omp/dispatch/sort.h \ - thrust/detail/device/omp/dispatch/copy.h \ - thrust/detail/device/omp/scan.h \ - thrust/detail/device/omp/reduce.h \ - thrust/detail/device/omp/copy_device_to_device.h \ - thrust/detail/device/omp/copy_device_to_host_or_any.h \ - thrust/detail/device/omp/copy.h \ - thrust/detail/device/omp/detail/stable_merge_sort.h \ - thrust/detail/device/internal_allocator.h \ - thrust/detail/device/remove.h \ - thrust/detail/device/scan.h \ - thrust/detail/device/fill.h \ - thrust/detail/device/reduce.h \ - thrust/detail/device/set_operations.h \ - thrust/detail/device/uninitialized_copy.h \ - thrust/detail/device/copy.h \ - thrust/detail/device/cuda/block/merging_sort.h \ - thrust/detail/device/cuda/block/inclusive_scan.h \ - thrust/detail/device/cuda/block/reduce.h \ - thrust/detail/device/cuda/block/odd_even_sort.h \ - thrust/detail/device/cuda/block/copy.h \ - thrust/detail/device/cuda/for_each.h \ - thrust/detail/device/cuda/malloc.h \ - thrust/detail/device/cuda/launch_closure.h \ - thrust/detail/device/cuda/partition.h \ - thrust/detail/device/cuda/trivial_copy.h \ - thrust/detail/device/cuda/sort.h \ - thrust/detail/device/cuda/synchronize.h \ - thrust/detail/device/cuda/copy_cross_space.h \ - thrust/detail/device/cuda/arch.h \ - thrust/detail/device/cuda/copy_if.h \ - thrust/detail/device/cuda/no_throw_free.h \ - thrust/detail/device/cuda/dispatch/scan.h \ - thrust/detail/device/cuda/dispatch/reduce.h \ - thrust/detail/device/cuda/dispatch/copy.h \ - thrust/detail/device/cuda/free.h \ - thrust/detail/device/cuda/scan.h \ - thrust/detail/device/cuda/segmented_scan.h \ - thrust/detail/device/cuda/fill.h \ - thrust/detail/device/cuda/scalar/binary_search.h \ - thrust/detail/device/cuda/scalar/rotate.h \ - thrust/detail/device/cuda/reduce.h \ - thrust/detail/device/cuda/copy_device_to_device.h \ - thrust/detail/device/cuda/warp/any.h \ - thrust/detail/device/cuda/warp/scan.h \ - thrust/detail/device/cuda/set_operations.h \ - thrust/detail/device/cuda/copy.h \ - thrust/detail/device/cuda/extern_shared_ptr.h \ - thrust/detail/device/cuda/detail/stable_radix_sort_util.h \ - thrust/detail/device/cuda/detail/trivial_copy.h \ - thrust/detail/device/cuda/detail/stable_radix_sort_bits.h \ - thrust/detail/device/cuda/detail/stable_radix_sort.h \ - thrust/detail/device/cuda/detail/stable_merge_sort.h \ - thrust/detail/device/cuda/detail/safe_scan.h \ - thrust/detail/device/cuda/detail/b40c/vector_types.h \ - thrust/detail/device/cuda/detail/b40c/radixsort_scanscatter_kernel.h \ - thrust/detail/device/cuda/detail/b40c/kernel_utils.h \ - thrust/detail/device/cuda/detail/b40c/radixsort_api.h \ - thrust/detail/device/cuda/detail/b40c/radixsort_kernel_common.h \ - thrust/detail/device/cuda/detail/b40c/radixsort_reduction_kernel.h \ - thrust/detail/device/cuda/detail/b40c/radixsort_key_conversion.h \ - thrust/detail/device/cuda/detail/b40c/radixsort_spine_kernel.h \ - thrust/detail/device/cuda/detail/fast_scan.h \ - thrust/detail/device/extrema.h \ - thrust/detail/type_traits/has_trivial_assign.h \ - thrust/detail/raw_buffer.h \ - thrust/detail/casts.h \ - thrust/detail/cstdint.h \ - thrust/detail/config.h \ - thrust/detail/vector_base.h \ - thrust/device_ptr.h \ - thrust/device_reference.h \ - thrust/device_free.h \ - thrust/iterator/detail/permutation_iterator.inl \ - thrust/iterator/detail/zip_iterator.inl \ - thrust/iterator/detail/counting_iterator.inl \ - thrust/iterator/detail/transform_iterator.inl \ - thrust/iterator/detail/iterator_adaptor.inl \ - thrust/iterator/detail/iterator_traits.inl \ - thrust/iterator/detail/constant_iterator.inl \ - thrust/iterator/detail/reverse_iterator.inl \ - thrust/iterator/detail/iterator_facade.inl \ - thrust/random/detail/linear_feedback_shift_engine.inl \ - thrust/random/detail/xor_combine_engine.inl \ - thrust/random/detail/discard_block_engine.inl \ - thrust/random/detail/uniform_int_distribution.inl \ - thrust/random/detail/linear_congruential_engine.inl \ - thrust/random/detail/uniform_real_distribution.inl \ - thrust/random/detail/normal_distribution.inl \ - thrust/random/detail/subtract_with_carry_engine.inl \ - thrust/experimental/cuda/detail/ogl_interop_allocator.inl \ - thrust/system/detail/error_code.inl \ - thrust/system/detail/system_error.inl \ - thrust/system/detail/error_category.inl \ - thrust/system/detail/error_condition.inl \ - thrust/system/detail/cuda_error.inl \ - thrust/detail/scan.inl \ - thrust/detail/host_vector.inl \ - thrust/detail/binary_search.inl \ - thrust/detail/device_reference.inl \ - thrust/detail/device_delete.inl \ - thrust/detail/device_free.inl \ - thrust/detail/inner_product.inl \ - thrust/detail/device_malloc.inl \ - thrust/detail/transform.inl \ - thrust/detail/device_ptr.inl \ - thrust/detail/mismatch.inl \ - thrust/detail/tuple.inl \ - thrust/detail/device_new.inl \ - thrust/detail/transform_scan.inl \ - thrust/detail/device_vector.inl \ - thrust/detail/swap.inl \ - thrust/detail/partition.inl \ - thrust/detail/advance.inl \ - thrust/detail/set_operations.inl \ - thrust/detail/count.inl \ - thrust/detail/host/for_each.inl \ - thrust/detail/host/detail/merge.inl \ - thrust/detail/host/detail/stable_merge_sort.inl \ - thrust/detail/host/sort.inl \ - thrust/detail/logical.inl \ - thrust/detail/uninitialized_copy.inl \ - thrust/detail/vector_base.inl \ - thrust/detail/reverse.inl \ - thrust/detail/generate.inl \ - thrust/detail/for_each.inl \ - thrust/detail/scatter.inl \ - thrust/detail/find.inl \ - thrust/detail/device/scan.inl \ - thrust/detail/device/generic/binary_search.inl \ - thrust/detail/device/generic/reduce_by_key.inl \ - thrust/detail/device/generic/partition.inl \ - thrust/detail/device/generic/scan_by_key.inl \ - thrust/detail/device/generic/copy_if.inl \ - thrust/detail/device/generic/find.inl \ - thrust/detail/device/generic/unique.inl \ - thrust/detail/device/generic/extrema.inl \ - thrust/detail/device/generic/adjacent_difference.inl \ - thrust/detail/device/generic/reduce.inl \ - thrust/detail/device/generic/remove.inl \ - thrust/detail/device/omp/copy_device_to_device.inl \ - thrust/detail/device/omp/scan.inl \ - thrust/detail/device/omp/copy_host_or_any_to_device.inl \ - thrust/detail/device/omp/for_each.inl \ - thrust/detail/device/omp/copy_device_to_host_or_any.inl \ - thrust/detail/device/omp/reduce.inl \ - thrust/detail/device/omp/detail/stable_merge_sort.inl \ - thrust/detail/device/omp/sort.inl \ - thrust/detail/device/for_each.inl \ - thrust/detail/device/reduce.inl \ - thrust/detail/device/fill.inl \ - thrust/detail/device/cuda/scan.inl \ - thrust/detail/device/cuda/synchronize.inl \ - thrust/detail/device/cuda/segmented_scan.inl \ - thrust/detail/device/cuda/no_throw_free.inl \ - thrust/detail/device/cuda/dispatch/reduce.inl \ - thrust/detail/device/cuda/set_operations.inl \ - thrust/detail/device/cuda/trivial_copy.inl \ - thrust/detail/device/cuda/copy_if.inl \ - thrust/detail/device/cuda/for_each.inl \ - thrust/detail/device/cuda/launch_closure.inl \ - thrust/detail/device/cuda/arch.inl \ - thrust/detail/device/cuda/reduce.inl \ - thrust/detail/device/cuda/free.inl \ - thrust/detail/device/cuda/fill.inl \ - thrust/detail/device/cuda/malloc.inl \ - thrust/detail/device/cuda/detail/stable_radix_sort_key_value.inl \ - thrust/detail/device/cuda/detail/stable_merge_sort.inl \ - thrust/detail/device/cuda/detail/safe_scan.inl \ - thrust/detail/device/cuda/detail/stable_radix_sort.inl \ - thrust/detail/device/cuda/detail/stable_radix_sort_merrill.inl \ - thrust/detail/device/cuda/detail/fast_scan.inl \ - thrust/detail/device/cuda/detail/stable_radix_sort_key.inl \ - thrust/detail/device/cuda/sort.inl \ - thrust/detail/device/sort.inl \ - thrust/detail/pair.inl \ - thrust/detail/gather.inl \ - thrust/detail/contiguous_storage.inl \ - thrust/detail/uninitialized_fill.inl \ - thrust/detail/unique.inl \ - thrust/detail/transform_reduce.inl \ - thrust/detail/sequence.inl \ - thrust/detail/extrema.inl \ - thrust/detail/replace.inl \ - thrust/detail/functional.inl \ - thrust/detail/copy.inl \ - thrust/detail/adjacent_difference.inl \ - thrust/detail/swap_ranges.inl \ - thrust/detail/reduce.inl \ - thrust/detail/remove.inl \ - thrust/detail/fill.inl \ - thrust/detail/distance.inl \ - thrust/detail/equal.inl \ - thrust/detail/sort.inl \ - thrust/detail/raw_buffer.inl \ - gmm/gmm_domain_decomp.h \ - gmm/gmm_least_squares_cg.h \ - gmm/gmm_dense_lu.h \ - gmm/gmm_dense_Householder.h \ - gmm/gmm_iter.h \ - gmm/gmm_kernel.h \ - gmm/gmm_solver_constrained_cg.h \ - gmm/gmm_lapack_interface.h \ - gmm/gmm_blas.h \ - gmm/gmm_algobase.h \ - gmm/gmm_solver_qmr.h \ - gmm/gmm_std.h \ - gmm/gmm_matrix.h \ - gmm/gmm_interface.h \ - gmm/gmm_interface_bgeot.h \ - gmm/gmm_solver_Schwarz_additive.h \ - gmm/gmm_dense_qr.h \ - gmm/gmm_sub_index.h \ - gmm/gmm_solver_bfgs.h \ - gmm/gmm_dense_sylvester.h \ - gmm/gmm_precond_diagonal.h \ - gmm/gmm_solver_gmres.h \ - gmm/gmm_except.h \ - gmm/gmm_precond_ildltt.h \ - gmm/gmm_precond_ilut.h \ - gmm/gmm_opt.h \ - gmm/gmm_solver_idgmres.h \ - gmm/gmm_iter_solvers.h \ - gmm/gmm.h \ - gmm/gmm_ref.h \ - gmm/gmm_def.h \ - gmm/gmm_conjugated.h \ - gmm/gmm_sub_vector.h \ - gmm/gmm_sub_matrix.h \ - gmm/gmm_vector_to_matrix.h \ - gmm/gmm_real_part.h \ - gmm/gmm_precond_ildlt.h \ - gmm/gmm_precond_ilutp.h \ - gmm/gmm_scaled.h \ - gmm/gmm_solver_cg.h \ - gmm/gmm_transposed.h \ - gmm/gmm_MUMPS_interface.h \ - gmm/gmm_vector.h \ - gmm/gmm_tri_solve.h \ - gmm/gmm_inoutput.h \ - gmm/gmm_precond_mr_approx_inverse.h \ - gmm/gmm_solver_bicgstab.h \ - gmm/gmm_condition_number.h \ - gmm/gmm_blas_interface.h \ - gmm/gmm_solver_Newton.h \ - gmm/gmm_superlu_interface.h \ - gmm/gmm_modified_gram_schmidt.h \ - gmm/gmm_precond.h \ - gmm/gmm_precond_ilu.h - -if BUILDCUDA -if HAVE_XXD - -# creates a file containing the output of nvcc --version, -# for use in printing info on the nvidia compiler for diagnostics. -BUILT_SOURCES=nvcc_version.h - -nvcc_version.h: - $(NVCC) --version > nvcc_version - echo "/* output of nvcc --version */" > nvcc_version.h - echo "/* example usage:" >> nvcc_version.h - echo "#include " >> nvcc_version.h - echo "#include \"nvcc_version.h\"" >> nvcc_version.h - echo "char buf[nvcc_version_len+1];" >> nvcc_version.h - echo "bcopy(nvcc_version,buf,nvcc_version_len);" >> nvcc_version.h - echo "buf[nvcc_version_len]=0;" >> nvcc_version.h - echo "printf(buf);" >> nvcc_version.h - echo "" >> nvcc_version.h - echo "nvcc_version.h was created by running:" >> nvcc_version.h - echo "nvcc --version > nvcc_version" >> nvcc_version.h - echo "xxd -i nvcc_version >> nvcc_version.h" >> nvcc_version.h - echo "*/" >> nvcc_version.h - xxd -i nvcc_version >> nvcc_version.h - -clean-local: - rm -f $(BUILT_SOURCES) nvcc_version - -EXTRA_DIST += nvcc_version.h -endif -endif - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/include/NrrdIO/Makefile.am b/include/NrrdIO/Makefile.am deleted file mode 100644 index de961d94f52..00000000000 --- a/include/NrrdIO/Makefile.am +++ /dev/null @@ -1,15 +0,0 @@ -EXTRA_DIST=\ - NrrdIO.h \ - privateAir.h \ - privateNrrd.h \ - teem32bit.h \ - teemDio.h \ - teemEndian.h \ - teemPng.h \ - teemQnanhibit.h - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/include/dicom/Makefile.am b/include/dicom/Makefile.am deleted file mode 100644 index b9998a9d3f9..00000000000 --- a/include/dicom/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -EXTRA_DIST=\ - condition.h \ - ctn_os.h \ - ctnthread.h \ - dcmprivate.h \ - dicom.h \ - dicom_objects.h \ - dicom_platform.h \ - dicom_uids.h \ - lst.h \ - lstprivate.h - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/include/fs_vnl/Makefile.am b/include/fs_vnl/Makefile.am deleted file mode 100644 index e88aa1fa39b..00000000000 --- a/include/fs_vnl/Makefile.am +++ /dev/null @@ -1,12 +0,0 @@ -EXTRA_DIST=\ - fs_cost_function.h \ - fs_lbfgs.h \ - fs_lbfgs_observer.h \ - fs_lbfgs_subject.h \ - fs_powell.h - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/include/pixrect/Makefile.am b/include/pixrect/Makefile.am deleted file mode 100644 index 9e007b041ae..00000000000 --- a/include/pixrect/Makefile.am +++ /dev/null @@ -1,38 +0,0 @@ -EXTRA_DIST=\ - bw2var.h \ - cg12_var.h \ - cg2reg.h \ - cg2var.h \ - cg3var.h \ - cg4var.h \ - cg8var.h \ - cg9var.h \ - gp1cmds.h \ - gp1reg.h \ - gp1var.h \ - gt_fbi.h \ - gt_rp.h \ - gtvar.h \ - mem32_var.h \ - memreg.h \ - mem_rop_impl_ops.h \ - mem_rop_impl_util.h \ - memvar.h \ - pixfont.h \ - pixrect.h \ - pixrect_hs.h \ - pr_dblbuf.h \ - pr_impl_make.h \ - pr_impl_util.h \ - pr_io.h \ - pr_line.h \ - pr_planegroups.h \ - pr_util.h \ - traprop.h \ - tv1var.h - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/include/sys/Makefile.am b/include/sys/Makefile.am deleted file mode 100644 index 27a88771759..00000000000 --- a/include/sys/Makefile.am +++ /dev/null @@ -1,7 +0,0 @@ -EXTRA_DIST=timeb.h - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/include/topology/Makefile.am b/include/topology/Makefile.am deleted file mode 100644 index c9f7feaf6e5..00000000000 --- a/include/topology/Makefile.am +++ /dev/null @@ -1,16 +0,0 @@ -EXTRA_DIST=\ - face.h \ - fastloop.h \ - globals.h \ - loop.h \ - patchdisk.h \ - segment.h \ - surface.h \ - topo_parms.h \ - vertex.h - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/include/xview/Makefile.am b/include/xview/Makefile.am deleted file mode 100644 index bcefaa88641..00000000000 --- a/include/xview/Makefile.am +++ /dev/null @@ -1,73 +0,0 @@ -EXTRA_DIST=\ - alert.h \ - attr.h \ - attrol.h \ - base.h \ - canvas.h \ - cms_grays.h \ - cms.h \ - cms_mono.h \ - cmsrainbow.h \ - cms_rgb.h \ - cursor.h \ - db.h \ - defaults.h \ - dragdrop.h \ - drawable.h \ - expandname.h \ - font.h \ - frame.h \ - fullscreen.h \ - generic.h \ - icon.h \ - icon_load.h \ - notice.h \ - notify.h \ - openmenu.h \ - openwin.h \ - panel.h \ - pixwin.h \ - pkg.h \ - pkg_public.h \ - rect.h \ - rectlist.h \ - screen.h \ - scrollbar.h \ - sel_attrs.h \ - sel_compat.h \ - selection.h \ - seln.h \ - sel_pkg.h \ - sel_svc.h \ - server.h \ - str_utils.h \ - sun.h \ - svrimage.h \ - termsw.h \ - text.h \ - textsw.h \ - tty.h \ - ttysw.h \ - window.h \ - window_hs.h \ - win_enum.h \ - win_env.h \ - win_event.h \ - win_input.h \ - win_notify.h \ - win_screen.h \ - win_struct.h \ - wmgr.h \ - xv_c_types.h \ - xv_error.h \ - xv_i18n.h \ - xview.h \ - xview_xvin.h \ - xv_version.h \ - xv_xrect.h - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/itkio/Makefile.am b/itkio/Makefile.am deleted file mode 100644 index 8d28ede2d9e..00000000000 --- a/itkio/Makefile.am +++ /dev/null @@ -1,41 +0,0 @@ -# -# Makefile.am for libitkio.a -# - -#itk is required for building poistats -# add ITK -if HAVE_ITK_LIBS - -ITK_THINGS=$(ITK_CFLAGS) -DHAVE_ITK_LIBS - -AM_CPPFLAGS = -Wno-deprecated \ - $(X_CFLAGS) \ - $(VXL_CFLAGS) \ - -I$(top_srcdir)/include \ - $(ITK_THINGS) \ - -DHAVE_ZLIB - -AM_LDFLAGS= - -noinst_LIBRARIES= libitkio.a - -libitkio_a_SOURCES= \ - itkMGHImageIO.cxx \ - itkMGHImageIOFactory.cxx - -am_libitkio_a_OBJECTS=$(libitkio_a_SOURCES:%.cxx=%.o) - -endif -#end itk - -EXTRA_DIST=\ - itkMGHImageIO.cxx \ - itkMGHImageIO.h \ - itkMGHImageIOFactory.cxx \ - itkMGHImageIOFactory.h - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/itkutils/Makefile.am b/itkutils/Makefile.am deleted file mode 100644 index d6a976f60a8..00000000000 --- a/itkutils/Makefile.am +++ /dev/null @@ -1,50 +0,0 @@ -# -# Makefile.am for libitkutils.a -# - -#itk is required for building poistats -# add ITK -if HAVE_ITK_LIBS - -ITK_THINGS=$(ITK_CFLAGS) -DHAVE_ITK_LIBS - -AM_CPPFLAGS = -Wno-deprecated \ - $(X_CFLAGS) \ - $(VXL_CFLAGS) \ - -I$(top_srcdir)/include \ - $(ITK_THINGS) \ - -DHAVE_ZLIB - -AM_LDFLAGS= - -noinst_LIBRARIES= libitkutils.a - -BSPLINES_SRCS = \ - bspline/itkBSplineKernelFunction.txx \ - bspline/itkBSplineKernelFunction.h \ - bspline/itkBSplineDataPointSetToImageFilter.txx \ - bspline/itkBSplineDataPointSetToImageFilter.h \ - bspline/itkPointSetToImageFilter.txx \ - bspline/itkPointSetToImageFilter.h - -UI_SRCS = \ - ui/CommandParser.cxx \ - ui/CommandParser.h \ - ui/FreeSurferExecutable.cxx \ - ui/FreeSurferExecutable.h - -libitkutils_a_SOURCES= \ - $(BSPLINES_SRCS) \ - $(UI_SRCS) \ - itkOrientedVectorImage.h itkOrientedVectorImage.txx - -endif -#end itk - -EXTRA_DIST=$(libitkutils_a_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES=ui/CVS -include $(top_srcdir)/Makefile.extra diff --git a/label2flat/Makefile.am b/label2flat/Makefile.am deleted file mode 100644 index 88682c7fc8d..00000000000 --- a/label2flat/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = label2flat -label2flat_SOURCES=label2flat.c -label2flat_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -label2flat_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/label2patch/Makefile.am b/label2patch/Makefile.am deleted file mode 100644 index 227f49182e1..00000000000 --- a/label2patch/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = label2patch -label2patch_SOURCES=label2patch.c -label2patch_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -label2patch_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/label_area/Makefile.am b/label_area/Makefile.am deleted file mode 100644 index 0d510fb3095..00000000000 --- a/label_area/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -# -# Makefile.am -# - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = label_area -label_area_SOURCES=label_area.c -label_area_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -label_area_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/label_border/Makefile.am b/label_border/Makefile.am deleted file mode 100644 index af9705919b5..00000000000 --- a/label_border/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -# -# Makefile.am -# - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = label_border -label_border_SOURCES=label_border.c -label_border_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -label_border_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/lineprof/Makefile.am b/lineprof/Makefile.am deleted file mode 100644 index ad479de5c5d..00000000000 --- a/lineprof/Makefile.am +++ /dev/null @@ -1,116 +0,0 @@ -# -# Makefile.am for liblineprof.a -# - -# For now skip the lineprof build when --disable-all-apps is set (hence, -# ENABLE_QT_APPS = false) because lineprof is only used by freeview. -if ENABLE_QT_APPS - -if USE_LOCAL_TIFF -TIFFCFLAGS=-I$(top_srcdir)/tiff -LIBTIFF=$(top_builddir)/tiff/libtiff.a -else -TIFFCFLAGS=$(TIFF_CFLAGS) -LIBTIFF=$(LIB_TIFF) -endif - -if HAVE_ITK45 -ITK_45_THINGS=-DHAVE_ITK45 -endif - -AM_CPPFLAGS= -Wno-deprecated \ - -I$(top_srcdir)/include \ - -I$(top_srcdir)/tetgen \ - $(VXL_CFLAGS) $(ITK_45_THINGS) \ - $(VTK_CXXFLAGS) \ - $(ITK_CFLAGS) -DHAVE_ITK_LIBS \ - $(PETSC_CFLAGS) $(TIFFCFLAGS) \ - $(BOOST_CFLAGS) - -if HAVE_MAC_OSX -AM_LDFLAGS=$(OS_LDFLAGS) -framework Accelerate -framework Cocoa -else -AM_LDFLAGS=$(OS_LDFLAGS) -z muldefs -endif - -AM_CXXFLAGS=$(AM_CPPFLAGS) $(VTK_COCOA_CXXFLAGS) - -noinst_LIBRARIES= liblineprof.a - -liblineprof_a_SOURCES= \ - Tracer.cpp \ - Preprocessor.cpp \ - PetscSolver.cpp \ - LineProf.cpp - -#foo_SOURCES= -#foo: -# if ! test -f "$(top_builddir)/vtkutils/vtkKWRGBATransferFunctionEditorTester-scalars.mgh"; then \ -# cp -v $(top_srcdir)/vtkutils/vtkKWRGBATransferFunctionEditorTester-scalars.mgh \ -# $(top_builddir)/vtkutils/; fi; -# if ! test -f "$(top_builddir)/vtkutils/IconLoaderTestIcons.txt"; then \ -# cp -v $(top_srcdir)/vtkutils/IconLoaderTestIcons.txt \ -# $(top_builddir)/vtkutils/; fi; -##check_PROGRAMS=foo LineProfTest - -check_PROGRAMS=LineProfTest -#NOTE: the testLineProf script calls the vtk setup script, which is -# necessary under normal circumstances, but since configure sets the -# TEST_ENVIRONMENT var already, it is not needed for make check -# (and in fact will not work for make distcheck), so LineProfTest -# can be called directly -TESTS=testLineProf -#TESTS=LineProfTest - -LineProfTest_SOURCES=LineProfTest.cpp - - -if HAVE_MAC_OSX -LineProfTest_LDADD=\ - $(top_builddir)/lineprof/liblineprof.a \ - $(VTK_COCOA_LIBS) $(VTK_VERDICT_LIB) $(VTK_SQLITE_LIB) \ - -lvtkIO -lvtkWidgets -lvtkGraphics \ - -lvtkImaging -lvtkFiltering \ - -lvtkCommon -lvtksys \ - -lvtkHybrid -lvtkexoIIc -lvtkNetCDF -lvtkDICOMParser \ - -lvtkVolumeRendering -lvtkRendering -lvtkftgl \ - -lexpat $(VTK_EXPAT_LIB) $(VTK_FREETYPE_LIB) \ - $(LIBTIFF) \ - $(VTK_PNG_LIB) $(VTK_Z_LIB) $(VTK_METAIO_LIB) \ - $(ITK_LIBS) \ - $(PETSC_LIBS) -lpetscts -lpetscsnes -lpetscksp \ - -lpetscdm -lpetscmat -lpetscvec -lpetsc -lmpich -lpmpich -else -LineProfTest_LDADD=\ - $(top_builddir)/lineprof/liblineprof.a \ - $(VTK_LIBS) $(VTK_VERDICT_LIB) $(VTK_SQLITE_LIB) \ - -lvtkIO -lvtkWidgets -lvtkGraphics \ - -lvtkImaging -lvtkFiltering \ - -lvtkCommon -lvtksys \ - -lvtkHybrid -lvtkexoIIc -lvtkNetCDF -lvtkDICOMParser \ - -lvtkVolumeRendering -lvtkRendering -lvtkftgl \ - -lexpat $(VTK_EXPAT_LIB) $(VTK_FREETYPE_LIB) \ - $(LIBTIFF) \ - $(VTK_PNG_LIB) $(VTK_Z_LIB) $(VTK_METAIO_LIB) \ - $(ITK_LIBS) \ - $(PETSC_LIBS) -lpetscts -lpetscsnes -lpetscksp \ - -lpetscdm -lpetscmat -lpetscvec -lpetsc -lmpich -lfmpich \ - $(LIB_GFORTRAN) $(LIB_LAPACK) $(LIB_BLAS) $(LIB_G2C_A) $(LIB_GFORTRAN) -endif - -endif -# endif ENABLE_QT_APPS - -EXTRA_DIST= \ -PetscSolver.h \ -Preprocessor.h \ -Tracer.h \ -LineProf.h \ -LineProfTest.cpp \ -testLineProf - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/log/Makefile.am b/log/Makefile.am deleted file mode 100644 index ca72f9d29fc..00000000000 --- a/log/Makefile.am +++ /dev/null @@ -1,16 +0,0 @@ -# -# Makefile.am -# - -AM_CPPFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -noinst_LIBRARIES= liblog.a -liblog_a_SOURCES = congraph.c h_logz.c map.c \ - connect.c lmedian.c runfuncs.c - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/lta_convert/Makefile.am b/lta_convert/Makefile.am deleted file mode 100644 index 66eb035e922..00000000000 --- a/lta_convert/Makefile.am +++ /dev/null @@ -1,27 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -BUILT_SOURCES=lta_convert.help.xml.h lta_convert.help.xml.html - -foodir=$(prefix)/docs/xml -foo_DATA=lta_convert.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=lta_convert.help.xml.html - -bin_PROGRAMS = lta_convert -lta_convert_SOURCES=lta_convert.cpp -lta_convert_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -lta_convert_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -clean-local: - rm -f $(BUILT_SOURCES) diff --git a/m4/autotroll.m4 b/m4/autotroll.m4 deleted file mode 100644 index 5e9873c30ae..00000000000 --- a/m4/autotroll.m4 +++ /dev/null @@ -1,601 +0,0 @@ -# Build Qt apps with the autotools (Autoconf/Automake). -# M4 macros. -# This file is part of AutoTroll. -# Copyright (C) 2006 Benoit Sigoure -# -# AutoTroll is free software; you can redistribute it and/or -# modify it under the terms of the GNU General Public License -# as published by the Free Software Foundation; either version 2 -# of the License, or (at your option) any later version. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU General Public License for more details. -# -# You should have received a copy of the GNU General Public License -# along with this program; if not, write to the Free Software -# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, -# USA. -# -# In addition, as a special exception, the copyright holders of AutoTroll -# give you unlimited permission to copy, distribute and modify the configure -# scripts that are the output of Autoconf when processing the macros of -# AutoTroll. You need not follow the terms of the GNU General Public License -# when using or distributing such scripts, even though portions of the text of -# AutoTroll appear in them. The GNU General Public License (GPL) does govern -# all other use of the material that constitutes AutoTroll. -# -# This special exception to the GPL applies to versions of AutoTroll -# released by the copyright holders of AutoTroll. Note that people who make -# modified versions of AutoTroll are not obligated to grant this special -# exception for their modified versions; it is their choice whether to do so. -# The GNU General Public License gives permission to release a modified version -# without this exception; this exception also makes it possible to release a -# modified version which carries forward this exception. - - # ------------- # - # DOCUMENTATION # - # ------------- # - -# Disclaimer: Never tested with anything else than Qt 4.2! Feedback welcome. -# Simply invoke AT_WITH_QT in your configure.ac. AT_WITH_QT can take -# arguments which are documented in depth below. The default arguments are -# equivalent to the default .pro file generated by qmake. -# -# Invoking AT_WITH_QT will do the following: -# - Add a --with-qt option to your configure -# - Find qmake, moc and uic and save them in the make variables $(QMAKE), -# $(MOC), $(UIC). -# - Save the path to Qt in $(QT_PATH) -# - Find the flags to use Qt, that is: -# * $(QT_DEFINES): -D's defined by qmake. -# * $(QT_CFLAGS): CFLAGS as defined by qmake (C?!) -# * $(QT_CXXFLAGS): CXXFLAGS as defined by qmake. -# * $(QT_INCPATH): -I's defined by qmake. -# * $(QT_CPPFLAGS): Same as $(QT_DEFINES) + $(QT_INCPATH) -# * $(QT_LFLAGS): LFLAGS defined by qmake. -# * $(QT_LDFLAGS): Same thing as $(QT_LFLAGS). -# * $(QT_LIBS): LIBS defined by qmake. -# -# You *MUST* invoke $(MOC) and/or $(UIC) where necessary. AutoTroll provides -# you with Makerules to ease this, here is a sample Makefile.am to use with -# AutoTroll which builds the code given in the chapter 7 of the Qt Tutorial: -# http://doc.trolltech.com/4.2/tutorial-t7.html -# -# ------------------------------------------------------------------------- -# include $(top_srcdir)/build-aux/autotroll.mk -# -# ACLOCAL_AMFLAGS = -I build-aux -# -# bin_PROGRAMS = lcdrange -# lcdrange_SOURCES = $(BUILT_SOURCES) lcdrange.cpp lcdrange.h main.cpp -# lcdrange_CXXFLAGS = $(QT_CXXFLAGS) $(AM_CXXFLAGS) -# lcdrange_CPPFLAGS = $(QT_CPPFLAGS) $(AM_CPPFLAGS) -# lcdrange_LDFLAGS = $(QT_LDFLAGS) $(LDFLAGS) -# lcdrange_LDADD = $(QT_LIBS) $(LDADD) -# -# BUILT_SOURCES = lcdrange.moc.cpp -# ------------------------------------------------------------------------- -# -# Note that your MOC, UIC and QRC files *MUST* be listed manually in -# BUILT_SOURCES. 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The "bug" has been fixed on 22 October 2006 - # by Peter O'Gorman but we provide backward compatibility here. - at_cv_env_QT_LIBS=`echo "$at_cv_env_QT_LIBS" \ - | sed 's/^-F/-Wl,-F/;s/ -F/ -Wl,-F/g'` - fi - ]) - AC_SUBST([QT_LIBS], [$at_cv_env_QT_LIBS]) - - cd .. && rm -rf conftest.dir - - # Run the user code - $5 - - done # end hack (useless for to be able to use break) -]) - -# AT_REQUIRE_QT_VERSION(QT_version, RUN-IF-FAILED, RUN-IF-OK) -# ----------------------------------------------------------- -# Check (using qmake) that Qt's version "matches" QT_version. -# Must be run AFTER AT_WITH_QT. Requires autoconf 2.60. -# -# RUN-IF-FAILED is arbitrary code to execute if Qt cannot be found or if any -# problem happens. If this argument is omitted, then AC_MSG_ERROR will be -# called. RUN-IF-OK is arbitrary code to execute if Qt was successfully found. -AC_DEFUN([AT_REQUIRE_QT_VERSION], -[ AC_PREREQ([2.60]) - # this is a hack to get decent flow control with 'break' - for _qt_ignored in once; do - - if test x"$QMAKE" = x; then - AC_MSG_WARN([\$QMAKE is empty.\ - Did you invoke AT@&t@_WITH_QT before AT@&t@_REQUIRE_QT_VERSION?. Disabling Qt apps]) - qt_enabled="no" - break - fi - AC_CACHE_CHECK([for Qt's version], [at_cv_QT_VERSION], - [echo "$as_me:$LINENO: Running $QMAKE --version:" >&AS_MESSAGE_LOG_FD - $QMAKE --version >&AS_MESSAGE_LOG_FD 2>&1 - qmake_version_sed=['/^.*\([0-9]\.[0-9]\.[0-9]\).*$/!d;s//\1/'] - at_cv_QT_VERSION=`$QMAKE --version 2>&1 | sed "$qmake_version_sed"`]) - if test x"$at_cv_QT_VERSION" = x; then - AC_MSG_WARN([Cannot detect Qt's version. Disabling Qt apps]) - qt_enabled="no" - break - fi - AC_SUBST([QT_VERSION], [$at_cv_QT_VERSION]) - AS_VERSION_COMPARE([$QT_VERSION], [$1], - [AC_MSG_WARN([This package requires Qt $1 or above.])]) - - # Run the user code - $3 - - done # end hack (useless for to be able to use break) -]) - -# _AT_TWEAK_PRO_FILE(QT_VAR, VALUE) -# --------------------------- -# @internal. Tweak the variable QT_VAR in the .pro. -# VALUE is an IFS-separated list of value and each value is rewritten -# as follows: -# +value => QT_VAR += value -# -value => QT_VAR -= value -# value => QT_VAR += value -AC_DEFUN([_AT_TWEAK_PRO_FILE], -[ # Tweak the value of $1 in the .pro file for $2. - - qt_conf='' - for at_mod in $2; do - at_mod=`echo "$at_mod" | sed 's/^-//; tough - s/^+//; beef - :ough - s/^/$1 -= /;n - :eef - s/^/$1 += /'` - qt_conf="$qt_conf -$at_mod" - done - echo "$qt_conf" | sed 1d >>"$pro_file" -]) diff --git a/matlab/Makefile.am b/matlab/Makefile.am deleted file mode 100644 index cf83aed5188..00000000000 --- a/matlab/Makefile.am +++ /dev/null @@ -1,330 +0,0 @@ -# -# Makefile.am for matlab files -# - - -foodir=$(prefix)/matlab/lme/geodesic -mfilesdir=$(prefix)/matlab -siemensdir=$(prefix)/matlab -lmefilesdir=$(prefix)/matlab/lme -lmegeofilesdir=$(prefix)/matlab/lme/geodesic -lmemassunifilesdir=$(prefix)/matlab/lme/mass_univariate -lmeunifilesdir=$(prefix)/matlab/lme/univariate -lmeQdecfilesdir=$(prefix)/matlab/lme/Qdec -samsegfilesdir=$(prefix)/matlab/samseg -survivalfilesdir=$(prefix)/matlab/Survival -survivalexdatafilesdir=$(prefix)/matlab/Survival/ex_data -survivalmassunifilesdir=$(prefix)/matlab/Survival/mass_univariate -survivalunifilesdir=$(prefix)/matlab/Survival/univariate - -mfiles_DATA=\ - angles2rotmat.m \ - barsegstats.m \ - bmmcost.m \ - bmm_mcvect.m \ - bmm_mcvhist.m \ - bmmroc.m \ - cc_cut_afd.m \ - cc_cut_dir_afd.m \ - cc_cut_table.m \ - combine_labels.m \ - compute_opt_volume.m \ - convert_fieldsign.m \ - convert_unwarp_resample.m \ - cortical_labeling_afd_txt.m \ - cortical_labeling_dir_afd_txt.m \ - cortical_labeling_table.m \ - dice_labels.m \ - dilate3d.m \ - dtifa.m \ - dtimatrix.m \ - erode3d.m \ - fisher_twoclass.m \ - fix_exvivo_dwi_drift.m \ - fread3.m \ - fwrite3.m \ - fs_ranksum.m \ - fs_signrank.m \ - fsgettmppath.m \ - irepierr.m \ - irepifit.m \ - irepifitvol.m \ - irepistructure.m \ - irepisynth.m \ - irepitiming.m \ - isdicomfile.m \ - juelichmat2mat.m \ - labelic.m \ - llbmm.m \ - load_analyze_hdr.m \ - load_analyze.m \ - load_cor.m \ - load_csd.m \ - load_dicom_fl.m \ - load_dicom_series.m \ - load_gca.m \ - load_ima.m \ - load_mgh2.m \ - load_mgh.m \ - load_nifti_hdr.m \ - load_nifti.m \ - load_segstats.m \ - lta_read.m \ - lta_write.m \ - mksubfov.m \ - mri_cdf2p.m \ - mri_glmfit_pcc.m \ - MRIeuler2Mdc.m \ - MRIextractImage.m \ - MRIfspec.m \ - MRIisBHDR.m \ - MRIisMGH.m \ - mri_kurtosis.m \ - MRImdc2euler.m \ - MRIread.m \ - MRIseg2labelxyz.m \ - MRIsegReg.m \ - mri_surfrft_jlbr.m \ - MRIvol2vol.m \ - MRIvote.m \ - MRIwrite.m \ - mri_zcdf.m \ - mris_display.m \ - peakfinder.m \ - pons_cut_afd.m \ - pons_cut_dir_afd.m \ - pons_cut_table.m \ - randb.m \ - read_all.m \ - read_annotation.m \ - read_ascii_curv.m \ - read_asc.m \ - read_cor.m \ - read_csf_patch.m \ - read_curv.m \ - read_eccen_patch.m \ - read_freq_patch.m \ - read_fscolorlut.m \ - read_genesis_image.m \ - read_label.m \ - read_label_old.m \ - read_moviebyu.m \ - read_patch.m \ - readrec.m \ - ReadSiemensPhysio.m\ - read_siemens_header.m \ - read_siemens_image.m \ - read_smooth_eccen.m \ - read_surf.m \ - read_type.m \ - read_vf.m \ - read_wfile.m \ - remove_spaces.m \ - ribbon_afd.m \ - ribbon_dir_afd.m \ - ribbon_table.m \ - rotmat.m \ - rotmat2angles.m \ - sampleSize.m \ - save_cor.m \ - save_mgh2.m \ - save_mgh.m \ - save_nifti.m \ - ssblochgrad.m \ - ssbloch.m \ - stringunique.m \ - strlen.m \ - subcortical_labeling_afd.m \ - subcortical_labeling_dir_afd.m \ - subcortical_labeling_table.m \ - surf_registration_afd.m \ - surf_registration_stats.m \ - surf_registration_table.m \ - talairaching_afd.m \ - talairaching_dir_afd.m \ - talairaching_stats.m \ - talairaching_table.m \ - unwarp_init_globals.m \ - unwarp_resample.m \ - unwarp_scanners_table.m \ - vox2ras_0to1.m \ - vox2ras_1to0.m \ - vox2ras_dfmeas.m \ - vox2ras_ksolve.m \ - vox2ras_rsolveAA.m \ - vox2ras_rsolve.m \ - vox2ras_tkreg.m \ - vox2rasToQform.m \ - wm_seg_afd.m \ - wm_seg_dir_afd.m \ - wm_seg_table.m \ - write_analyze_hdr.m \ - write_annotation.m \ - write_ascii_curv.m \ - write_curv.m \ - write_label.m \ - write_surf.m \ - write_wfile.m \ - xfm_read.m - -if NMR_INSTALL -siemens_DATA=\ - read_meas_dat.m \ - read_meas_prot.m \ - read_meas_prot__struct.m -else -siemens_DATA= -endif - -lmefiles_DATA=\ - lme/usage.txt \ - lme/fs_read_label.m \ - lme/fs_read_surf.m \ - lme/fs_read_Y.m \ - lme/fs_write_fstats.m \ - lme/fs_write_Y.m \ - lme/sortData.m - -lmegeofiles_DATA=\ - lme/geodesic/geodesic_license.txt \ - lme/geodesic/geodesic_readme.txt \ - lme/geodesic/geodesic_matlab_api.h \ - lme/geodesic/create_flat_triangular_mesh.m \ - lme/geodesic/create_hedgehog_mesh.m \ - lme/geodesic/create_subdivision_pattern.m \ - lme/geodesic/example1.m \ - lme/geodesic/example2.m \ - lme/geodesic/example3.m \ - lme/geodesic/example4.m \ - lme/geodesic/example5.m \ - lme/geodesic/extract_coordinates_from_path.m \ - lme/geodesic/geodesic_convert_surface_points.m \ - lme/geodesic/geodesic_create_surface_point.m \ - lme/geodesic/geodesic_delete.m \ - lme/geodesic/geodesic_distance_and_source.m \ - lme/geodesic/geodesic_new_algorithm.m \ - lme/geodesic/geodesic_new_mesh.m \ - lme/geodesic/geodesic_propagate.m \ - lme/geodesic/geodesic_trace_back.m - -lmemassunifiles_DATA=\ - lme/mass_univariate/AdjMtx.m \ - lme/mass_univariate/lme_FSfit.m \ - lme/mass_univariate/lme_mass_FDR2.m \ - lme/mass_univariate/lme_mass_FDR.m \ - lme/mass_univariate/lme_mass_fit_EMinit.m \ - lme/mass_univariate/lme_mass_fit_init.m \ - lme/mass_univariate/lme_mass_fit.m \ - lme/mass_univariate/lme_mass_fit_Rgw.m \ - lme/mass_univariate/lme_mass_fit_vw.m \ - lme/mass_univariate/lme_mass_F.m \ - lme/mass_univariate/lme_mass_LR.m \ - lme/mass_univariate/lme_mass_RgDist.m \ - lme/mass_univariate/lme_mass_RgEI1.m \ - lme/mass_univariate/lme_mass_RgEI.m \ - lme/mass_univariate/lme_mass_RgFSfit.m \ - lme/mass_univariate/lme_mass_RgGradient1.m \ - lme/mass_univariate/lme_mass_RgGradient.m \ - lme/mass_univariate/lme_mass_RgGrow.m \ - lme/mass_univariate/lme_mass_RgMean.m \ - lme/mass_univariate/lme_RgFSfit.m \ - lme/mass_univariate/parfor_progress.m \ - lme/mass_univariate/sphCoord.m - -lmeunifiles_DATA=\ - lme/univariate/lme_EI.m \ - lme/univariate/lme_fit_EMinit.m \ - lme/univariate/lme_fit_EM.m \ - lme/univariate/lme_fit_FSinit.m \ - lme/univariate/lme_fit_FS.m \ - lme/univariate/lme_fit_init.m \ - lme/univariate/lme_fit_NR.m \ - lme/univariate/lme_F.m \ - lme/univariate/lme_Gradient.m \ - lme/univariate/lme_Hessian.m \ - lme/univariate/lme_lowessPlot.m \ - lme/univariate/lme_LR.m \ - lme/univariate/lme_plannedPower.m \ - lme/univariate/lme_plannedSampleSize.m \ - lme/univariate/lme_realizedPower.m \ - lme/univariate/lme_timePlot.m \ - lme/univariate/vec.m - -lmeQdecfiles_DATA=\ - lme/Qdec/findQdecVar.m \ - lme/Qdec/fReadQdec.m \ - lme/Qdec/fWriteQdec.m \ - lme/Qdec/getQdecVarData.m \ - lme/Qdec/getQdecVars.m \ - lme/Qdec/num2Qdec.m \ - lme/Qdec/Qdec2num.m \ - lme/Qdec/rmQdecCol.m - -samsegfiles_DATA=\ - samseg/run_samseg.m \ - samseg/samsegment.m \ - samseg/getCollage.m \ - samseg/inspectHistory.m \ - samseg/prepareExVivoImages.m \ - samseg/samseg_registerAtlas.m - -samseg_binfiles=\ - samseg/samseg - -survivalfiles_DATA=\ - Survival/SStat_lmeX_ext.m - -survivalexdatafiles_datafiles=\ - Survival/ex_data/addicts.mat \ - Survival/ex_data/addicts.dat \ - Survival/ex_data/Qdec_addicts.dat \ - Survival/ex_data/vets.dat \ - Survival/ex_data/vets.mat - -survivalmassunifiles_DATA=\ - Survival/mass_univariate/SStat_mass_FDR.m \ - Survival/mass_univariate/SStat_mass_FDR2.m \ - Survival/mass_univariate/SStat_mass_HR.m \ - Survival/mass_univariate/SStat_mass_CoxPH.m \ - Survival/mass_univariate/SStat_mass_PHTest.m \ - Survival/mass_univariate/parfor_progress.m \ - Survival/mass_univariate/SStat_mass_CoxExt.m \ - Survival/mass_univariate/SStat_mass_CoxStratPH.m - -survivalunifiles_DATA=\ - Survival/univariate/SStat_PHTest.m \ - Survival/univariate/SStat_CoxExt.m \ - Survival/univariate/SStat_KM.m \ - Survival/univariate/SStat_CoxPH.m \ - Survival/univariate/SStat_X_ext.m \ - Survival/univariate/SStat_CoxStratPH.m \ - Survival/univariate/SStat_HR.m - -foo_datafiles=lme/geodesic/geodesic_src.tar.gz - -install-data-local: - test -z $(DESTDIR)$(survivalexdatafilesdir) || $(mkdir_p) $(DESTDIR)$(survivalexdatafilesdir) - $(INSTALL_DATA) $(survivalexdatafiles_datafiles) $(DESTDIR)$(survivalexdatafilesdir) - test -z $(DESTDIR)$(foodir) || $(mkdir_p) $(DESTDIR)$(foodir) - $(INSTALL_DATA) $(foo_datafiles) $(DESTDIR)$(foodir) - test -z $(DESTDIR)$(bindir) || $(mkdir_p) $(DESTDIR)$(bindir) - $(INSTALL_PROGRAM) $(samseg_binfiles) $(DESTDIR)$(bindir) - - -EXTRA_DIST=$(mfiles_DATA) \ - $(lmefiles_DATA) \ - $(lmegeofiles_DATA) \ - $(lmeunifiles_DATA) \ - $(lmemassunifiles_DATA) \ - $(lmeQdecfiles_DATA) \ - $(samsegfiles_DATA) \ - $(survivalfiles_DATA) \ - $(survivalexdatafiles_DATA) \ - $(survivalmassunifiles_DATA) \ - $(survivalunifiles_DATA) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES=$(siemens_DATA) -include $(top_srcdir)/Makefile.extra diff --git a/mkxsubjreg/Makefile.am b/mkxsubjreg/Makefile.am deleted file mode 100644 index b55ae520af9..00000000000 --- a/mkxsubjreg/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mkxsubjreg -mkxsubjreg_SOURCES=mkxsubjreg.c -mkxsubjreg_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mkxsubjreg_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_add_xform_to_header/Makefile.am b/mri_add_xform_to_header/Makefile.am deleted file mode 100644 index d24ffcef819..00000000000 --- a/mri_add_xform_to_header/Makefile.am +++ /dev/null @@ -1,33 +0,0 @@ -## -# Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -BUILT_SOURCES=mri_add_xform_to_header.help.xml.h \ - mri_add_xform_to_header.help.xml.html - -bin_PROGRAMS = mri_add_xform_to_header - -mri_add_xform_to_header_SOURCES=mri_add_xform_to_header.c -mri_add_xform_to_header_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_add_xform_to_header_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mri_add_xform_to_header.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mri_add_xform_to_header.help.xml.html - -TESTS=$(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=$(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_and/Makefile.am b/mri_and/Makefile.am deleted file mode 100644 index eb54f70259e..00000000000 --- a/mri_and/Makefile.am +++ /dev/null @@ -1,22 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_and mri_or - -mri_and_SOURCES=mri_and.c -mri_and_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_and_LDFLAGS=$(OS_LDFLAGS) - -mri_or_SOURCES=mri_or.c -mri_or_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_or_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_annotation2label/Makefile.am b/mri_annotation2label/Makefile.am deleted file mode 100644 index e190a0d1a23..00000000000 --- a/mri_annotation2label/Makefile.am +++ /dev/null @@ -1,22 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mri_annotation2label -mri_annotation2label_SOURCES=mri_annotation2label.c -mri_annotation2label_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_annotation2label_LDFLAGS=$(OS_LDFLAGS) - -TESTS=test.py - -EXTRA_DIST=runit test.py - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - diff --git a/mri_aparc2aseg/Makefile.am b/mri_aparc2aseg/Makefile.am deleted file mode 100644 index af3990dde97..00000000000 --- a/mri_aparc2aseg/Makefile.am +++ /dev/null @@ -1,46 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_aparc2aseg - -mri_aparc2aseg_SOURCES=mri_aparc2aseg.c mri_aparc2aseg.help.xml.h -mri_aparc2aseg_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_aparc2aseg_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mri_aparc2aseg.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mri_aparc2aseg.help.xml.html - -# trick to get test data into the build directory -foo_SOURCES= -foo: - if ! test -f "$(top_builddir)/mri_aparc2aseg/testdata.tar.gz"; then \ - cp -v $(top_srcdir)/mri_aparc2aseg/testdata.tar.gz \ - $(top_builddir)/mri_aparc2aseg/; fi; - if ! test -f "$(top_builddir)/mri_aparc2aseg/testdata2.tar.gz"; then \ - cp -v $(top_srcdir)/mri_aparc2aseg/testdata2.tar.gz \ - $(top_builddir)/mri_aparc2aseg/; fi; - -check_PROGRAMS=foo - -TESTS=test_mri_aparc2aseg $(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=test_mri_aparc2aseg testdata.tar.gz testdata2.tar.gz \ - $(BUILT_SOURCES) $(foo_DATA) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mri_aparc2aseg.help.xml.h mri_aparc2aseg.help.xml.html - diff --git a/mri_aparc2wmseg/Makefile.am b/mri_aparc2wmseg/Makefile.am deleted file mode 100644 index 9b524851dac..00000000000 --- a/mri_aparc2wmseg/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mri_aparc2wmseg -mri_aparc2wmseg_SOURCES=mri_aparc2wmseg.c -mri_aparc2wmseg_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_aparc2wmseg_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_apply_inu_correction/Makefile.am b/mri_apply_inu_correction/Makefile.am deleted file mode 100644 index 9e3eee3597e..00000000000 --- a/mri_apply_inu_correction/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mri_apply_inu_correction -mri_apply_inu_correction_SOURCES=mri_apply_inu_correction.c -mri_apply_inu_correction_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_apply_inu_correction_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_aseg_edit_reclassify/Makefile.am b/mri_aseg_edit_reclassify/Makefile.am deleted file mode 100644 index 52c27024a97..00000000000 --- a/mri_aseg_edit_reclassify/Makefile.am +++ /dev/null @@ -1,18 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_aseg_edit_reclassify -mri_aseg_edit_reclassify_SOURCES=mri_aseg_edit_reclassify.c -mri_aseg_edit_reclassify_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - ../svm-lib/libsvm.a -mri_aseg_edit_reclassify_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_aseg_edit_train/Makefile.am b/mri_aseg_edit_train/Makefile.am deleted file mode 100644 index dc451c51d4b..00000000000 --- a/mri_aseg_edit_train/Makefile.am +++ /dev/null @@ -1,18 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_aseg_edit_train -mri_aseg_edit_train_SOURCES=mri_aseg_edit_train.c -mri_aseg_edit_train_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - ../svm-lib/libsvm.a -mri_aseg_edit_train_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_auto_fill/Makefile.am b/mri_auto_fill/Makefile.am deleted file mode 100644 index 231aa221315..00000000000 --- a/mri_auto_fill/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_auto_fill -mri_auto_fill_SOURCES=mri_auto_fill.c -mri_auto_fill_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_auto_fill_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_average/Makefile.am b/mri_average/Makefile.am deleted file mode 100644 index 85a6c17a3bf..00000000000 --- a/mri_average/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_average -mri_average_SOURCES=mri_average.c -mri_average_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_average_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_bc_sc_bias_correct/Makefile.am b/mri_bc_sc_bias_correct/Makefile.am deleted file mode 100644 index 473c7c13431..00000000000 --- a/mri_bc_sc_bias_correct/Makefile.am +++ /dev/null @@ -1,16 +0,0 @@ -## -## Makefile.am -## -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mri_bc_sc_bias_correct -mri_bc_sc_bias_correct_SOURCES=mri_bc_sc_bias_correct.c -mri_bc_sc_bias_correct_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_bc_sc_bias_correct_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_bias/Makefile.am b/mri_bias/Makefile.am deleted file mode 100644 index 5f81708995d..00000000000 --- a/mri_bias/Makefile.am +++ /dev/null @@ -1,22 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mri_compute_bias mri_apply_bias - -mri_apply_bias_SOURCES=mri_apply_bias.c -mri_apply_bias_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_apply_bias_LDFLAGS=$(OS_LDFLAGS) - -mri_compute_bias_SOURCES=mri_compute_bias.c -mri_compute_bias_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_compute_bias_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_binarize/Makefile.am b/mri_binarize/Makefile.am deleted file mode 100644 index 9f417d1228c..00000000000 --- a/mri_binarize/Makefile.am +++ /dev/null @@ -1,29 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mri_binarize -mri_binarize_SOURCES=mri_binarize.c -mri_binarize_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_binarize_LDFLAGS=$(OS_LDFLAGS) - -# mri_binarize is called by Eugenios hippocampal subfield binaries. -# Mac OSX systems 10.11 (El Capitan) and greater implemented SIP -# which necessitates a wrapper script to all binaries called by other binaries -# in order to pass the DYLD_LIBRARY_PATH env var. - -TESTS=test.py - -EXTRA_DIST= test.py - -install-exec-hook: - cp $(top_builddir)/mri_binarize/mri_binarize $(DESTDIR)$(bindir)/mri_binarize.bin - echo "#!/bin/bash" > $(DESTDIR)$(bindir)/mri_binarize - echo "source \$$FREESURFER_HOME/sources.sh" >> $(DESTDIR)$(bindir)/mri_binarize - echo "mri_binarize.bin \"\$$@\"" >> $(DESTDIR)$(bindir)/mri_binarize - -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_build_priors/Makefile.am b/mri_build_priors/Makefile.am deleted file mode 100644 index 9234c40083c..00000000000 --- a/mri_build_priors/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_build_priors -mri_build_priors_SOURCES=mri_build_priors.c -mri_build_priors_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_build_priors_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_ca_label/Makefile.am b/mri_ca_label/Makefile.am deleted file mode 100644 index 9d13d242e79..00000000000 --- a/mri_ca_label/Makefile.am +++ /dev/null @@ -1,42 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mri_ca_label - -mri_ca_label_SOURCES=mri_ca_label.c mri_ca_label.help.xml.h -mri_ca_label_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_ca_label_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mri_ca_label.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mri_ca_label.help.xml.html - -# this one weird trick to get test data into the build directory -# that doctors don't want you to know about -foo_SOURCES= -foo: - if ! test -f "$(top_builddir)/mri_ca_label/testdata.tar.gz"; then \ - cp -v $(top_srcdir)/mri_ca_label/testdata.tar.gz \ - $(top_builddir)/mri_ca_label/; fi; - -check_PROGRAMS=foo - -TESTS=test_mri_ca_label $(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=$(foo_DATA) $(BUILT_SOURCES) test_mri_ca_label - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mri_ca_label.help.xml.h mri_ca_label.help.xml.html diff --git a/mri_ca_normalize/Makefile.am b/mri_ca_normalize/Makefile.am deleted file mode 100644 index 1974ae72cb8..00000000000 --- a/mri_ca_normalize/Makefile.am +++ /dev/null @@ -1,49 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_cal_normalize mri_ca_normalize -mri_cal_normalize_SOURCES=mri_cal_normalize.c -mri_cal_normalize_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_cal_normalize_LDFLAGS=$(OS_LDFLAGS) - - -mri_ca_normalize_SOURCES=mri_ca_normalize.c -mri_ca_normalize_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_ca_normalize_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mri_ca_normalize.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mri_ca_normalize.help.xml.html - -# trick to get test data into the build directory (during make distcheck) -foo_SOURCES= -foo: - if ! test -f "$(top_builddir)/distribution/average/RB_all_2016-05-10.vc700.gca"; \ - then \ - cp -v $(top_srcdir)/distribution/average/RB_all_2016-05-10.vc700.gca \ - $(top_builddir)/distribution/average/; fi; - if ! test -f "$(top_builddir)/mri_ca_normalize/testdata.tar.gz"; then \ - cp -v $(top_srcdir)/mri_ca_normalize/testdata.tar.gz \ - $(top_builddir)/mri_ca_normalize/; fi; - -check_PROGRAMS=foo - -TESTS=test_mri_ca_normalize $(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=testdata.tar.gz test_mri_ca_normalize $(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mri_ca_normalize.help.xml.h mri_ca_normalize.help.xml.html diff --git a/mri_ca_register/Makefile.am b/mri_ca_register/Makefile.am deleted file mode 100644 index 8b15274dc19..00000000000 --- a/mri_ca_register/Makefile.am +++ /dev/null @@ -1,72 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include - -AM_CXXFLAGS=-I$(top_srcdir)/include \ - $(BOOST_CFLAGS) - -AM_LDFLAGS= - -bin_PROGRAMS = mri_ca_register - -mri_ca_register_SOURCES=mri_ca_register.c -mri_ca_register_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_ca_register_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mri_ca_register.help.xml mri_ca_register_cuda.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mri_ca_register.help.xml.html mri_ca_register_cuda.help.xml.html - -## ---- -## CUDA -## ---- - -# BUILDCUDA is defined if configure.in finds CUDA -if BUILDCUDA - -# rules for building cuda files -.cu.o: - $(NVCC) -o $@ -c $< $(NVCCFLAGS) $(CUDA_CFLAGS) $(AM_CFLAGS) $(MNI_CFLAGS) - -bin_PROGRAMS += mri_ca_register_cuda - -mri_ca_register_cuda_SOURCES = mri_ca_register.c \ - mri_ca_register_cuda.help.xml.h -mri_ca_register_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -mri_ca_register_cuda_CXXFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -mri_ca_register_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) -mri_ca_register_cuda_LDFLAGS = $(OS_LDFLAGS) -mri_ca_register_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(mri_ca_register_cuda_CFLAGS) \ - $(CFLAGS) $(mri_ca_register_cuda_LDFLAGS) $(LDFLAGS) -o $@ - -endif -# endif BUILDCUDA - -# trick to get test data into the build directory -foo_SOURCES= -foo: - if ! test -f "$(top_builddir)/mri_ca_register/testdata.tar.gz"; then \ - cp -v $(top_srcdir)/mri_ca_register/testdata.tar.gz \ - $(top_builddir)/mri_ca_register/; fi; - -check_PROGRAMS=foo - -TESTS=test_mri_ca_register $(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=$(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mri_ca_register.help.xml.h mri_ca_register_cuda.help.xml.h \ - mri_ca_register.help.xml.html mri_ca_register_cuda.help.xml.html diff --git a/mri_ca_tissue_parms/Makefile.am b/mri_ca_tissue_parms/Makefile.am deleted file mode 100644 index 180a39d6ae1..00000000000 --- a/mri_ca_tissue_parms/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_ca_tissue_parms -mri_ca_tissue_parms_SOURCES=mri_ca_tissue_parms.c -mri_ca_tissue_parms_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_ca_tissue_parms_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_ca_train/Makefile.am b/mri_ca_train/Makefile.am deleted file mode 100644 index 4526f631293..00000000000 --- a/mri_ca_train/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_ca_train -mri_ca_train_SOURCES=mri_ca_train.c -mri_ca_train_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_ca_train_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_cal_renormalize_gca/Makefile.am b/mri_cal_renormalize_gca/Makefile.am deleted file mode 100644 index cfa3e8a7362..00000000000 --- a/mri_cal_renormalize_gca/Makefile.am +++ /dev/null @@ -1,42 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include - -AM_CXXFLAGS=-I$(top_srcdir)/include \ - $(BOOST_CFLAGS) - -AM_LDFLAGS= - -bin_PROGRAMS = mri_cal_renormalize_gca - -mri_cal_renormalize_gca_SOURCES=mri_cal_renormalize_gca.c -mri_cal_renormalize_gca_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_cal_renormalize_gca_LDFLAGS=$(OS_LDFLAGS) - -#foodir=$(prefix)/docs/xml -#foo_DATA=mri_cal_renormalize_gca.help.xml mri_cal_renormalize_gca_cuda.help.xml -#foo2dir=$(prefix)/docs/html -#foo2_DATA=mri_cal_renormalize_gca.help.xml.html mri_cal_renormalize_gca_cuda.help.xml.html - -## ---- -## CUDA -## ---- - - -TESTS=$(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=$(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mri_cal_renormalize_gca.help.xml.h \ - mri_cal_renormalize_gca.help.xml.html diff --git a/mri_cc/Makefile.am b/mri_cc/Makefile.am deleted file mode 100644 index 95896cc7cab..00000000000 --- a/mri_cc/Makefile.am +++ /dev/null @@ -1,33 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mri_cc - -mri_cc_SOURCES=mri_cc.c mri_cc.help.xml.h -mri_cc_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_cc_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mri_cc.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mri_cc.help.xml.html - -TESTS=$(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=$(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mri_cc.help.xml.h mri_cc.help.xml.html - diff --git a/mri_cht2p/Makefile.am b/mri_cht2p/Makefile.am deleted file mode 100644 index 00ae3a23ebb..00000000000 --- a/mri_cht2p/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_cht2p -mri_cht2p_SOURCES=mri_cht2p.c -mri_cht2p_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_cht2p_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_classify/Makefile.am b/mri_classify/Makefile.am deleted file mode 100644 index 37c9371ac79..00000000000 --- a/mri_classify/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_classify -mri_classify_SOURCES=mri_classify.c -mri_classify_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_classify_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_cnr/Makefile.am b/mri_cnr/Makefile.am deleted file mode 100644 index 9186d67dc23..00000000000 --- a/mri_cnr/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_cnr -mri_cnr_SOURCES=mri_cnr.c -mri_cnr_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_cnr_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_compile_edits/Makefile.am b/mri_compile_edits/Makefile.am deleted file mode 100644 index 9a62dfdeed2..00000000000 --- a/mri_compile_edits/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_compile_edits -mri_compile_edits_SOURCES=mri_compile_edits.c -mri_compile_edits_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_compile_edits_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_compute_change_map/Makefile.am b/mri_compute_change_map/Makefile.am deleted file mode 100644 index f5b62f7c3c8..00000000000 --- a/mri_compute_change_map/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_compute_change_map -mri_compute_change_map_SOURCES=mri_compute_change_map.c -mri_compute_change_map_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_compute_change_map_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_compute_overlap/Makefile.am b/mri_compute_overlap/Makefile.am deleted file mode 100644 index f8652a1ea43..00000000000 --- a/mri_compute_overlap/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_compute_overlap -mri_compute_overlap_SOURCES=mri_compute_overlap.c -mri_compute_overlap_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_compute_overlap_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_compute_seg_overlap/Makefile.am b/mri_compute_seg_overlap/Makefile.am deleted file mode 100644 index e888ead2f26..00000000000 --- a/mri_compute_seg_overlap/Makefile.am +++ /dev/null @@ -1,33 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_compute_seg_overlap -mri_compute_seg_overlap_SOURCES=mri_compute_seg_overlap.c \ - mri_compute_seg_overlap.help.xml.h -mri_compute_seg_overlap_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_compute_seg_overlap_LDFLAGS=$(OS_LDFLAGS) - -TESTS=$(top_builddir)/scripts/help_xml_validate - -foodir=$(prefix)/docs/xml -foo_DATA=mri_compute_seg_overlap.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mri_compute_seg_overlap.help.xml.html - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=$(foo_DATA) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mri_compute_seg_overlap.help.xml.h \ - mri_compute_seg_overlap.help.xml.html diff --git a/mri_compute_structure_transforms/Makefile.am b/mri_compute_structure_transforms/Makefile.am deleted file mode 100644 index 6a4dba0c390..00000000000 --- a/mri_compute_structure_transforms/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_compute_structure_transforms -mri_compute_structure_transforms_SOURCES=mri_compute_structure_transforms.c -mri_compute_structure_transforms_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_compute_structure_transforms_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_compute_volume_fractions/Makefile.am b/mri_compute_volume_fractions/Makefile.am deleted file mode 100644 index be6816fa22f..00000000000 --- a/mri_compute_volume_fractions/Makefile.am +++ /dev/null @@ -1,29 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_compute_volume_fractions mri_compute_layer_fractions mris_compute_layer_intensities mri_compute_volume_intensities -mri_compute_volume_fractions_SOURCES=mri_compute_volume_fractions.c -mri_compute_volume_fractions_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_compute_volume_fractions_LDFLAGS=$(OS_LDFLAGS) - -mri_compute_volume_intensities_SOURCES=mri_compute_volume_intensities.c -mri_compute_volume_intensities_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_compute_volume_intensities_LDFLAGS=$(OS_LDFLAGS) - -mri_compute_layer_fractions_SOURCES=mri_compute_layer_fractions.c -mri_compute_layer_fractions_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_compute_layer_fractions_LDFLAGS=$(OS_LDFLAGS) - -mris_compute_layer_intensities_SOURCES=mris_compute_layer_intensities.c -mris_compute_layer_intensities_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_compute_layer_intensities_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_concat/Makefile.am b/mri_concat/Makefile.am deleted file mode 100644 index f05be4ca05e..00000000000 --- a/mri_concat/Makefile.am +++ /dev/null @@ -1,31 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mri_concat -mri_concat_SOURCES=mri_concat.c -mri_concat_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_concat_LDFLAGS=$(OS_LDFLAGS) - -# mri_concat is called by qdec. On Mac OSX -# systems 10.11 (El Capitan) and greater implemented SIP -# which necessitates a wrapper script to pass the DYLD_LIBRARY_PATH env var. - -TESTS=test.py - -EXTRA_DIST= test.py - -install-exec-hook: - cp $(top_builddir)/mri_concat/mri_concat $(DESTDIR)$(bindir)/mri_concat.bin - echo "#!/bin/bash" > $(DESTDIR)$(bindir)/mri_concat - echo "source \$$FREESURFER_HOME/sources.sh" >> $(DESTDIR)$(bindir)/mri_concat - echo "mri_concat.bin \"\$$@\"" >> $(DESTDIR)$(bindir)/mri_concat - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_concatenate_gcam/Makefile.am b/mri_concatenate_gcam/Makefile.am deleted file mode 100644 index a5bd7bb5a46..00000000000 --- a/mri_concatenate_gcam/Makefile.am +++ /dev/null @@ -1,26 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS=mri_concatenate_gcam -mri_concatenate_gcam_SOURCES=mri_concatenate_gcam.cpp mri_concatenate_gcam.help.xml.h -mri_concatenate_gcam_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_concatenate_gcam_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mri_concatenate_gcam.help.xml - -TESTS=$(top_builddir)/scripts/help_xml_validate - -EXTRA_DIST=$(foo_DATA) $(BUILT_SOURCES) - -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mri_concatenate_gcam.help.xml.h - -clean-local: -rm -f $(BUILT_SOURCES) diff --git a/mri_concatenate_lta/Makefile.am b/mri_concatenate_lta/Makefile.am deleted file mode 100644 index aff10d730af..00000000000 --- a/mri_concatenate_lta/Makefile.am +++ /dev/null @@ -1,40 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_concatenate_lta -mri_concatenate_lta_SOURCES=mri_concatenate_lta.c -mri_concatenate_lta_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_concatenate_lta_LDFLAGS=$(OS_LDFLAGS) - -# trick to get test data into the build directory during make distcheck -foo_SOURCES= -foo: - if ! test -f "$(top_builddir)/mri_concatenate_lta/testdata.tar.gz"; then \ - cp -vf $(top_srcdir)/mri_concatenate_lta/testdata.tar.gz \ - $(top_builddir)/mri_concatenate_lta/; fi; - -check_PROGRAMS=foo - -TESTS=test_mri_concatenate_lta - -EXTRA_DIST=test_mri_concatenate_lta testdata.tar.gz - -# mri_concatenate_lta is called by Eugenios hippocampal subfield binaries. -# Mac OSX systems 10.11 (El Capitan) and greater implemented SIP -# which necessitates a wrapper script to all binaries called by other binaries -# in order to pass the DYLD_LIBRARY_PATH env var. - -install-exec-hook: - cp $(top_builddir)/mri_concatenate_lta/mri_concatenate_lta $(DESTDIR)$(bindir)/mri_concatenate_lta.bin - echo "#!/bin/bash" > $(DESTDIR)$(bindir)/mri_concatenate_lta - echo "source \$$FREESURFER_HOME/sources.sh" >> $(DESTDIR)$(bindir)/mri_concatenate_lta - echo "mri_concatenate_lta.bin \"\$$@\"" >> $(DESTDIR)$(bindir)/mri_concatenate_lta - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_convert/Makefile.am b/mri_convert/Makefile.am deleted file mode 100644 index d0ae46cd7fb..00000000000 --- a/mri_convert/Makefile.am +++ /dev/null @@ -1,54 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mri_convert mri_make_uchar -mri_convert_SOURCES=mri_convert.c mri_convert.help.xml.h -mri_convert_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_convert_LDFLAGS=$(OS_LDFLAGS) - -mri_make_uchar_SOURCES=mri_make_uchar.c -mri_make_uchar_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_make_uchar_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mri_convert.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mri_convert.help.xml.html - -# trick to get test data into the build directory -foo_SOURCES= -foo: - if ! test -f "$(top_builddir)/mri_convert/testdata.tar.gz"; then \ - cp -v $(top_srcdir)/mri_convert/testdata.tar.gz \ - $(top_builddir)/mri_convert/; fi; - -check_PROGRAMS=foo - -TESTS=test.py $(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=test.py testdata.tar.gz $(foo_DATA) $(BUILT_SOURCES) - -# mri_convert is called by Eugenio's hippocampal subfield code. -# Mac OSX systems 10.11 (El Capitan) and greater implemented SIP -# which necessitates a wrapper script for all binaries called by -# other binaries to pass the DYLD_LIBRARY_PATH env var. - -install-exec-hook: - cp $(top_builddir)/mri_convert/mri_convert $(DESTDIR)$(bindir)/mri_convert.bin - echo "#!/bin/bash" > $(DESTDIR)$(bindir)/mri_convert - echo "source \$$FREESURFER_HOME/sources.sh" >> $(DESTDIR)$(bindir)/mri_convert - echo "mri_convert.bin \"\$$@\"" >> $(DESTDIR)$(bindir)/mri_convert - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mri_convert.help.xml.h mri_convert.help.xml.html diff --git a/mri_convert_mdh/Makefile.am b/mri_convert_mdh/Makefile.am deleted file mode 100644 index f28d89ffaf6..00000000000 --- a/mri_convert_mdh/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_convert_mdh -mri_convert_mdh_SOURCES=mri_convert_mdh.c -mri_convert_mdh_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_convert_mdh_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_copy_values/Makefile.am b/mri_copy_values/Makefile.am deleted file mode 100644 index d129c52f066..00000000000 --- a/mri_copy_values/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_copy_values -mri_copy_values_SOURCES=mri_copy_values.c -mri_copy_values_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_copy_values_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_cor2label/Makefile.am b/mri_cor2label/Makefile.am deleted file mode 100644 index c7a6eb0f741..00000000000 --- a/mri_cor2label/Makefile.am +++ /dev/null @@ -1,22 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mri_cor2label -mri_cor2label_SOURCES=mri_cor2label.c -mri_cor2label_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_cor2label_LDFLAGS=$(OS_LDFLAGS) - -# mri_vol2label is the better name -install-exec-hook:mri_cor2label - cp $(top_builddir)/mri_cor2label/mri_cor2label \ - $(DESTDIR)$(bindir)/mri_vol2label - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_coreg/Makefile.am b/mri_coreg/Makefile.am deleted file mode 100644 index 88c5700d39d..00000000000 --- a/mri_coreg/Makefile.am +++ /dev/null @@ -1,74 +0,0 @@ -## -## Makefile.am -## - -####################################################################### -# When you create your own program directory, copy the 'from' to the -# 'to' lines to your Makefile.am and change dummy to your program name. -# -# 0. mkdir dev/yourdir and put .c file in there -# 1. modify dev/configure.in to have yourdir/Makefile -# 2. modify dev/Makefile.am to have yourdir as one of SUBDIRS -# 3. create dev/yourdir/Makefile.am (follow dummy/Makefile.am) -# i.e. replace dummy with your program name. -# -# 4. ./setup_configure at the top directory, i.e. dev/ (which will create -# Makefile.in in yourdir directory and configure from configure.in) -# 5. ./configure .... and make to make sure that your new thing is working -# 6. try make to make sure that yourthing is compiled. -# -# After confirming everything working: -# 7. checkin yourdir/Makefile.am, yourdir/yourprog.c or cpp. -# (Don't checkin Makefile or Makefile.in.) -# 8. commit dev/configure.in, dev/Makefile.am -# -# 9. lastly, delete this help text from your own Makefile.am! -# -# If you have problems, please let us know (zkaufman@nmr.mgh.harvard.edu -# or nicks@nmr.mgh.harvard.edu). -######################################################################### -# from ------------------------------------------------ - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_coreg -mri_coreg_SOURCES=mri_coreg.c -mri_coreg_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_coreg_LDFLAGS=$(OS_LDFLAGS) - -foo_SOURCES= -foo: - if ! test -f "$(top_builddir)/mri_coreg/testdata.tar.gz"; then \ - cp -v $(top_srcdir)/mri_coreg/testdata.tar.gz \ - $(top_builddir)/mri_coreg/; fi; - -check_PROGRAMS=foo -TESTS=test_mri_coreg -EXTRA_DIST=test_mri_coreg testdata.tar.gz - - -# to -------------------------------------------------- -# -# Where $(OS_LDFLAGS) is to compile programs statically for Linux. -# -# You can have multiple bin_PROGRAMS in the same directory. -# -######################################################################## -# When you want to create your program to test, use the following -# framework: -# You can have as many programs (separated by space) in check_PROGRAMS. -# Your program can consist of many sources (you add to _SOURCES= line). -# You can do "make myown" to compile. The default CFLAGS="-g -O2", but -# you can do "make CFLAGS=-g myown" to create a debugging version. -# -# The program listed as check_PROGRAMS are not compiled under standard -# "make". Only "make check" will compile them. See mri_convert's -# Makefile.am for an example of its 'make check' test setup. -# - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_correct_segmentations/Makefile.am b/mri_correct_segmentations/Makefile.am deleted file mode 100644 index e37dd8a6172..00000000000 --- a/mri_correct_segmentations/Makefile.am +++ /dev/null @@ -1,40 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_correct_segmentations -mri_correct_segmentations_SOURCES=mri_correct_segmentations.c -mri_correct_segmentations_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_correct_segmentations_LDFLAGS=$(OS_LDFLAGS) - -# -# Where $(OS_LDFLAGS) is to compile programs statically for Linux. -# -# You can have multiple bin_PROGRAMS in the same directory. -# -######################################################################## -# When you want to create your program to test, use the following -# framework: -# You can have as many programs (separated by space) in check_PROGRAMS. -# Your program can consist of many sources (you add to _SOURCES= line). -# You can do "make myown" to compile. The default CFLAGS="-g -O2", but -# you can do "make CFLAGS=-g myown" to create a debugging version. -# -# The program listed as check_PROGRAMS are not compiled under standard -# "make". Only "make check" will compile them. -# -# Please don't remove myown.c from this mri_correct_segmentations directory. -######################################################################## -#check_PROGRAMS=myown - -#myown_SOURCES=myown.c -#myown_LDADD=$(addprefix $(top_builddir)/, $(LIBS_MGH)) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_cvs_register/Makefile.am b/mri_cvs_register/Makefile.am deleted file mode 100644 index 0a24c3d7b14..00000000000 --- a/mri_cvs_register/Makefile.am +++ /dev/null @@ -1,32 +0,0 @@ -# -# Makefile.am -# - -dist_bin_SCRIPTS = mri_cvs_register mri_cvs_check mri_cvs_data_copy - -foodir=$(bindir) -foo_DATA= \ - id.xfm \ - mri_cvs_requiredfiles.txt - -xmldir=$(prefix)/docs/xml -xml_DATA=mri_cvs_register.help.xml -htmldir=$(prefix)/docs/html -html_DATA=mri_cvs_register.help.xml.html - -install-exec-hook: - $(top_builddir)/utils/fsPrintHelp $(srcdir)/mri_cvs_register.help.xml \ - >> $(DESTDIR)$(bindir)/mri_cvs_register - -TESTS = $(top_builddir)/scripts/help_xml_validate - -EXTRA_DIST=$(foo_DATA) $(xml_DATA) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -clean-local: - rm -f *.help.xml.html diff --git a/mri_dct_align/Makefile.am b/mri_dct_align/Makefile.am deleted file mode 100644 index f484978f7bb..00000000000 --- a/mri_dct_align/Makefile.am +++ /dev/null @@ -1,21 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_dct_align_binary mri_dct_align -mri_dct_align_binary_SOURCES=mri_dct_align_binary.c -mri_dct_align_binary_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_dct_align_binary_LDFLAGS=$(OS_LDFLAGS) - -mri_dct_align_SOURCES=mri_dct_align.c -mri_dct_align_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_dct_align_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_deface/Makefile.am b/mri_deface/Makefile.am deleted file mode 100644 index 3eb78b35c78..00000000000 --- a/mri_deface/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS=-static - -bin_PROGRAMS = mri_deface -mri_deface_SOURCES=mri_deface.c -mri_deface_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_deface_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_diff/Makefile.am b/mri_diff/Makefile.am deleted file mode 100644 index 89e22c26946..00000000000 --- a/mri_diff/Makefile.am +++ /dev/null @@ -1,21 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mri_diff -mri_diff_SOURCES=mri_diff.c -mri_diff_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_diff_LDFLAGS=$(OS_LDFLAGS) - -TESTS=test.py - -EXTRA_DIST= test.py - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_distance_transform/Makefile.am b/mri_distance_transform/Makefile.am deleted file mode 100644 index ba86985f79f..00000000000 --- a/mri_distance_transform/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mri_distance_transform -mri_distance_transform_SOURCES=mri_distance_transform.cpp -mri_distance_transform_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH) utilscpp/libutilscpp.a ) -mri_distance_transform_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_divide_segmentation/Makefile.am b/mri_divide_segmentation/Makefile.am deleted file mode 100644 index 0fba1d413e6..00000000000 --- a/mri_divide_segmentation/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_divide_segmentation -mri_divide_segmentation_SOURCES=mri_divide_segmentation.c -mri_divide_segmentation_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_divide_segmentation_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_edit_segmentation/Makefile.am b/mri_edit_segmentation/Makefile.am deleted file mode 100644 index 3ef738a24af..00000000000 --- a/mri_edit_segmentation/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_edit_segmentation -mri_edit_segmentation_SOURCES=mri_edit_segmentation.c -mri_edit_segmentation_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_edit_segmentation_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_edit_segmentation_with_surfaces/Makefile.am b/mri_edit_segmentation_with_surfaces/Makefile.am deleted file mode 100644 index b8dd0207ca5..00000000000 --- a/mri_edit_segmentation_with_surfaces/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mri_edit_segmentation_with_surfaces -mri_edit_segmentation_with_surfaces_SOURCES=mri_edit_segmentation_with_surfaces.c -mri_edit_segmentation_with_surfaces_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_edit_segmentation_with_surfaces_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_edit_wm_with_aseg/Makefile.am b/mri_edit_wm_with_aseg/Makefile.am deleted file mode 100644 index 37243fadc2d..00000000000 --- a/mri_edit_wm_with_aseg/Makefile.am +++ /dev/null @@ -1,34 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_edit_wm_with_aseg - -mri_edit_wm_with_aseg_SOURCES=mri_edit_wm_with_aseg.c \ - mri_edit_wm_with_aseg.help.xml.h -mri_edit_wm_with_aseg_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_edit_wm_with_aseg_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mri_edit_wm_with_aseg.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mri_edit_wm_with_aseg.help.xml.html - -TESTS=$(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=$(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mri_edit_wm_with_aseg.help.xml.h \ - mri_edit_wm_with_aseg.help.xml.html diff --git a/mri_elastic_energy/Makefile.am b/mri_elastic_energy/Makefile.am deleted file mode 100644 index 175f99b816d..00000000000 --- a/mri_elastic_energy/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_elastic_energy -mri_elastic_energy_SOURCES=mri_elastic_energy.c -mri_elastic_energy_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_elastic_energy_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_em_register/Makefile.am b/mri_em_register/Makefile.am deleted file mode 100644 index 0aad1cefb72..00000000000 --- a/mri_em_register/Makefile.am +++ /dev/null @@ -1,76 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include - -AM_CXXFLAGS=-I$(top_srcdir)/include\ - $(BOOST_CFLAGS)\ - -Wall -Wextra - -AM_LDFLAGS= - -bin_PROGRAMS = mri_em_register -mri_em_register_SOURCES=mri_em_register.c\ - findtranslation.cpp findtranslation.h\ - emregisterutils.cpp emregisterutils.h -mri_em_register_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_em_register_LDFLAGS=$(OS_LDFLAGS) - - -foodir=$(prefix)/docs/xml -foo_DATA=mri_em_register.help.xml mri_em_register_cuda.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mri_em_register.help.xml mri_em_register_cuda.help.xml.html - - -## ---- -## CUDA -## ---- - -# BUILDCUDA is defined if configure.in finds CUDA -if BUILDCUDA -# rules for building cuda files -.cu.o: - $(NVCC) -o $@ -c $< $(NVCCFLAGS) $(CUDA_CFLAGS) $(AM_CFLAGS) $(MNI_CFLAGS) - -bin_PROGRAMS += mri_em_register_cuda - -mri_em_register_cuda_SOURCES = mri_em_register.c \ - em_register_cuda.cu em_register_cuda.h\ - findtranslation.cpp findtranslation.h\ - emregisterutils.cpp emregisterutils.h -mri_em_register_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -mri_em_register_cuda_CXXFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -mri_em_register_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) -mri_em_register_cuda_LDFLAGS = $(OS_LDFLAGS) -mri_em_register_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(mri_em_register_cuda_CFLAGS) \ - $(CFLAGS) $(mri_em_register_cuda_LDFLAGS) $(LDFLAGS) -o $@ -endif - -# trick to get test data into the build directory -foo_SOURCES= -foo: - if ! test -f "$(top_builddir)/mri_em_register/testdata.tar.gz"; then \ - cp -v $(top_srcdir)/mri_em_register/testdata.tar.gz \ - $(top_builddir)/mri_em_register/; fi; - -check_PROGRAMS=foo - -TESTS=test_mri_em_register $(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=$(foo_DATA) $(BUILT_SOURCES) test_mri_em_register - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mri_em_register.help.xml.h mri_em_register_cuda.help.xml.h \ - mri_em_register.help.xml.html mri_em_register_cuda.help.xml.html - diff --git a/mri_estimate_tissue_parms/Makefile.am b/mri_estimate_tissue_parms/Makefile.am deleted file mode 100644 index 028e93f1eba..00000000000 --- a/mri_estimate_tissue_parms/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_estimate_tissue_parms -mri_estimate_tissue_parms_SOURCES=mri_estimate_tissue_parms.c -mri_estimate_tissue_parms_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_estimate_tissue_parms_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_evaluate_morph/Makefile.am b/mri_evaluate_morph/Makefile.am deleted file mode 100644 index d57e4521375..00000000000 --- a/mri_evaluate_morph/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_evaluate_morph -mri_evaluate_morph_SOURCES=mri_evaluate_morph.c -mri_evaluate_morph_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_evaluate_morph_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_extract/Makefile.am b/mri_extract/Makefile.am deleted file mode 100644 index 05521dba1e7..00000000000 --- a/mri_extract/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_extract -mri_extract_SOURCES=mri_extract.c -mri_extract_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_extract_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_extract_conditions/Makefile.am b/mri_extract_conditions/Makefile.am deleted file mode 100644 index 2a828b656f0..00000000000 --- a/mri_extract_conditions/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_extract_conditions -mri_extract_conditions_SOURCES=mri_extract_conditions.c -mri_extract_conditions_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_extract_conditions_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_extract_fcd_features/Makefile.am b/mri_extract_fcd_features/Makefile.am deleted file mode 100644 index 7cf59ea5000..00000000000 --- a/mri_extract_fcd_features/Makefile.am +++ /dev/null @@ -1,19 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_extract_fcd_features - -mri_extract_fcd_features_SOURCES=mri_extract_fcd_features.c -mri_extract_fcd_features_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_extract_fcd_features_LDFLAGS=$(OS_LDFLAGS) - - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_extract_label/Makefile.am b/mri_extract_label/Makefile.am deleted file mode 100644 index 99a34f04e8b..00000000000 --- a/mri_extract_label/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_extract_label -mri_extract_label_SOURCES=mri_extract_label.c -mri_extract_label_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_extract_label_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_extract_largest_CC/Makefile.am b/mri_extract_largest_CC/Makefile.am deleted file mode 100644 index ca72d4a388f..00000000000 --- a/mri_extract_largest_CC/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mri_extract_largest_CC -mri_extract_largest_CC_SOURCES=mri_extract_largest_CC.c -mri_extract_largest_CC_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_extract_largest_CC_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_fcili/Makefile.am b/mri_fcili/Makefile.am deleted file mode 100644 index 3518d888be4..00000000000 --- a/mri_fcili/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_fcili -mri_fcili_SOURCES=mri_fcili.c -mri_fcili_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_fcili_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_fdr/Makefile.am b/mri_fdr/Makefile.am deleted file mode 100644 index cd0b4f7045c..00000000000 --- a/mri_fdr/Makefile.am +++ /dev/null @@ -1,63 +0,0 @@ -## -## Makefile.am -## - -####################################################################### -# When you create your own program directory, copy the 'from' to the -# 'to' lines to your Makefile.am and change dummy to your program name. -# -# 0. mkdir dev/yourdir and put .c file in there -# 1. modify dev/configure.in to have yourdir/Makefile -# 2. modify dev/Makefile.am to have yourdir as one of SUBDIRS -# 3. create dev/yourdir/Makefile.am (follow dummy/Makefile.am) -# i.e. replace dummy with your program name. -# -# 4. ./setup_configure at the top directory, i.e. dev/ (which will create -# Makefile.in in yourdir directory and configure from configure.in) -# 5. ./configure .... and make to make sure that your new thing is working -# 6. try make to make sure that yourthing is compiled. -# -# After confirming everything working: -# 7. checkin yourdir/Makefile.am, yourdir/yourprog.c or cpp. -# (Don't checkin Makefile or Makefile.in.) -# 8. commit dev/configure.in, dev/Makefile.am -# -# 9. lastly, delete this help text from your own Makefile.am! -# -# If you have problems, please let us know (zkaufman@nmr.mgh.harvard.edu -# or nicks@nmr.mgh.harvard.edu). -######################################################################### -# from ------------------------------------------------ - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_fdr -mri_fdr_SOURCES=mri_fdr.c -mri_fdr_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_fdr_LDFLAGS=$(OS_LDFLAGS) - -# to -------------------------------------------------- -# -# Where $(OS_LDFLAGS) is to compile programs statically for Linux. -# -# You can have multiple bin_PROGRAMS in the same directory. -# -######################################################################## -# When you want to create your program to test, use the following -# framework: -# You can have as many programs (separated by space) in check_PROGRAMS. -# Your program can consist of many sources (you add to _SOURCES= line). -# You can do "make myown" to compile. The default CFLAGS="-g -O2", but -# you can do "make CFLAGS=-g myown" to create a debugging version. -# -# The program listed as check_PROGRAMS are not compiled under standard -# "make". Only "make check" will compile them. See mri_convert's -# Makefile.am for an example of its 'make check' test setup. -# - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_fieldsign/Makefile.am b/mri_fieldsign/Makefile.am deleted file mode 100644 index e77b0971a70..00000000000 --- a/mri_fieldsign/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_fieldsign -mri_fieldsign_SOURCES=mri_fieldsign.c -mri_fieldsign_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_fieldsign_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_fill/Makefile.am b/mri_fill/Makefile.am deleted file mode 100644 index d6a982c30b9..00000000000 --- a/mri_fill/Makefile.am +++ /dev/null @@ -1,32 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_fill - -mri_fill_SOURCES=mri_fill.c -mri_fill_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_fill_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mri_fill.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mri_fill.help.xml.html - -TESTS=$(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=$(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mri_fill.help.xml.h mri_fill.help.xml.html diff --git a/mri_fit_bias/Makefile.am b/mri_fit_bias/Makefile.am deleted file mode 100644 index 052bd7a1afd..00000000000 --- a/mri_fit_bias/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_fit_bias -mri_fit_bias_SOURCES=mri_fit_bias.c -mri_fit_bias_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_fit_bias_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_fslmat_to_lta/Makefile.am b/mri_fslmat_to_lta/Makefile.am deleted file mode 100644 index 5d6e624dff7..00000000000 --- a/mri_fslmat_to_lta/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mri_fslmat_to_lta -mri_fslmat_to_lta_SOURCES=mri_fslmat_to_lta.c -mri_fslmat_to_lta_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_fslmat_to_lta_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_fuse_intensity_images/Makefile.am b/mri_fuse_intensity_images/Makefile.am deleted file mode 100644 index 275bf1462d7..00000000000 --- a/mri_fuse_intensity_images/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_fuse_intensity_images -mri_fuse_intensity_images_SOURCES=mri_fuse_intensity_images.c -mri_fuse_intensity_images_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_fuse_intensity_images_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_fuse_segmentations/Makefile.am b/mri_fuse_segmentations/Makefile.am deleted file mode 100644 index a981572f6f5..00000000000 --- a/mri_fuse_segmentations/Makefile.am +++ /dev/null @@ -1,31 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -BUILT_SOURCES=mri_fuse_segmentations.help.xml.h mri_fuse_segmentations.help.xml.html - -foodir=$(prefix)/docs/xml -foo_DATA=mri_fuse_segmentations.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mri_fuse_segmentations.help.xml.html - -bin_PROGRAMS = mri_fuse_segmentations -mri_fuse_segmentations_SOURCES=mri_fuse_segmentations.cpp -mri_fuse_segmentations_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_fuse_segmentations_LDFLAGS=$(OS_LDFLAGS) - -TESTS=test.py - -EXTRA_DIST= test.py - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -clean-local: -rm -f $(BUILT_SOURCES) diff --git a/mri_fwhm/Makefile.am b/mri_fwhm/Makefile.am deleted file mode 100644 index 2a734798e9b..00000000000 --- a/mri_fwhm/Makefile.am +++ /dev/null @@ -1,21 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_fwhm -mri_fwhm_SOURCES=mri_fwhm.c -mri_fwhm_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_fwhm_LDFLAGS=$(OS_LDFLAGS) - -TESTS=test.py - -EXTRA_DIST= test.py - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_gca_ambiguous/Makefile.am b/mri_gca_ambiguous/Makefile.am deleted file mode 100644 index eb01157a6a2..00000000000 --- a/mri_gca_ambiguous/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_gca_ambiguous -mri_gca_ambiguous_SOURCES=mri_gca_ambiguous.c -mri_gca_ambiguous_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_gca_ambiguous_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_gcab_train/Makefile.am b/mri_gcab_train/Makefile.am deleted file mode 100644 index 9f7edb24336..00000000000 --- a/mri_gcab_train/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_gcab_train -mri_gcab_train_SOURCES=mri_gcab_train.c -mri_gcab_train_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_gcab_train_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_gcut/Makefile.am b/mri_gcut/Makefile.am deleted file mode 100644 index 98f091b3f49..00000000000 --- a/mri_gcut/Makefile.am +++ /dev/null @@ -1,26 +0,0 @@ -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_gcut - -mri_gcut_SOURCES=mri_gcut.cpp mri_gcut.help.xml.h -mri_gcut_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_gcut_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mri_gcut.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mri_gcut.help.xml.html - -TESTS=$(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST = gcut.h graphcut.h graphcut.cpp pre_pro.cpp \ - $(foo_DATA) $(BUILT_SOURCES) - -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mri_gcut.help.xml.h mri_gcut.help.xml.html diff --git a/mri_gdfglm/Makefile.am b/mri_gdfglm/Makefile.am deleted file mode 100644 index 8feee9683f1..00000000000 --- a/mri_gdfglm/Makefile.am +++ /dev/null @@ -1,18 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mri_gdfglm - -mri_gdfglm_SOURCES=mri_gdfglm.c $(top_srcdir)/fsgdf/fsgdf.c -mri_gdfglm_LDADD=$(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_gdfglm_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_glmfit/Makefile.am b/mri_glmfit/Makefile.am deleted file mode 100644 index dee82ea1515..00000000000 --- a/mri_glmfit/Makefile.am +++ /dev/null @@ -1,40 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_glmfit -mri_glmfit_SOURCES=mri_glmfit.c $(top_srcdir)/fsgdf/fsgdf.c -mri_glmfit_LDADD=$(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_glmfit_LDFLAGS=$(OS_LDFLAGS) - -# trick to get test data into the build directory -foo_SOURCES= -foo: - if ! test -f "$(top_builddir)/mri_glmfit/teststats.tar.gz"; then \ - cp -v $(top_srcdir)/mri_glmfit/teststats.tar.gz \ - $(top_builddir)/mri_glmfit/; fi; - -check_PROGRAMS=foo - -TESTS=test_mri_glmfit - -# mri_glmfit is called by qdec. On Mac OSX -# systems 10.11 (El Capitan) and greater implemented SIP -# which necessitates a wrapper script to pass the DYLD_LIBRARY_PATH env var. - -install-exec-hook: - cp $(top_builddir)/mri_glmfit/mri_glmfit $(DESTDIR)$(bindir)/mri_glmfit.bin - echo "#!/bin/bash" > $(DESTDIR)$(bindir)/mri_glmfit - echo "source \$$FREESURFER_HOME/sources.sh" >> $(DESTDIR)$(bindir)/mri_glmfit - echo "mri_glmfit.bin \"\$$@\"" >> $(DESTDIR)$(bindir)/mri_glmfit - -EXTRA_DIST=test_mri_glmfit teststats.tar.gz - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_gtmpvc/Makefile.am b/mri_gtmpvc/Makefile.am deleted file mode 100644 index b8203183d5f..00000000000 --- a/mri_gtmpvc/Makefile.am +++ /dev/null @@ -1,14 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_gtmpvc -mri_gtmpvc_SOURCES=mri_gtmpvc.c -mri_gtmpvc_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_gtmpvc_LDFLAGS=$(OS_LDFLAGS) - -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_gtmseg/Makefile.am b/mri_gtmseg/Makefile.am deleted file mode 100644 index 69b71012fa5..00000000000 --- a/mri_gtmseg/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_gtmseg -mri_gtmseg_SOURCES=mri_gtmseg.c -mri_gtmseg_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_gtmseg_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_hausdorff_dist/Makefile.am b/mri_hausdorff_dist/Makefile.am deleted file mode 100644 index 5d117648f25..00000000000 --- a/mri_hausdorff_dist/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_hausdorff_dist -mri_hausdorff_dist_SOURCES=mri_hausdorff_dist.c -mri_hausdorff_dist_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_hausdorff_dist_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_head/Makefile.am b/mri_head/Makefile.am deleted file mode 100644 index bb390196753..00000000000 --- a/mri_head/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_head -mri_head_SOURCES=mri_head.c -mri_head_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_head_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_hires_register/Makefile.am b/mri_hires_register/Makefile.am deleted file mode 100644 index 7b0896ce60e..00000000000 --- a/mri_hires_register/Makefile.am +++ /dev/null @@ -1,45 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_hires_register \ - mri_nl_align_binary \ - mri_linear_align_binary \ - mri_compute_distances \ - mri_linear_align \ - mri_nl_align - -mri_hires_register_SOURCES=mri_hires_register.c -mri_hires_register_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_hires_register_LDFLAGS=$(OS_LDFLAGS) - -mri_nl_align_binary_SOURCES=mri_nl_align_binary.c -mri_nl_align_binary_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_nl_align_binary_LDFLAGS=$(OS_LDFLAGS) - -mri_linear_align_binary_SOURCES=mri_linear_align_binary.c -mri_linear_align_binary_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_linear_align_binary_LDFLAGS=$(OS_LDFLAGS) - -mri_compute_distances_SOURCES=mri_compute_distances.c -mri_compute_distances_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_compute_distances_LDFLAGS=$(OS_LDFLAGS) - -mri_nl_align_SOURCES=mri_nl_align.c -mri_nl_align_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_nl_align_LDFLAGS=$(OS_LDFLAGS) - -mri_linear_align_SOURCES=mri_linear_align.c -mri_linear_align_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_linear_align_LDFLAGS=$(OS_LDFLAGS) - -EXTRA_DIST = make_movie.tcl - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_histo_eq/Makefile.am b/mri_histo_eq/Makefile.am deleted file mode 100644 index f8b1f3471cb..00000000000 --- a/mri_histo_eq/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_histo_eq -mri_histo_eq_SOURCES=mri_histo_eq.c -mri_histo_eq_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_histo_eq_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_histo_normalize/Makefile.am b/mri_histo_normalize/Makefile.am deleted file mode 100644 index f6bf9b6a588..00000000000 --- a/mri_histo_normalize/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mri_histo_normalize -mri_histo_normalize_SOURCES=mri_histo_normalize.c -mri_histo_normalize_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_histo_normalize_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_ibmc/Makefile.am b/mri_ibmc/Makefile.am deleted file mode 100644 index 8865f4e85f2..00000000000 --- a/mri_ibmc/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_ibmc -mri_ibmc_SOURCES=mri_ibmc.c -mri_ibmc_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_ibmc_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_iic/Makefile.am b/mri_iic/Makefile.am deleted file mode 100644 index 17c469075f9..00000000000 --- a/mri_iic/Makefile.am +++ /dev/null @@ -1,30 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include $(VXL_CFLAGS) - -check_PROGRAMS = testTCS \ - testMatrix \ - testMultiplication - -testTCS_SOURCES=testTCS.cpp tensorCubicSmoothing.cpp matrix3d.cpp -testTCS_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -testTCS_LDFLAGS=$(OS_LDFLAGS) - -testMatrix_SOURCES=testMatrix.cpp matrix3d.cpp -testMatrix_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -testMatrix_LDFLAGS=$(OS_LDFLAGS) - -testMultiplication_SOURCES=testMultiplication.cpp matrix3d.cpp -testMultiplication_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -testMultiplication_LDFLAGS=$(OS_LDFLAGS) - -TESTS=testMultiplication testTCS - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_info/Makefile.am b/mri_info/Makefile.am deleted file mode 100644 index 20ba4a3308a..00000000000 --- a/mri_info/Makefile.am +++ /dev/null @@ -1,21 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_info -mri_info_SOURCES=mri_info.c -mri_info_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_info_LDFLAGS=$(OS_LDFLAGS) - -# TESTS=test.py - -# EXTRA_DIST= test.py - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_interpolate/Makefile.am b/mri_interpolate/Makefile.am deleted file mode 100644 index ac6b0ffa43d..00000000000 --- a/mri_interpolate/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_interpolate -mri_interpolate_SOURCES=mri_interpolate.c -mri_interpolate_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_interpolate_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_jacobian/Makefile.am b/mri_jacobian/Makefile.am deleted file mode 100644 index 19a44f2d737..00000000000 --- a/mri_jacobian/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mri_jacobian -mri_jacobian_SOURCES=mri_jacobian.c -mri_jacobian_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_jacobian_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_joint_density/Makefile.am b/mri_joint_density/Makefile.am deleted file mode 100644 index 306facaea34..00000000000 --- a/mri_joint_density/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_joint_density -mri_joint_density_SOURCES=mri_joint_density.c -mri_joint_density_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_joint_density_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_label2label/Makefile.am b/mri_label2label/Makefile.am deleted file mode 100644 index ffc3345ec81..00000000000 --- a/mri_label2label/Makefile.am +++ /dev/null @@ -1,31 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_label2label -mri_label2label_SOURCES=mri_label2label.c -mri_label2label_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_label2label_LDFLAGS=$(OS_LDFLAGS) - -TESTS=test.py - -EXTRA_DIST= test.py - -# mri_label2label is called by qdec. On Mac OSX -# systems 10.11 (El Capitan) and greater implemented SIP -# which necessitates a wrapper script to pass the DYLD_LIBRARY_PATH env var. - -install-exec-hook: - cp $(top_builddir)/mri_label2label/mri_label2label $(DESTDIR)$(bindir)/mri_label2label.bin - echo "#!/bin/bash" > $(DESTDIR)$(bindir)/mri_label2label - echo "source \$$FREESURFER_HOME/sources.sh" >> $(DESTDIR)$(bindir)/mri_label2label - echo "mri_label2label.bin \"\$$@\"" >> $(DESTDIR)$(bindir)/mri_label2label - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_label2vol/Makefile.am b/mri_label2vol/Makefile.am deleted file mode 100644 index 8681ee704cb..00000000000 --- a/mri_label2vol/Makefile.am +++ /dev/null @@ -1,21 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_label2vol -mri_label2vol_SOURCES=mri_label2vol.c -mri_label2vol_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_label2vol_LDFLAGS=$(OS_LDFLAGS) - -# TESTS=test.py - -# EXTRA_DIST= test.py - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_label_accuracy/Makefile.am b/mri_label_accuracy/Makefile.am deleted file mode 100644 index fa95f5ab440..00000000000 --- a/mri_label_accuracy/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_label_accuracy -mri_label_accuracy_SOURCES=mri_label_accuracy.c -mri_label_accuracy_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_label_accuracy_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_label_histo/Makefile.am b/mri_label_histo/Makefile.am deleted file mode 100644 index c3a89ac2213..00000000000 --- a/mri_label_histo/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_label_histo -mri_label_histo_SOURCES=mri_label_histo.c -mri_label_histo_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_label_histo_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_label_vals/Makefile.am b/mri_label_vals/Makefile.am deleted file mode 100644 index e37cb663710..00000000000 --- a/mri_label_vals/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_label_vals -mri_label_vals_SOURCES=mri_label_vals.c -mri_label_vals_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_label_vals_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_label_volume/Makefile.am b/mri_label_volume/Makefile.am deleted file mode 100644 index 3bc45e8a295..00000000000 --- a/mri_label_volume/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mri_label_volume -mri_label_volume_SOURCES=mri_label_volume.c -mri_label_volume_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_label_volume_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_linear_register/Makefile.am b/mri_linear_register/Makefile.am deleted file mode 100644 index ee75c24a49b..00000000000 --- a/mri_linear_register/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_linear_register -mri_linear_register_SOURCES=mri_linear_register.c -mri_linear_register_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_linear_register_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_log_likelihood/Makefile.am b/mri_log_likelihood/Makefile.am deleted file mode 100644 index 826e8141c68..00000000000 --- a/mri_log_likelihood/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_log_likelihood -mri_log_likelihood_SOURCES=mri_log_likelihood.c -mri_log_likelihood_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_log_likelihood_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_make_bem_surfaces/Makefile.am b/mri_make_bem_surfaces/Makefile.am deleted file mode 100644 index 08c7d7ca94f..00000000000 --- a/mri_make_bem_surfaces/Makefile.am +++ /dev/null @@ -1,18 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mri_make_bem_surfaces -mri_make_bem_surfaces_SOURCES=mri_make_bem_surfaces.c ../utils/machine.c -# cyclic dependency between rgb and utils on swapInt etc. -mri_make_bem_surfaces_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_make_bem_surfaces_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_make_density_map/Makefile.am b/mri_make_density_map/Makefile.am deleted file mode 100644 index f56077f775b..00000000000 --- a/mri_make_density_map/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mri_make_density_map -mri_make_density_map_SOURCES=mri_make_density_map.c -mri_make_density_map_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_make_density_map_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_make_labels/Makefile.am b/mri_make_labels/Makefile.am deleted file mode 100644 index f4e78b83f5f..00000000000 --- a/mri_make_labels/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_make_labels -mri_make_labels_SOURCES=mri_make_labels.c -mri_make_labels_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_make_labels_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_make_register/Makefile.am b/mri_make_register/Makefile.am deleted file mode 100644 index 0bf2fec0b4c..00000000000 --- a/mri_make_register/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_make_register -mri_make_register_SOURCES=mri_make_register.c -mri_make_register_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_make_register_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_make_template/Makefile.am b/mri_make_template/Makefile.am deleted file mode 100644 index 965c05268da..00000000000 --- a/mri_make_template/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_make_template -mri_make_template_SOURCES=mri_make_template.c -mri_make_template_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_make_template_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_map_cpdat/Makefile.am b/mri_map_cpdat/Makefile.am deleted file mode 100644 index 4f1fa9cacb7..00000000000 --- a/mri_map_cpdat/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_map_cpdat -mri_map_cpdat_SOURCES=mri_map_cpdat.cpp -mri_map_cpdat_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_map_cpdat_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_mark_temporal_lobe/Makefile.am b/mri_mark_temporal_lobe/Makefile.am deleted file mode 100644 index b29605ac7fb..00000000000 --- a/mri_mark_temporal_lobe/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_mark_temporal_lobe -mri_mark_temporal_lobe_SOURCES=mri_mark_temporal_lobe.c -mri_mark_temporal_lobe_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_mark_temporal_lobe_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_mask/Makefile.am b/mri_mask/Makefile.am deleted file mode 100644 index 12b0dfd51aa..00000000000 --- a/mri_mask/Makefile.am +++ /dev/null @@ -1,44 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mri_mask - -mri_mask_SOURCES=mri_mask.c mri_mask.help.xml.h -mri_mask_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_mask_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mri_mask.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mri_mask.help.xml.html - -TESTS=$(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=$(foo_DATA) $(BUILT_SOURCES) - -# mri_mask is called by Eugenios hippocampal subfield binaries. -# Mac OSX systems 10.11 (El Capitan) and greater implemented SIP -# which necessitates a wrapper script to all binaries called by other binaries -# in order to pass the DYLD_LIBRARY_PATH env var. - -install-exec-hook: - cp $(top_builddir)/mri_mask/mri_mask $(DESTDIR)$(bindir)/mri_mask.bin - echo "#!/bin/bash" > $(DESTDIR)$(bindir)/mri_mask - echo "source \$$FREESURFER_HOME/sources.sh" >> $(DESTDIR)$(bindir)/mri_mask - echo "mri_mask.bin \"\$$@\"" >> $(DESTDIR)$(bindir)/mri_mask - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mri_mask.help.xml.h mri_mask.help.xml.html - diff --git a/mri_matrix_multiply/Makefile.am b/mri_matrix_multiply/Makefile.am deleted file mode 100644 index 6a22189eaa6..00000000000 --- a/mri_matrix_multiply/Makefile.am +++ /dev/null @@ -1,21 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_matrix_multiply -mri_matrix_multiply_SOURCES=mri_matrix_multiply.c -mri_matrix_multiply_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_matrix_multiply_LDFLAGS=$(OS_LDFLAGS) - -TESTS=test.py - -EXTRA_DIST= test.py - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_mc/Makefile.am b/mri_mc/Makefile.am deleted file mode 100644 index be9db32a2ac..00000000000 --- a/mri_mc/Makefile.am +++ /dev/null @@ -1,52 +0,0 @@ -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_mc mri_pretess mris_extract_main_component - -mri_mc_SOURCES=mri_mc.c -mri_mc_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) - -foodir=$(prefix)/docs/xml -foo_DATA=mri_pretess.help.xml mris_extract_main_component.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mri_pretess.help.xml.html mris_extract_main_component.help.xml.html - -# trick to get test data into build dir -foo_SOURCES= -foo: - if ! test -f "$(top_builddir)/mri_mc/test_volume_reference.mgz"; then \ - cp -v $(top_srcdir)/mri_mc/test_volume_reference.mgz \ - $(top_builddir)/mri_mc/; fi; - -check_PROGRAMS=foo build_test_volume -#build_MC_table - -TESTS=test.py compare_test_volumes $(top_builddir)/scripts/help_xml_validate - -build_test_volume_SOURCES=build_test_volume.c -build_test_volume_LDADD=$(addprefix $(top_builddir)/, $(LIBS_MGH)) - -mri_pretess_SOURCES=mri_pretess.c mri_pretess.help.xml.h -mri_pretess_LDADD=$(addprefix $(top_builddir)/, $(LIBS_MGH)) - -mris_extract_main_component_SOURCES=mris_extract_main_component.c \ - mris_extract_main_component.help.xml.h -mris_extract_main_component_LDADD=$(addprefix $(top_builddir)/, $(LIBS_MGH)) - -#build_MC_table_SOURCES=build_MC_table.c -#build_MC_table_LDADD=$(addprefix $(top_builddir)/, $(LIBS_MGH)) - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=test.py compare_test_volumes test_volume_reference.mgz $(foo_DATA) \ - build_MC_table.c mc_table.gif $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mri_pretess.help.xml.h mris_extract_main_component.help.xml.h \ - mri_pretess.help.xml.html mris_extract_main_component.help.xml.html diff --git a/mri_mcsim/Makefile.am b/mri_mcsim/Makefile.am deleted file mode 100644 index f876580580c..00000000000 --- a/mri_mcsim/Makefile.am +++ /dev/null @@ -1,14 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_mcsim -mri_mcsim_SOURCES=mri_mcsim.c -mri_mcsim_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_mcsim_LDFLAGS=$(OS_LDFLAGS) - -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_mi/Makefile.am b/mri_mi/Makefile.am deleted file mode 100644 index 7f82fb731e7..00000000000 --- a/mri_mi/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_mi -mri_mi_SOURCES=mri_mi.c -mri_mi_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_mi_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_modify/Makefile.am b/mri_modify/Makefile.am deleted file mode 100644 index 19cf4f43138..00000000000 --- a/mri_modify/Makefile.am +++ /dev/null @@ -1,21 +0,0 @@ -## -## Makefile.am -## - -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_modify mri_copy_params -mri_modify_SOURCES=mri_modify.cpp -mri_modify_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_modify_LDFLAGS=$(OS_LDFLAGS) - -mri_copy_params_SOURCES=mri_copy_params.cpp -mri_copy_params_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_copy_params_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_morphology/Makefile.am b/mri_morphology/Makefile.am deleted file mode 100644 index 85384230f13..00000000000 --- a/mri_morphology/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mri_morphology -mri_morphology_SOURCES=mri_morphology.c -mri_morphology_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_morphology_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_mosaic/Makefile.am b/mri_mosaic/Makefile.am deleted file mode 100644 index a1568ba954c..00000000000 --- a/mri_mosaic/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_mosaic -mri_mosaic_SOURCES=mri_mosaic.c -mri_mosaic_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_mosaic_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_ms_EM/Makefile.am b/mri_ms_EM/Makefile.am deleted file mode 100644 index f7deb018882..00000000000 --- a/mri_ms_EM/Makefile.am +++ /dev/null @@ -1,18 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mri_ms_EM -mri_ms_EM_SOURCES=mri_ms_EM.c \ - PoissonSolver.c PoissonSolver.h -mri_ms_EM_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_ms_EM_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_ms_EM_with_atlas/Makefile.am b/mri_ms_EM_with_atlas/Makefile.am deleted file mode 100644 index b7e92462ede..00000000000 --- a/mri_ms_EM_with_atlas/Makefile.am +++ /dev/null @@ -1,18 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mri_ms_EM_with_atlas -mri_ms_EM_with_atlas_SOURCES=mri_ms_EM_with_atlas.c \ - PoissonSolver.c PoissonSolver.h -mri_ms_EM_with_atlas_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_ms_EM_with_atlas_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_ms_LDA/Makefile.am b/mri_ms_LDA/Makefile.am deleted file mode 100644 index d0ba9916ba3..00000000000 --- a/mri_ms_LDA/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mri_ms_LDA -mri_ms_LDA_SOURCES=mri_ms_LDA.c -mri_ms_LDA_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_ms_LDA_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_ms_fitparms/Makefile.am b/mri_ms_fitparms/Makefile.am deleted file mode 100644 index a63df0b7870..00000000000 --- a/mri_ms_fitparms/Makefile.am +++ /dev/null @@ -1,31 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mri_ms_fitparms -mri_ms_fitparms_SOURCES=mri_ms_fitparms.c mri_ms_fitparms.help.xml.h -mri_ms_fitparms_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_ms_fitparms_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mri_ms_fitparms.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mri_ms_fitparms.help.xml.html - -TESTS=$(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=$(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mri_ms_fitparms.help.xml.h mri_ms_fitparms.help.xml.html diff --git a/mri_multiscale_segment/Makefile.am b/mri_multiscale_segment/Makefile.am deleted file mode 100644 index d8fc30b031b..00000000000 --- a/mri_multiscale_segment/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_multiscale_segment -mri_multiscale_segment_SOURCES=mri_multiscale_segment.c -mri_multiscale_segment_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_multiscale_segment_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_multispectral_segment/Makefile.am b/mri_multispectral_segment/Makefile.am deleted file mode 100644 index 99e8570c326..00000000000 --- a/mri_multispectral_segment/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mri_multispectral_segment -mri_multispectral_segment_SOURCES=mri_multispectral_segment.c -mri_multispectral_segment_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_multispectral_segment_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_nlfilter/Makefile.am b/mri_nlfilter/Makefile.am deleted file mode 100644 index aff4f576ae9..00000000000 --- a/mri_nlfilter/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_nlfilter -mri_nlfilter_SOURCES=mri_nlfilter.c -mri_nlfilter_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_nlfilter_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_normalize/Makefile.am b/mri_normalize/Makefile.am deleted file mode 100644 index 25b010dd2af..00000000000 --- a/mri_normalize/Makefile.am +++ /dev/null @@ -1,35 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mri_normalize mri_long_normalize -mri_normalize_SOURCES=mri_normalize.c mri_normalize.help.xml.h -mri_normalize_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_normalize_LDFLAGS=$(OS_LDFLAGS) - -mri_long_normalize_SOURCES=mri_long_normalize.c mri_long_normalize.help.xml.h -mri_long_normalize_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_long_normalize_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mri_normalize.help.xml mri_long_normalize.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mri_normalize.help.xml.html mri_long_normalize.help.xml.html - -TESTS=test.py $(top_builddir)/scripts/help_xml_validate - -EXTRA_DIST=test.py testdata.tar.gz $(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mri_normalize.help.xml.h mri_normalize.help.xml.html mri_long_normalize.help.xml.h mri_long_normalize.help.xml.html - -clean-local: - rm -f $(BUILT_SOURCES) diff --git a/mri_normalize_tp2/Makefile.am b/mri_normalize_tp2/Makefile.am deleted file mode 100644 index fd7a66d6982..00000000000 --- a/mri_normalize_tp2/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mri_normalize_tp2 -mri_normalize_tp2_SOURCES=mri_normalize_tp2.c -mri_normalize_tp2_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_normalize_tp2_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_otl/Makefile.am b/mri_otl/Makefile.am deleted file mode 100644 index 5611ac0a11f..00000000000 --- a/mri_otl/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = list_otl_labels -list_otl_labels_SOURCES= list_otl_labels.c -list_otl_labels_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -list_otl_labels_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_paint/Makefile.am b/mri_paint/Makefile.am deleted file mode 100644 index d1b181aa8ef..00000000000 --- a/mri_paint/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_paint -mri_paint_SOURCES=mri_paint.c -mri_paint_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_paint_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_parse_sdcmdir/Makefile.am b/mri_parse_sdcmdir/Makefile.am deleted file mode 100644 index e6b028de915..00000000000 --- a/mri_parse_sdcmdir/Makefile.am +++ /dev/null @@ -1,31 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS=mri_parse_sdcmdir -mri_parse_sdcmdir_SOURCES=mri_parse_sdcmdir.c -mri_parse_sdcmdir_LDADD=$(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_parse_sdcmdir_LDFLAGS=$(OS_LDFLAGS) - -# trick to get test data into build dir -foo_SOURCES= -foo: - if ! test -f "$(top_builddir)/mri_parse_sdcmdir/98915109"; then \ - cp -v $(top_srcdir)/mri_parse_sdcmdir/98915109 \ - $(top_srcdir)/mri_parse_sdcmdir/test_dicomdir.sumfile \ - $(top_builddir)/mri_parse_sdcmdir/; fi; - -check_PROGRAMS=foo - -TESTS=test_mri_parse_sdcmdir - -EXTRA_DIST=test_mri_parse_sdcmdir 98915109 test_dicomdir.sumfile - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_parselabel/Makefile.am b/mri_parselabel/Makefile.am deleted file mode 100644 index 8c252ac10a7..00000000000 --- a/mri_parselabel/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_parselabel -mri_parselabel_SOURCES=mri_parselabel.cpp -mri_parselabel_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_parselabel_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_partial_ribbon/Makefile.am b/mri_partial_ribbon/Makefile.am deleted file mode 100644 index 7e4e01ff60d..00000000000 --- a/mri_partial_ribbon/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_partial_ribbon -mri_partial_ribbon_SOURCES=mri_partial_ribbon.c -mri_partial_ribbon_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_partial_ribbon_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_path2label/Makefile.am b/mri_path2label/Makefile.am deleted file mode 100644 index 7c8ca89c3f0..00000000000 --- a/mri_path2label/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mri_path2label -mri_path2label_SOURCES=mri_path2label.c -mri_path2label_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_path2label_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_polv/Makefile.am b/mri_polv/Makefile.am deleted file mode 100644 index 7eb1e6b1e39..00000000000 --- a/mri_polv/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_polv -mri_polv_SOURCES=mri_polv.c -mri_polv_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_polv_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_probe_ima/Makefile.am b/mri_probe_ima/Makefile.am deleted file mode 100644 index 69b522a9444..00000000000 --- a/mri_probe_ima/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_probe_ima -mri_probe_ima_SOURCES=mri_probe_ima.c -mri_probe_ima_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_probe_ima_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_probedicom/Makefile.am b/mri_probedicom/Makefile.am deleted file mode 100644 index c5339e92dda..00000000000 --- a/mri_probedicom/Makefile.am +++ /dev/null @@ -1,33 +0,0 @@ -## -# Makefile.am -## - -AM_LDFLAGS= - -if HAVE_OPENGL_LIBS -AM_CFLAGS=-I$(top_srcdir)/glut $(GL_CFLAGS) \ - -I$(top_srcdir)/include \ - -I$(top_srcdir)/include/dicom \ - -DHAVE_OPENGL - -bin_PROGRAMS = mri_probedicom -mri_probedicom_SOURCES=mri_probedicom.c -mri_probedicom_LDADD=$(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(LIBS_OPENGL) $(top_builddir)/glut/libglut.a $(X_LIBS) -mri_probedicom_LDFLAGS= -else -# built w/o image rendering portion -AM_CFLAGS=-I$(top_srcdir)/include \ - -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mri_probedicom -mri_probedicom_SOURCES=mri_probedicom.c -mri_probedicom_LDADD=$(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_probedicom_LDFLAGS= -endif - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_rbvpvc/Makefile.am b/mri_rbvpvc/Makefile.am deleted file mode 100644 index 2b4324fde82..00000000000 --- a/mri_rbvpvc/Makefile.am +++ /dev/null @@ -1,14 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_rbvpvc -mri_rbvpvc_SOURCES=mri_rbvpvc.c -mri_rbvpvc_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_rbvpvc_LDFLAGS=$(OS_LDFLAGS) - -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_reduce/Makefile.am b/mri_reduce/Makefile.am deleted file mode 100644 index 9c345425198..00000000000 --- a/mri_reduce/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_reduce -mri_reduce_SOURCES=mri_reduce.c -mri_reduce_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_reduce_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_register/Makefile.am b/mri_register/Makefile.am deleted file mode 100644 index ab18006b428..00000000000 --- a/mri_register/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_register -mri_register_SOURCES=mri_register.c -mri_register_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_register_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_relabel_hypointensities/Makefile.am b/mri_relabel_hypointensities/Makefile.am deleted file mode 100644 index 7ff1bf89448..00000000000 --- a/mri_relabel_hypointensities/Makefile.am +++ /dev/null @@ -1,24 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_relabel_hypointensities -mri_relabel_hypointensities_SOURCES=mri_relabel_hypointensities.c -mri_relabel_hypointensities_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_relabel_hypointensities_LDFLAGS=$(OS_LDFLAGS) - -# TESTS=test.py test_mri_relabel_hypointensities -TESTS=test.py - -# EXTRA_DIST=test.py test_mri_relabel_hypointensities testdata.tar.gz $(foo_DATA) $(BUILT_SOURCES) -EXTRA_DIST=test.py testdata.tar.gz $(foo_DATA) $(BUILT_SOURCES) - - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_relabel_nonwm_hypos/Makefile.am b/mri_relabel_nonwm_hypos/Makefile.am deleted file mode 100644 index e4e1efd9f6f..00000000000 --- a/mri_relabel_nonwm_hypos/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_relabel_nonwm_hypos -mri_relabel_nonwm_hypos_SOURCES=mri_relabel_nonwm_hypos.c -mri_relabel_nonwm_hypos_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_relabel_nonwm_hypos_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_remove_neck/Makefile.am b/mri_remove_neck/Makefile.am deleted file mode 100644 index f17c4abe6d8..00000000000 --- a/mri_remove_neck/Makefile.am +++ /dev/null @@ -1,31 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_remove_neck -mri_remove_neck_SOURCES=mri_remove_neck.c -mri_remove_neck_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_remove_neck_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mri_remove_neck.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mri_remove_neck.help.xml.html - -TESTS=$(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=$(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mri_remove_neck.help.xml.h mri_remove_neck.help.xml.html diff --git a/mri_rf_label/Makefile.am b/mri_rf_label/Makefile.am deleted file mode 100644 index 60690fdd014..00000000000 --- a/mri_rf_label/Makefile.am +++ /dev/null @@ -1,31 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_rf_label -mri_rf_label_SOURCES=mri_rf_label.c mri_rf_label.help.xml.h -mri_rf_label_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_rf_label_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mri_rf_label.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mri_rf_label.help.xml.html - -TESTS=$(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=$(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mri_rf_label.help.xml.h mri_rf_label.help.xml.html diff --git a/mri_rf_long_label/Makefile.am b/mri_rf_long_label/Makefile.am deleted file mode 100644 index acbe3b41704..00000000000 --- a/mri_rf_long_label/Makefile.am +++ /dev/null @@ -1,33 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_rf_long_label -#mri_rf_long_label_SOURCES=mri_rf_long_label.c mri_rf_long_label.help.xml.h -mri_rf_long_label_SOURCES=mri_rf_long_label.c -mri_rf_long_label_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_rf_long_label_LDFLAGS=$(OS_LDFLAGS) - -#foodir=$(prefix)/docs/xml -#foo_DATA=mri_rf_long_label.help.xml -#foo2dir=$(prefix)/docs/html -#foo2_DATA=mri_rf_long_label.help.xml.html - -#TESTS=$(top_builddir)/scripts/help_xml_validate -TESTS= - -#EXTRA_DIST=$(foo_DATA) $(BUILT_SOURCES) -EXTRA_DIST=$(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -#BUILT_SOURCES=mri_rf_long_label.help.xml.h mri_rf_long_label.help.xml.html -#clean-local: -# rm -f $(BUILT_SOURCES) \ No newline at end of file diff --git a/mri_rf_long_train/Makefile.am b/mri_rf_long_train/Makefile.am deleted file mode 100644 index aa7c049fda3..00000000000 --- a/mri_rf_long_train/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_rf_long_train -mri_rf_long_train_SOURCES=mri_rf_long_train.c -mri_rf_long_train_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_rf_long_train_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_rf_train/Makefile.am b/mri_rf_train/Makefile.am deleted file mode 100644 index 0834c2efb9b..00000000000 --- a/mri_rf_train/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_rf_train -mri_rf_train_SOURCES=mri_rf_train.c -mri_rf_train_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_rf_train_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_ribbon/Makefile.am b/mri_ribbon/Makefile.am deleted file mode 100644 index e9bbf4e295a..00000000000 --- a/mri_ribbon/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mri_ribbon -mri_ribbon_SOURCES=mri_ribbon.c -mri_ribbon_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_ribbon_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_rigid_register/Makefile.am b/mri_rigid_register/Makefile.am deleted file mode 100644 index 02ac15bd194..00000000000 --- a/mri_rigid_register/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_rigid_register -mri_rigid_register_SOURCES=mri_rigid_register.c -mri_rigid_register_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_rigid_register_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_robust_register/Makefile.am b/mri_robust_register/Makefile.am deleted file mode 100644 index cfd459ac3ab..00000000000 --- a/mri_robust_register/Makefile.am +++ /dev/null @@ -1,99 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include $(VXL_CFLAGS) - -if HAVE_MAC_OSX -OTHERLDFLAGS=-framework Accelerate -else -OTHERLDFLAGS=-z muldefs -endif - -BUILT_SOURCES=mri_robust_template.help.xml.h \ - mri_robust_template.help.xml.html \ - mri_robust_register.help.xml.h \ - mri_robust_register.help.xml.html \ - lta_diff.help.xml.h \ - lta_diff.help.xml.html - -foodir=$(prefix)/docs/xml -foo_DATA=mri_robust_template.help.xml mri_robust_register.help.xml lta_diff.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mri_robust_template.help.xml.html mri_robust_register.help.xml.html lta_diff.help.xml.html - -bin_PROGRAMS = mri_robust_register \ - mri_robust_template \ - lta_diff \ - mri_create_tests \ - mri_gradient_info - -mri_robust_register_SOURCES= JointHisto.cpp \ - CostFunctions.cpp MyMatrix.cpp MyMRI.cpp \ - Quaternion.cpp Registration.cpp RegRobust.cpp RegPowell.cpp \ - mri_robust_register.cpp mri_robust_register.help.xml.h -mri_robust_register_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(LIB_LAPACK) $(LIB_BLAS) $(LIB_G2C_A) $(LIB_GFORTRAN) -mri_robust_register_LDFLAGS=$(OS_LDFLAGS) $(OTHERLDFLAGS) - -mri_robust_template_SOURCES= Registration.cpp RegRobust.cpp \ - CostFunctions.cpp MyMatrix.cpp MyMRI.cpp Quaternion.cpp \ - MultiRegistration.cpp mri_robust_template.cpp mri_robust_template.help.xml.h -mri_robust_template_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(LIB_LAPACK) $(LIB_BLAS) $(LIB_G2C_A) $(LIB_GFORTRAN) -mri_robust_template_LDFLAGS=$(OS_LDFLAGS) $(OTHERLDFLAGS) - -lta_diff_SOURCES=lta_diff.help.xml.h lta_diff.cpp Registration.cpp \ - CostFunctions.cpp MyMatrix.cpp MyMRI.cpp Quaternion.cpp -lta_diff_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(LIB_LAPACK) $(LIB_BLAS) $(LIB_G2C_A) $(LIB_GFORTRAN) -lta_diff_LDFLAGS=$(OS_LDFLAGS) $(OTHERLDFLAGS) - -mri_create_tests_SOURCES=mri_create_tests.cpp Quaternion.cpp \ - MyMatrix.cpp MyMRI.cpp CostFunctions.cpp -mri_create_tests_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(LIB_LAPACK) $(LIB_BLAS) $(LIB_G2C_A) $(LIB_GFORTRAN) -mri_create_tests_LDFLAGS=$(OS_LDFLAGS) $(OTHERLDFLAGS) - -mri_gradient_info_SOURCES=mri_gradient_info.cpp -mri_gradient_info_LDADD = $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_gradient_info_LDFLAGS=$(OS_LDFLAGS) $(OTHERLDFLAGS) - -# trick to get test data into the build directory -foo_SOURCES= -foo: - if ! test -f "$(top_builddir)/mri_robust_register/testdata.tar.gz"; then \ - cp -v $(top_srcdir)/mri_robust_register/testdata.tar.gz \ - $(top_builddir)/mri_robust_register/; fi; - -check_PROGRAMS=foo - -TESTS=test_libgfortran test_mri_robust_template $(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=Regression.h Regression.cpp Registration.h RegistrationStep.h \ - MultiRegistration.h Quaternion.h RobustGaussian.cpp RegPowell.cpp \ - CostFunctions.h RobustGaussian.h RegPowell.h MyMatrix.h MyMRI.h \ - testdata.tar.gz $(foo_DATA) Registration.cpp test_mri_robust_template \ - $(BUILT_SOURCES) JointHisto.h RegRobust.h Transformation.h test_libgfortran - -# mri_robust_register is called by Eugenios hippocampal subfield binaries. -# Mac OSX systems 10.11 (El Capitan) and greater implemented SIP -# which necessitates a wrapper script to all binaries called by other binaries -# in order to pass the DYLD_LIBRARY_PATH env var. - -install-exec-hook: - cp $(top_builddir)/mri_robust_register/mri_robust_register $(DESTDIR)$(bindir)/mri_robust_register.bin - echo "#!/bin/bash" > $(DESTDIR)$(bindir)/mri_robust_register - echo "source \$$FREESURFER_HOME/sources.sh" >> $(DESTDIR)$(bindir)/mri_robust_register - echo "mri_robust_register.bin \"\$$@\"" >> $(DESTDIR)$(bindir)/mri_robust_register - - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_sbbr/Makefile.am b/mri_sbbr/Makefile.am deleted file mode 100644 index 1a10d211f82..00000000000 --- a/mri_sbbr/Makefile.am +++ /dev/null @@ -1,69 +0,0 @@ -## -## Makefile.am -## - -####################################################################### -# When you create your own program directory, copy the 'from' to the -# 'to' lines to your Makefile.am and change mri_sbbr to your program name. -# -# 0. mkdir dev/yourdir and put .c file in there -# 1. modify dev/configure.in to have yourdir/Makefile -# 2. modify dev/Makefile.am to have yourdir as one of SUBDIRS -# 3. create dev/yourdir/Makefile.am (follow dummy/Makefile.am) -# i.e. replace dummy with your program name. -# -# 4. ./setup_configure at the top directory, i.e. dev/ (which will create -# Makefile.in in yourdir directory and configure from configure.in) -# 5. ./configure .... and make to make sure that your new thing is working -# 6. try make to make sure that yourthing is compiled. -# -# After confirming everything working: -# 7. checkin yourdir/Makefile.am, yourdir/yourprog.c or cpp. -# (Don't checkin Makefile or Makefile.in.) -# 8. commit dev/configure.in, dev/Makefile.am -# -# 9. lastly, delete this help text from your own Makefile.am! -# -# If you have problems, please let us know (zkaufman@nmr.mgh.harvard.edu -# or nicks@nmr.mgh.harvard.edu). -######################################################################### -# from ------------------------------------------------ - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_sbbr -mri_sbbr_SOURCES=mri_sbbr.c -mri_sbbr_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_sbbr_LDFLAGS=$(OS_LDFLAGS) - -# to -------------------------------------------------- -# -# Where $(OS_LDFLAGS) is to compile programs statically for Linux. -# -# You can have multiple bin_PROGRAMS in the same directory. -# -######################################################################## -# When you want to create your program to test, use the following -# framework: -# You can have as many programs (separated by space) in check_PROGRAMS. -# Your program can consist of many sources (you add to _SOURCES= line). -# You can do "make myown" to compile. The default CFLAGS="-g -O2", but -# you can do "make CFLAGS=-g myown" to create a debugging version. -# -# The program listed as check_PROGRAMS are not compiled under standard -# "make". Only "make check" will compile them. See mri_convert's -# Makefile.am for an example of its 'make check' test setup. -# -# Please don't remove myown.c from this dummy directory. -######################################################################## -#check_PROGRAMS=myown - -#myown_SOURCES=myown.c -#myown_LDADD=$(addprefix $(top_builddir)/, $(LIBS_MGH)) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_seg_diff/Makefile.am b/mri_seg_diff/Makefile.am deleted file mode 100644 index 581bbc53b41..00000000000 --- a/mri_seg_diff/Makefile.am +++ /dev/null @@ -1,18 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_seg_diff -mri_seg_diff_SOURCES=mri_seg_diff.c -mri_seg_diff_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_seg_diff_LDFLAGS=$(OS_LDFLAGS) - -TESTS=test.py - -EXTRA_DIST= test.py - -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_segcentroids/Makefile.am b/mri_segcentroids/Makefile.am deleted file mode 100644 index a40af273b7b..00000000000 --- a/mri_segcentroids/Makefile.am +++ /dev/null @@ -1,30 +0,0 @@ -## -## Makefile.am -## - -#AM_CXXFLAGS=-std=c++11 -I$(top_srcdir)/include -D$(target_cpu) -AM_CXXFLAGS=-std=c++0x -I$(top_srcdir)/include -D$(target_cpu) -AM_LDFLAGS= - -bin_PROGRAMS=mri_segcentroids - -mri_segcentroids_SOURCES=mri_segcentroids.cpp mri_segcentroids.help.xml.h -mri_segcentroids_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_segcentroids_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mri_segcentroids.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mri_segcentroids.help.xml.html - -TESTS=$(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=$(foo_DATA) $(BUILT_SOURCES) - -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mri_segcentroids.help.xml.h mri_segcentroids.help.xml.html diff --git a/mri_seghead/Makefile.am b/mri_seghead/Makefile.am deleted file mode 100644 index 4c3bcbf6416..00000000000 --- a/mri_seghead/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_seghead -mri_seghead_SOURCES=mri_seghead.c -mri_seghead_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_seghead_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_segment/Makefile.am b/mri_segment/Makefile.am deleted file mode 100644 index 4f4ebc47dcd..00000000000 --- a/mri_segment/Makefile.am +++ /dev/null @@ -1,33 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mri_segment - -mri_segment_SOURCES=mri_segment.c mri_segment.help.xml.h -mri_segment_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_segment_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mri_segment.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mri_segment.help.xml.html - -TESTS=test.py $(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=test.py $(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mri_segment.help.xml.h mri_segment.help.xml.html - diff --git a/mri_segment_tumor/Makefile.am b/mri_segment_tumor/Makefile.am deleted file mode 100644 index c9b71c8262e..00000000000 --- a/mri_segment_tumor/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_segment_tumor -mri_segment_tumor_SOURCES=mri_segment_tumor.c -mri_segment_tumor_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_segment_tumor_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_segment_wm_damage/Makefile.am b/mri_segment_wm_damage/Makefile.am deleted file mode 100644 index 34b2643fab0..00000000000 --- a/mri_segment_wm_damage/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mri_segment_wm_damage -mri_segment_wm_damage_SOURCES=mri_segment_wm_damage.c -mri_segment_wm_damage_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_segment_wm_damage_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_segreg/Makefile.am b/mri_segreg/Makefile.am deleted file mode 100644 index 2786a4e20e0..00000000000 --- a/mri_segreg/Makefile.am +++ /dev/null @@ -1,16 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_segreg -mri_segreg_SOURCES=mri_segreg.c -mri_segreg_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_segreg_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_segstats/Makefile.am b/mri_segstats/Makefile.am deleted file mode 100644 index 4b23d55bfb5..00000000000 --- a/mri_segstats/Makefile.am +++ /dev/null @@ -1,69 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_segstats - -mri_segstats_SOURCES=mri_segstats.c mri_segstats.help.xml.h -mri_segstats_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_segstats_LDFLAGS=$(OS_LDFLAGS) - - -## ---- -## CUDA -## ---- - -# BUILDCUDA is defined if configure.in finds CUDA -if BUILDCUDA - -# rules for building cuda files -.cu.o: - $(NVCC) -o $@ -c $< $(NVCCFLAGS) $(CUDA_CFLAGS) $(AM_CFLAGS) $(MNI_CFLAGS) - -bin_PROGRAMS += mri_segstats_cuda - -mri_segstats_cuda_SOURCES = mri_segstats.c -mri_segstats_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -mri_segstats_cuda_CXXFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -mri_segstats_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) -mri_segstats_cuda_LDFLAGS = $(OS_LDFLAGS) -mri_segstats_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(mri_segstats_cuda_CFLAGS) \ - $(CFLAGS) $(mri_segstats_cuda_LDFLAGS) $(LDFLAGS) -o $@ - -endif -# endif BUILDCUDA - - -foodir=$(prefix)/docs/xml -foo_DATA=mri_segstats.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mri_segstats.help.xml.html - -# trick to get test data into the build directory -foo_SOURCES= -foo: - if ! test -f "$(top_builddir)/mri_segstats/testdata.tar.gz"; then \ - cp -v $(top_srcdir)/mri_segstats/testdata.tar.gz \ - $(top_builddir)/mri_segstats/; fi; - -check_PROGRAMS=foo - -TESTS=test_mri_segstats $(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=test_mri_segstats testdata.tar.gz $(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mri_segstats.help.xml.h mri_segstats.help.xml.html - diff --git a/mri_simulate_atrophy/Makefile.am b/mri_simulate_atrophy/Makefile.am deleted file mode 100644 index 33305a085e5..00000000000 --- a/mri_simulate_atrophy/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_simulate_atrophy -mri_simulate_atrophy_SOURCES=mri_simulate_atrophy.c -mri_simulate_atrophy_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_simulate_atrophy_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_stats2seg/Makefile.am b/mri_stats2seg/Makefile.am deleted file mode 100644 index 40c17cbd520..00000000000 --- a/mri_stats2seg/Makefile.am +++ /dev/null @@ -1,14 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mri_stats2seg -mri_stats2seg_SOURCES=mri_stats2seg.c $(top_srcdir)/fsgdf/fsgdf.c -mri_stats2seg_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_stats2seg_LDFLAGS=$(OS_LDFLAGS) - -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_strip_nonwhite/Makefile.am b/mri_strip_nonwhite/Makefile.am deleted file mode 100644 index 19df69abaaf..00000000000 --- a/mri_strip_nonwhite/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_strip_nonwhite -mri_strip_nonwhite_SOURCES=mri_strip_nonwhite.c -mri_strip_nonwhite_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_strip_nonwhite_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_strip_subject_info/Makefile.am b/mri_strip_subject_info/Makefile.am deleted file mode 100644 index bb017c8ec38..00000000000 --- a/mri_strip_subject_info/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_strip_subject_info -mri_strip_subject_info_SOURCES=mri_strip_subject_info.c -mri_strip_subject_info_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_strip_subject_info_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_surf2surf/Makefile.am b/mri_surf2surf/Makefile.am deleted file mode 100644 index 3be5a512b72..00000000000 --- a/mri_surf2surf/Makefile.am +++ /dev/null @@ -1,21 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_surf2surf -mri_surf2surf_SOURCES=mri_surf2surf.c -mri_surf2surf_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_surf2surf_LDFLAGS=$(OS_LDFLAGS) - -TESTS=test.py - -EXTRA_DIST= test.py - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_surf2vol/Makefile.am b/mri_surf2vol/Makefile.am deleted file mode 100644 index a05ee878f29..00000000000 --- a/mri_surf2vol/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mri_surf2vol -mri_surf2vol_SOURCES=mri_surf2vol.c -mri_surf2vol_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_surf2vol_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_surfacemask/Makefile.am b/mri_surfacemask/Makefile.am deleted file mode 100644 index f9f9d83e8b1..00000000000 --- a/mri_surfacemask/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_surfacemask -mri_surfacemask_SOURCES=mri_surfacemask.cpp -mri_surfacemask_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_surfacemask_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_surfcluster/Makefile.am b/mri_surfcluster/Makefile.am deleted file mode 100644 index 87be6781176..00000000000 --- a/mri_surfcluster/Makefile.am +++ /dev/null @@ -1,27 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_surfcluster -mri_surfcluster_SOURCES=mri_surfcluster.c -mri_surfcluster_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_surfcluster_LDFLAGS=$(OS_LDFLAGS) - -# mri_surfcluster is called by qdec. On Mac OSX -# systems 10.11 (El Capitan) and greater implemented SIP -# which necessitates a wrapper script to pass the DYLD_LIBRARY_PATH env var. - -install-exec-hook: - cp $(top_builddir)/mri_surfcluster/mri_surfcluster $(DESTDIR)$(bindir)/mri_surfcluster.bin - echo "#!/bin/bash" > $(DESTDIR)$(bindir)/mri_surfcluster - echo "source \$$FREESURFER_HOME/sources.sh" >> $(DESTDIR)$(bindir)/mri_surfcluster - echo "mri_surfcluster.bin \"\$$@\"" >> $(DESTDIR)$(bindir)/mri_surfcluster - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_synthesize/Makefile.am b/mri_synthesize/Makefile.am deleted file mode 100644 index 796f8b8f7e1..00000000000 --- a/mri_synthesize/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_synthesize -mri_synthesize_SOURCES=mri_synthesize.c -mri_synthesize_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_synthesize_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_tessellate/Makefile.am b/mri_tessellate/Makefile.am deleted file mode 100644 index 2f6ad0c94ca..00000000000 --- a/mri_tessellate/Makefile.am +++ /dev/null @@ -1,35 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mri_tessellate ico_supersample -mri_tessellate_SOURCES=mri_tessellate.c mri_tessellate.help.xml.h -mri_tessellate_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_tessellate_LDFLAGS=$(OS_LDFLAGS) - -ico_supersample_SOURCES=ico_supersample.c trilib.h systemid.h -ico_supersample_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -ico_supersample_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mri_tessellate.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mri_tessellate.help.xml.html - -TESTS=$(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=$(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mri_tessellate.help.xml.h mri_tessellate.help.xml.html diff --git a/mri_threshold/Makefile.am b/mri_threshold/Makefile.am deleted file mode 100644 index 1dfa46511af..00000000000 --- a/mri_threshold/Makefile.am +++ /dev/null @@ -1,16 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mri_threshold -mri_threshold_SOURCES=mri_threshold.c -mri_threshold_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_threshold_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_topologycorrection/Makefile.am b/mri_topologycorrection/Makefile.am deleted file mode 100644 index 01933e67756..00000000000 --- a/mri_topologycorrection/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mri_topologycorrection -mri_topologycorrection_SOURCES=mri_topologycorrection.c -mri_topologycorrection_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_topologycorrection_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_train/Makefile.am b/mri_train/Makefile.am deleted file mode 100644 index 3bc5d9e9106..00000000000 --- a/mri_train/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_train -mri_train_SOURCES=mri_train.c -mri_train_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_train_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_train_autoencoder/Makefile.am b/mri_train_autoencoder/Makefile.am deleted file mode 100644 index 40c1cc05cb8..00000000000 --- a/mri_train_autoencoder/Makefile.am +++ /dev/null @@ -1,21 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_train_autoencoder mri_apply_autoencoder -mri_train_autoencoder_SOURCES=mri_train_autoencoder.c -mri_train_autoencoder_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_train_autoencoder_LDFLAGS=$(OS_LDFLAGS) - -mri_apply_autoencoder_SOURCES=mri_apply_autoencoder.c -mri_apply_autoencoder_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_apply_autoencoder_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_transform/Makefile.am b/mri_transform/Makefile.am deleted file mode 100644 index 6aad243308d..00000000000 --- a/mri_transform/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_transform -mri_transform_SOURCES=mri_transform.c -mri_transform_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_transform_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_transform_to_COR/Makefile.am b/mri_transform_to_COR/Makefile.am deleted file mode 100644 index 8bc95b69220..00000000000 --- a/mri_transform_to_COR/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mri_transform_to_COR -mri_transform_to_COR_SOURCES=mri_transform_to_COR.c -mri_transform_to_COR_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_transform_to_COR_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_twoclass/Makefile.am b/mri_twoclass/Makefile.am deleted file mode 100644 index 9a14554b3ee..00000000000 --- a/mri_twoclass/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_twoclass -mri_twoclass_SOURCES=mri_twoclass.c -mri_twoclass_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_twoclass_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_update_gca/Makefile.am b/mri_update_gca/Makefile.am deleted file mode 100644 index 2ccd0bafeb3..00000000000 --- a/mri_update_gca/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_update_gca -mri_update_gca_SOURCES=mri_update_gca.c -mri_update_gca_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_update_gca_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_vol2roi/Makefile.am b/mri_vol2roi/Makefile.am deleted file mode 100644 index 89202ca540a..00000000000 --- a/mri_vol2roi/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_vol2roi -mri_vol2roi_SOURCES=mri_vol2roi.c -mri_vol2roi_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_vol2roi_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_vol2surf/Makefile.am b/mri_vol2surf/Makefile.am deleted file mode 100644 index c49aaa83f89..00000000000 --- a/mri_vol2surf/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_vol2surf -mri_vol2surf_SOURCES=mri_vol2surf.c -mri_vol2surf_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_vol2surf_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_vol2vol/Makefile.am b/mri_vol2vol/Makefile.am deleted file mode 100644 index a23d320bdc8..00000000000 --- a/mri_vol2vol/Makefile.am +++ /dev/null @@ -1,51 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_vol2vol -mri_vol2vol_SOURCES=mri_vol2vol.c -mri_vol2vol_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_vol2vol_LDFLAGS=$(OS_LDFLAGS) - -# mri_vol2vol is called by qdec. On Mac OSX -# systems 10.11 (El Capitan) and greater implemented SIP -# which necessitates a wrapper script to pass the DYLD_LIBRARY_PATH env var. - -install-exec-hook: - cp $(top_builddir)/mri_vol2vol/mri_vol2vol $(DESTDIR)$(bindir)/mri_vol2vol.bin - echo "#!/bin/bash" > $(DESTDIR)$(bindir)/mri_vol2vol - echo "source \$$FREESURFER_HOME/sources.sh" >> $(DESTDIR)$(bindir)/mri_vol2vol - echo "mri_vol2vol.bin \"\$$@\"" >> $(DESTDIR)$(bindir)/mri_vol2vol - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - -## ---- -## CUDA -## ---- - -# BUILDCUDA is defined if configure.in finds CUDA -if BUILDCUDA - -# rules for building cuda files -.cu.o: - $(NVCC) -o $@ -c $< $(NVCCFLAGS) $(CUDA_CFLAGS) $(AM_CFLAGS) $(MNI_CFLAGS) - -bin_PROGRAMS += mri_vol2vol_cuda - -mri_vol2vol_cuda_SOURCES = mri_vol2vol.c - -mri_vol2vol_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -mri_vol2vol_cuda_CXXFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -mri_vol2vol_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) -mri_vol2vol_cuda_LDFLAGS = $(OS_LDFLAGS) -mri_vol2vol_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(mri_em_register_cuda_CFLAGS) \ - $(CFLAGS) $(mri_em_register_cuda_LDFLAGS) $(LDFLAGS) -o $@ - -endif diff --git a/mri_volcluster/Makefile.am b/mri_volcluster/Makefile.am deleted file mode 100644 index be7dfe7509f..00000000000 --- a/mri_volcluster/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_volcluster -mri_volcluster_SOURCES=mri_volcluster.c -mri_volcluster_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_volcluster_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_voldiff/Makefile.am b/mri_voldiff/Makefile.am deleted file mode 100644 index c2e555f8e73..00000000000 --- a/mri_voldiff/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mri_voldiff -mri_voldiff_SOURCES=mri_voldiff.c -mri_voldiff_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_voldiff_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_volsynth/Makefile.am b/mri_volsynth/Makefile.am deleted file mode 100644 index 54d3316f564..00000000000 --- a/mri_volsynth/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mri_volsynth -mri_volsynth_SOURCES=mri_volsynth.c -mri_volsynth_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_volsynth_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_warp_convert/Makefile.am b/mri_warp_convert/Makefile.am deleted file mode 100644 index 71fd3bbbc71..00000000000 --- a/mri_warp_convert/Makefile.am +++ /dev/null @@ -1,27 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -BUILT_SOURCES=mri_warp_convert.help.xml.h mri_warp_convert.help.xml.html - -foodir=$(prefix)/docs/xml -foo_DATA=mri_warp_convert.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mri_warp_convert.help.xml.html - -bin_PROGRAMS = mri_warp_convert -mri_warp_convert_SOURCES=mri_warp_convert.cpp -mri_warp_convert_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_warp_convert_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -clean-local: - rm -f $(BUILT_SOURCES) diff --git a/mri_watershed/Makefile.am b/mri_watershed/Makefile.am deleted file mode 100644 index e26cfee2e96..00000000000 --- a/mri_watershed/Makefile.am +++ /dev/null @@ -1,38 +0,0 @@ -## -## Makefile.am -## - -AM_CXXFLAGS=-I$(top_srcdir)/include -D$(target_cpu) -AM_LDFLAGS= - -bin_PROGRAMS = mri_watershed mri_validate_skull_stripped - -mri_watershed_SOURCES=mri_watershed.cpp mri_watershed.help.xml.h -mri_watershed_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_watershed_LDFLAGS=$(OS_LDFLAGS) - -mri_validate_skull_stripped_SOURCES=mri_validate_skull_stripped.cpp -mri_validate_skull_stripped_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_validate_skull_stripped_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mri_watershed.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mri_watershed.help.xml.html - -SUBDIRS=brain_volume - -TESTS=$(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=$(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mri_watershed.help.xml.h mri_watershed.help.xml.html diff --git a/mri_watershed/brain_volume/Makefile.am b/mri_watershed/brain_volume/Makefile.am deleted file mode 100644 index 56ce883581c..00000000000 --- a/mri_watershed/brain_volume/Makefile.am +++ /dev/null @@ -1,27 +0,0 @@ -## -## Makefile.am -## - -AM_CXXFLAGS=-I$(top_srcdir)/include -if USE_LOCAL_MINC -AM_CXXFLAGS+=-I$(top_srcdir)/netcdf_3_6_0_p1 -endif -AM_LDFLAGS= - -bin_PROGRAMS = mri_brain_volume -mri_brain_volume_SOURCES=mri_brain_volume.cpp mrivariables.h TVector.h -mri_brain_volume_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_brain_volume_LDFLAGS=$(OS_LDFLAGS) - -check_PROGRAMS = test -test_SOURCES=test.cpp TVector.h -test_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -test_LDFLAGS=$(OS_LDFLAGS) - -TESTS = test - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_wbc/Makefile.am b/mri_wbc/Makefile.am deleted file mode 100644 index 163b8c566f9..00000000000 --- a/mri_wbc/Makefile.am +++ /dev/null @@ -1,63 +0,0 @@ -## -## Makefile.am -## - -####################################################################### -# When you create your own program directory, copy the 'from' to the -# 'to' lines to your Makefile.am and change dummy to your program name. -# -# 0. mkdir dev/yourdir and put .c file in there -# 1. modify dev/configure.in to have yourdir/Makefile -# 2. modify dev/Makefile.am to have yourdir as one of SUBDIRS -# 3. create dev/yourdir/Makefile.am (follow dummy/Makefile.am) -# i.e. replace dummy with your program name. -# -# 4. ./setup_configure at the top directory, i.e. dev/ (which will create -# Makefile.in in yourdir directory and configure from configure.in) -# 5. ./configure .... and make to make sure that your new thing is working -# 6. try make to make sure that yourthing is compiled. -# -# After confirming everything working: -# 7. checkin yourdir/Makefile.am, yourdir/yourprog.c or cpp. -# (Don't checkin Makefile or Makefile.in.) -# 8. commit dev/configure.in, dev/Makefile.am -# -# 9. lastly, delete this help text from your own Makefile.am! -# -# If you have problems, please let us know (zkaufman@nmr.mgh.harvard.edu -# or nicks@nmr.mgh.harvard.edu). -######################################################################### -# from ------------------------------------------------ - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_wbc -mri_wbc_SOURCES=mri_wbc.c -mri_wbc_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_wbc_LDFLAGS=$(OS_LDFLAGS) - -# to -------------------------------------------------- -# -# Where $(OS_LDFLAGS) is to compile programs statically for Linux. -# -# You can have multiple bin_PROGRAMS in the same directory. -# -######################################################################## -# When you want to create your program to test, use the following -# framework: -# You can have as many programs (separated by space) in check_PROGRAMS. -# Your program can consist of many sources (you add to _SOURCES= line). -# You can do "make myown" to compile. The default CFLAGS="-g -O2", but -# you can do "make CFLAGS=-g myown" to create a debugging version. -# -# The program listed as check_PROGRAMS are not compiled under standard -# "make". Only "make check" will compile them. See mri_convert's -# Makefile.am for an example of its 'make check' test setup. -# - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_wmfilter/Makefile.am b/mri_wmfilter/Makefile.am deleted file mode 100644 index 3817852a638..00000000000 --- a/mri_wmfilter/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mri_wmfilter -mri_wmfilter_SOURCES=mri_wmfilter.c -mri_wmfilter_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_wmfilter_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_xcorr/Makefile.am b/mri_xcorr/Makefile.am deleted file mode 100644 index e8be7be6b10..00000000000 --- a/mri_xcorr/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mri_xcorr -mri_xcorr_SOURCES=mri_xcorr.c -mri_xcorr_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_xcorr_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mri_xvolavg/Makefile.am b/mri_xvolavg/Makefile.am deleted file mode 100644 index 5d1238f4719..00000000000 --- a/mri_xvolavg/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mri_xvolavg -mri_xvolavg_SOURCES=mri_xvolavg.c -mri_xvolavg_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_xvolavg_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mri_z2p/Makefile.am b/mri_z2p/Makefile.am deleted file mode 100644 index 57a799b5fd1..00000000000 --- a/mri_z2p/Makefile.am +++ /dev/null @@ -1,19 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mri_z2p -mri_z2p_SOURCES=mri_z2p.c -mri_z2p_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mri_z2p_LDFLAGS=$(OS_LDFLAGS) - -check_PROGRAMS= - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris2rgb/Makefile.am b/mris2rgb/Makefile.am deleted file mode 100644 index c504070ec41..00000000000 --- a/mris2rgb/Makefile.am +++ /dev/null @@ -1,37 +0,0 @@ -## -# Makefile.am -## - -if USE_LOCAL_TIFF -TIFFCFLAGS=-I$(top_srcdir)/tiff -LIBTIFF=$(top_builddir)/tiff/libtiff.a -else -TIFFCFLAGS=$(TIFF_CFLAGS) -LIBTIFF=$(LIB_TIFF) -endif - -AM_CPPFLAGS=\ - -I$(top_srcdir)/glut \ - -I$(top_srcdir)/include \ - -I$(top_srcdir)/dicom \ - -I$(top_srcdir)/unix \ - $(GL_CFLAGS) $(TIFFCFLAGS) - -AM_LDFLAGS=$(X_LIBS) $(TIFF_LIBS) - -if HAVE_OPENGL_LIBS -bin_PROGRAMS = mris2rgb -mris2rgb_SOURCES=mris2rgb.c -mris2rgb_LDADD= $(addprefix $(top_builddir)/,$(LIBS_MGH)) \ - $(LIBS_OPENGL) -lGL $(LIBTIFF) \ - $(top_builddir)/glut/libglut.a -mris2rgb_LDFLAGS= -else -bin_PROGRAMS= -endif - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_BA_segment/Makefile.am b/mris_BA_segment/Makefile.am deleted file mode 100644 index 8fee9eb5baa..00000000000 --- a/mris_BA_segment/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_BA_segment -mris_BA_segment_SOURCES=mris_BA_segment.c -mris_BA_segment_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_BA_segment_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_add_template/Makefile.am b/mris_add_template/Makefile.am deleted file mode 100644 index 8759fd564c5..00000000000 --- a/mris_add_template/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_add_template -mris_add_template_SOURCES=mris_add_template.c -mris_add_template_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_add_template_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_anatomical_stats/Makefile.am b/mris_anatomical_stats/Makefile.am deleted file mode 100644 index 7b4066378c2..00000000000 --- a/mris_anatomical_stats/Makefile.am +++ /dev/null @@ -1,51 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mris_anatomical_stats - -mris_anatomical_stats_SOURCES=mris_anatomical_stats.c \ - mris_anatomical_stats.help.xml.h -mris_anatomical_stats_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_anatomical_stats_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mris_anatomical_stats.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mris_anatomical_stats.help.xml.html - -# trick to get test data into build dir -foo_SOURCES= -foo: - if ! test -f "$(top_builddir)/mris_ca_label/testdata.tar.gz"; then \ - cp -v $(top_srcdir)/mris_ca_label/testdata.tar.gz \ - $(top_builddir)/mris_ca_label/; fi; - if ! test -f "$(top_builddir)/mris_anatomical_stats/test1.expected"; then \ - cp -v $(top_srcdir)/mris_anatomical_stats/*.expected \ - $(top_builddir)/mris_anatomical_stats/; fi; - -check_PROGRAMS=foo - -TESTS=test_mris_anatomical_stats $(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - rm -f mris_anatomical_stats *.o - rm -Rf testdata2 *.observed *.table *.out - -EXTRA_DIST=test_mris_anatomical_stats test1.expected test2.expected \ -test2_logfile.expected test3.expected test4.expected \ -test6.expected $(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mris_anatomical_stats.help.xml.h \ - mris_anatomical_stats.help.xml.html - diff --git a/mris_annot_to_segmentation/Makefile.am b/mris_annot_to_segmentation/Makefile.am deleted file mode 100644 index e27c5c98a2e..00000000000 --- a/mris_annot_to_segmentation/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_annot_to_segmentation -mris_annot_to_segmentation_SOURCES=mris_annot_to_segmentation.c -mris_annot_to_segmentation_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_annot_to_segmentation_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_apply_reg/Makefile.am b/mris_apply_reg/Makefile.am deleted file mode 100644 index 412fd184b9e..00000000000 --- a/mris_apply_reg/Makefile.am +++ /dev/null @@ -1,26 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_apply_reg -mris_apply_reg_SOURCES=mris_apply_reg.c mris_apply_reg.help.xml.h -mris_apply_reg_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_apply_reg_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mris_apply_reg.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mris_apply_reg.help.xml.html - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=$(foo_DATA) $(BUILT_SOURCES) - -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mris_apply_reg.help.xml.h mris_apply_reg.help.xml.html diff --git a/mris_aseg_distance/Makefile.am b/mris_aseg_distance/Makefile.am deleted file mode 100644 index 12beeb89daf..00000000000 --- a/mris_aseg_distance/Makefile.am +++ /dev/null @@ -1,14 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_aseg_distance -mris_aseg_distance_SOURCES=mris_aseg_distance.c -mris_aseg_distance_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_aseg_distance_LDFLAGS=$(OS_LDFLAGS) - -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_average_curvature/Makefile.am b/mris_average_curvature/Makefile.am deleted file mode 100644 index be57abb70a8..00000000000 --- a/mris_average_curvature/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_average_curvature -mris_average_curvature_SOURCES=mris_average_curvature.c -mris_average_curvature_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_average_curvature_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_average_parcellation/Makefile.am b/mris_average_parcellation/Makefile.am deleted file mode 100644 index b5f5a0b4dc2..00000000000 --- a/mris_average_parcellation/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_average_parcellation -mris_average_parcellation_SOURCES=mris_average_parcellation.c -mris_average_parcellation_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_average_parcellation_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_ca_label/Makefile.am b/mris_ca_label/Makefile.am deleted file mode 100644 index e172674bb90..00000000000 --- a/mris_ca_label/Makefile.am +++ /dev/null @@ -1,45 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mris_ca_label - -mris_ca_label_SOURCES=mris_ca_label.c mris_ca_label.help.xml.h -mris_ca_label_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_ca_label_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mris_ca_label.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mris_ca_label.help.xml.html - -# trick to get test data into the build directory -foo_SOURCES= -foo: - if ! test -f "$(top_builddir)/mris_ca_label/testdata.tar.gz"; then \ - cp -v $(top_srcdir)/mris_ca_label/testdata.tar.gz \ - $(top_builddir)/mris_ca_label/; fi; - if ! test -f "$(top_builddir)/distribution/average/lh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs"; then \ - cp -v $(top_srcdir)/distribution/average/*.gcs \ - $(top_builddir)/distribution/average/; fi; - -check_PROGRAMS=foo - -TESTS=test_mris_ca_label $(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=test_mris_ca_label testdata.tar.gz $(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mris_ca_label.help.xml.h mris_ca_label.help.xml.html - diff --git a/mris_ca_train/Makefile.am b/mris_ca_train/Makefile.am deleted file mode 100644 index 0d09cfb52aa..00000000000 --- a/mris_ca_train/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_ca_train -mris_ca_train_SOURCES=mris_ca_train.c -mris_ca_train_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_ca_train_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_calc/Makefile.am b/mris_calc/Makefile.am deleted file mode 100644 index 98f075414b4..00000000000 --- a/mris_calc/Makefile.am +++ /dev/null @@ -1,30 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_calc - -mris_calc_SOURCES=mris_calc.c mris_calc.help.xml.h -mris_calc_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_calc_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mris_calc.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mris_calc.help.xml.html - -TESTS=$(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=$(foo_DATA) $(BUILT_SOURCES) - -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mris_calc.help.xml.h mris_calc.help.xml.html - diff --git a/mris_classify_thickness/Makefile.am b/mris_classify_thickness/Makefile.am deleted file mode 100644 index 051094a2f22..00000000000 --- a/mris_classify_thickness/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_classify_thickness -mris_classify_thickness_SOURCES=mris_classify_thickness.c -mris_classify_thickness_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_classify_thickness_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_compute_acorr/Makefile.am b/mris_compute_acorr/Makefile.am deleted file mode 100644 index e4267d0e5b8..00000000000 --- a/mris_compute_acorr/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_compute_acorr -mris_compute_acorr_SOURCES=mris_compute_acorr.c -mris_compute_acorr_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_compute_acorr_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_compute_lgi/Makefile.am b/mris_compute_lgi/Makefile.am deleted file mode 100644 index 6225cd2e368..00000000000 --- a/mris_compute_lgi/Makefile.am +++ /dev/null @@ -1,45 +0,0 @@ -## -## Makefile.am -## - -dist_bin_SCRIPTS = mris_compute_lgi - -foodir=$(prefix)/matlab -foo_DATA=\ - ComputeGeodesicProjection.m \ - compute_lgi.m \ - createMeshFacesOfVertex.m \ - dijk.m \ - find_corresponding_center_FSformat.m \ - freesurfer_fread3.m \ - freesurfer_read_surf.m \ - getFaceArea.m \ - getFacesArea.m \ - getMeshArea.m \ - getOrthogonalVector.m \ - getVerticesAndFacesInSphere.m \ - isInGeodesicROI.m \ - isVertexInRadius.m \ - MakeGeodesicOuterROI.m \ - make_outer_surface.m \ - make_roi_paths.m \ - mesh_adjacency.m \ - mesh_vertex_nearest.m \ - pred2path.m \ - PropagateGeodesic.m \ - read_normals.m \ - read_ROIlabel.m \ - redo_lgi.m \ - reorganize_verticeslist.m \ - SearchProjectionOnPial.m \ - transVertexToNormalAxisBase.m \ - write_lgi.m \ - write_path.m - -EXTRA_DIST=$(foo_DATA) - -# Our release target. Include files to be excluded here. They will be \ -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_compute_optimal_kernel/Makefile.am b/mris_compute_optimal_kernel/Makefile.am deleted file mode 100644 index c2d949e92f5..00000000000 --- a/mris_compute_optimal_kernel/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_compute_optimal_kernel -mris_compute_optimal_kernel_SOURCES=mris_compute_optimal_kernel.c -mris_compute_optimal_kernel_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_compute_optimal_kernel_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_compute_overlap/Makefile.am b/mris_compute_overlap/Makefile.am deleted file mode 100644 index ac5e6765e27..00000000000 --- a/mris_compute_overlap/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_compute_overlap -mris_compute_overlap_SOURCES=mris_compute_overlap.c -mris_compute_overlap_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_compute_overlap_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_compute_parc_overlap/Makefile.am b/mris_compute_parc_overlap/Makefile.am deleted file mode 100644 index 129db9544ba..00000000000 --- a/mris_compute_parc_overlap/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_compute_parc_overlap -mris_compute_parc_overlap_SOURCES=mris_compute_parc_overlap.c -mris_compute_parc_overlap_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_compute_parc_overlap_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_compute_volume_fractions/Makefile.am b/mris_compute_volume_fractions/Makefile.am deleted file mode 100644 index 25fab571132..00000000000 --- a/mris_compute_volume_fractions/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_compute_volume_fractions -mris_compute_volume_fractions_SOURCES=mris_compute_volume_fractions.c -mris_compute_volume_fractions_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_compute_volume_fractions_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_congeal/Makefile.am b/mris_congeal/Makefile.am deleted file mode 100644 index eb08c919653..00000000000 --- a/mris_congeal/Makefile.am +++ /dev/null @@ -1,43 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include $(PETSC_CFLAGS) -AM_LDFLAGS=$(PETSC_LIBS) - -# if there is a need to activate petsc support, delete the #PETSC text - -#PETSC if HAVE_PETSC_LIBS -#PETSC LIBS_PETSC=-lpetsc -lmpiuni -#PETSC else -LIBS_PETSC= -#PETSC endif - -bin_PROGRAMS = mris_congeal -mris_congeal_SOURCES=mris_congeal.c -mris_congeal_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_congeal_LDFLAGS=$(OS_LDFLAGS) - - -#PETSC if HAVE_PETSC_LIBS -#PETSC install-exec-hook: -#PETSC # put a wrapper around the bin, used to setup Petsc enviro vars -#PETSC cp $(srcdir)/mris_congeal $(DESTDIR)$(bindir)/mris_congeal.bin -#PETSC echo "#!/bin/tcsh -ef" > $(DESTDIR)$(bindir)/mris_congeal -#PETSC echo "source \$$FREESURFER_HOME/bin/petsc_setup" \ -#PETSC >> $(DESTDIR)$(bindir)/mris_congeal -#PETSC echo "mris_congeal.bin \$$argv" >> $(DESTDIR)$(bindir)/mris_congeal -#PETSC chmod a+x $(DESTDIR)$(bindir)/mris_congeal -#PETSC uninstall-hook: -#PETSC rm -f $(DESTDIR)$(bindir)/mris_congeal.bin -#PETSC else -#PETSC install-exec-hook: -#PETSC endif - -EXTRA_DIST=render_surface.tcl make_movie.csh - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_convert/Makefile.am b/mris_convert/Makefile.am deleted file mode 100644 index a3878f94f89..00000000000 --- a/mris_convert/Makefile.am +++ /dev/null @@ -1,39 +0,0 @@ -## -## Makefile.am -## - -if USE_LOCAL_EXPAT -EXPAT_THINGS=-I$(top_srcdir)/expat -else -EXPAT_THINGS= -endif - -AM_CFLAGS=-I$(top_srcdir)/include $(EXPAT_THINGS) -AM_LDFLAGS= - -bin_PROGRAMS = mris_convert -mris_convert_SOURCES=mris_convert.c -mris_convert_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_convert_LDFLAGS=$(OS_LDFLAGS) - -# trick to get test data into the build directory (mris_expand testdat is used) -foo_SOURCES= -foo: - if ! test -f "$(top_builddir)/mris_expand/testdata.tar.gz"; then \ - cp -v $(top_srcdir)/mris_expand/testdata.tar.gz \ - $(top_builddir)/mris_expand/; fi; - if ! test -f "$(top_builddir)/mris_convert/giftidata.tar.gz"; then \ - cp -v $(top_srcdir)/mris_convert/giftidata.tar.gz \ - $(top_builddir)/mris_convert/; fi; - -check_PROGRAMS=foo - -TESTS=test_mris_convert test_gifti - -EXTRA_DIST=test_mris_convert test_gifti giftidata.tar.gz - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_copy_header/Makefile.am b/mris_copy_header/Makefile.am deleted file mode 100644 index a2043036edb..00000000000 --- a/mris_copy_header/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_copy_header -mris_copy_header_SOURCES=mris_copy_header.c -mris_copy_header_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_copy_header_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_curvature/Makefile.am b/mris_curvature/Makefile.am deleted file mode 100644 index 20a0c1cf6eb..00000000000 --- a/mris_curvature/Makefile.am +++ /dev/null @@ -1,33 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mris_curvature - -mris_curvature_SOURCES=mris_curvature.c mris_curvature.help.xml.h -mris_curvature_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_curvature_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mris_curvature.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mris_curvature.help.xml.html - -TESTS=test_mris_curvature $(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=$(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mris_curvature.help.xml.h mris_curvature.help.xml.html - diff --git a/mris_curvature_stats/Makefile.am b/mris_curvature_stats/Makefile.am deleted file mode 100644 index 60e74cb4cdb..00000000000 --- a/mris_curvature_stats/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_curvature_stats -mris_curvature_stats_SOURCES=mris_curvature_stats.c -mris_curvature_stats_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_curvature_stats_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_curvature_vectors/Makefile.am b/mris_curvature_vectors/Makefile.am deleted file mode 100644 index 0d20f137447..00000000000 --- a/mris_curvature_vectors/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_curvature_vectors -mris_curvature_vectors_SOURCES=mris_curvature_vectors.c -mris_curvature_vectors_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_curvature_vectors_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_decimate/Makefile.am b/mris_decimate/Makefile.am deleted file mode 100644 index dbcb0ec686d..00000000000 --- a/mris_decimate/Makefile.am +++ /dev/null @@ -1,33 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include $(GTS_CFLAGS) -Wno-deprecated - -if HAVE_GTS_LIBS - bin_PROGRAMS = mris_decimate - mris_decimate_SOURCES=mris_decimate.cpp mris_decimate.h main.cpp - mris_decimate_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(GTS_LIBS) - mris_decimate_LDFLAGS=$(OS_LDFLAGS) -endif - -TESTS = ../scripts/help_xml_validate - -foodir=$(prefix)/docs/xml -foo_DATA=mris_decimate.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mris_decimate.help.xml.html - -BUILT_SOURCES=mris_decimate.help.xml.h mris_decimate.help.xml.html - -EXTRA_DIST=$(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -clean-local: - rm -f $(BUILT_SOURCES) diff --git a/mris_decimate_gui/Makefile.am b/mris_decimate_gui/Makefile.am deleted file mode 100644 index 5e443dcb1a1..00000000000 --- a/mris_decimate_gui/Makefile.am +++ /dev/null @@ -1,121 +0,0 @@ -## -## Makefile.am - build with the GUI -## - -AM_CXXFLAGS=\ - -fno-strict-aliasing \ - -Wno-deprecated \ - -I$(top_srcdir)/include \ - $(TCL_CFLAGS) \ - $(GL_CFLAGS) \ - $(VTK_CXXFLAGS) \ - -I$(top_srcdir)/vtkfsio \ - -I$(top_srcdir)/vtkutils \ - -I$(top_srcdir)/mris_decimate_gui/res \ - -I$(top_srcdir)/mris_decimate \ - $(WXWIDGETS_CXXFLAGS) $(GTS_CFLAGS) \ - $(X_LIBS) - -if ENABLE_WXWIDGETS_APPS -if HAVE_GTS_LIBS -if HAVE_VTK_LIBS - bin_PROGRAMS = mris_decimate_gui - mris_decimate_gui_SOURCES=\ - ../mris_decimate/mris_decimate.cpp \ - ../mris_decimate/mris_decimate.h \ - DecimatePanel.cpp \ - DecimatePanel.h \ - MainApp.cpp \ - MainApp.h \ - MainWindow.cpp \ - MainWindow.h \ - MyCmdLineParser.cpp \ - MyCmdLineParser.h \ - RenderPanel.cpp \ - RenderPanel.h \ - wxVTKRenderWindowInteractor.cpp \ - wxVTKRenderWindowInteractor.h \ - res/MainWindowBase.cpp \ - res/MainWindowBase.h \ - res/MainWindowBase.fbp \ - res/DecimatePanelBase.cpp \ - res/DecimatePanelBase.h \ - res/DecimatePanelBase.fbp - mris_decimate_gui_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(VTK_LIBS) $(VTK_VERDICT_LIB) -lvtkGraphics \ - $(VTK_EXPAT_LIB) $(VTK_FREETYPE_LIB) \ - $(VTK_TIFF_LIB) $(VTK_JPEG_LIB) \ - $(VTK_METAIO_LIB) $(VTK_PNG_LIB) $(VTK_Z_LIB) \ - $(VTK_SQLITE_LIB) \ - -lvtkexoIIc -lvtkNetCDF $(VTK_NETCDFCXX_LIB) \ - -lvtkVolumeRendering -lvtkRendering -lvtkftgl \ - -lvtkHybrid $(VTK_HDF5_LIB) \ - -lvtkWidgets \ - -lvtkGraphics \ - -lvtkCommon \ - -lvtksys \ - -lvtkImaging \ - -lvtkFiltering \ - -lvtkRendering \ - -lvtkIO $(VTK_LSDYNA_LIB) -lvtkDICOMParser \ - $(WXWIDGETS_LIBS) $(WXWIDGETS_GL_LIBS) $(GTS_LIBS) - mris_decimate_gui_LDFLAGS=$(OS_LDFLAGS) - -# put a wrapper around the bin, used to setup vtk enviro vars - -# and if the OS is MACOSX have a different install-hook to create a bundle -if HAVE_MAC_OSX -install-exec-hook:mris_decimate_gui - mkdir -p $(DESTDIR)$(bindir)/MrisDecimate.app - mkdir -p $(DESTDIR)$(bindir)/MrisDecimate.app/Contents - mkdir -p $(DESTDIR)$(bindir)/MrisDecimate.app/Contents/MacOS - mkdir -p $(DESTDIR)$(bindir)/MrisDecimate.app/Contents/Resources - mkdir -p $(DESTDIR)$(bindir)/MrisDecimate.app/Contents/Resources/English.lproj - cp $(top_builddir)/mris_decimate_gui/Info.plist $(DESTDIR)$(bindir)/MrisDecimate.app/Contents - echo -n 'APPL????' > $(DESTDIR)$(bindir)/MrisDecimate.app/Contents/PkgInfo - cp $(top_builddir)/mris_decimate_gui/mris_decimate_gui $(DESTDIR)$(bindir)/MrisDecimate.app/Contents/MacOS/mris_decimate_gui.bin - echo "#!/bin/tcsh -ef" > $(DESTDIR)$(bindir)/mris_decimate_gui - echo "source \$$FREESURFER_HOME/bin/tcl_setup" \ - >> $(DESTDIR)$(bindir)/mris_decimate_gui - echo "source \$$FREESURFER_HOME/bin/vtk_setup" \ - >> $(DESTDIR)$(bindir)/mris_decmris_deci - echo "exec $(DESTDIR)$(bindir)/MrisDecimate.app/Contents/MacOS/mris_decimate_gui.bin \$$*" >> $(DESTDIR)$(bindir)/mris_decimate_gui - chmod a+x $(DESTDIR)$(bindir)/mris_decimate_gui - if [[ -f /usr/pubsw/bin/chrpath ]]; then \ - /usr/pubsw/bin/chrpath -d $(DESTDIR)$(bindir)/MrisDecimate.app/Contents/MacOS/mris_decimate_gui.bin; fi - -uninstall-hook: - rm -f $(DESTDIR)$(bindir)/mris_decimate_gui - rm -rf $(DESTDIR)$(bindir)/MrisDecimatey.app -else -install-exec-hook:mris_decimate_gui - cp $(top_builddir)/mris_decimate_gui/mris_decimate_gui $(DESTDIR)$(bindir)/mris_decimate_gui.bin - echo "#!/bin/tcsh -ef" > $(DESTDIR)$(bindir)/mris_decimate_gui - echo "source \$$FREESURFER_HOME/bin/vtk_setup" \ - >> $(DESTDIR)$(bindir)/mris_decimate_gui - echo "if (-e /bin/pwd) then" >> $(DESTDIR)$(bindir)/mris_decimate_gui - echo " setenv HOME \`cd \$$HOME; /bin/pwd\`" \ - >> $(DESTDIR)$(bindir)/mris_decimate_gui - echo " setenv SUBJECTS_DIR \`cd \$$SUBJECTS_DIR; /bin/pwd\`" \ - >> $(DESTDIR)$(bindir)/mris_decimate_gui - echo "endif" >> $(DESTDIR)$(bindir)/mris_decimate_gui - echo "mris_decimate_gui.bin \$$argv" >> $(DESTDIR)$(bindir)/mris_decimate_gui - chmod a+x $(DESTDIR)$(bindir)/mris_decimate_gui - if [[ -f /usr/pubsw/bin/chrpath ]]; then \ - /usr/pubsw/bin/chrpath -d $(DESTDIR)$(bindir)/mris_decimate_gui.bin; fi - -uninstall-hook: - rm -f $(DESTDIR)$(bindir)/mris_decimate_gui.bin -endif - -endif -endif -endif - -EXTRA_DIST=Info.plist - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_deform/Makefile.am b/mris_deform/Makefile.am deleted file mode 100644 index 2b1c3a00934..00000000000 --- a/mris_deform/Makefile.am +++ /dev/null @@ -1,26 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mris_deform mris_ca_deform mris_nudge -mris_deform_SOURCES=mris_deform.c -mris_deform_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_deform_LDFLAGS=$(OS_LDFLAGS) - -mris_ca_deform_SOURCES=mris_ca_deform.c -mris_ca_deform_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_ca_deform_LDFLAGS=$(OS_LDFLAGS) - -mris_nudge_SOURCES=mris_nudge.c -mris_nudge_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_nudge_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - diff --git a/mris_density/Makefile.am b/mris_density/Makefile.am deleted file mode 100644 index 189ed9e3f2e..00000000000 --- a/mris_density/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_density -mris_density_SOURCES=mris_density.c -mris_density_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_density_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_diff/Makefile.am b/mris_diff/Makefile.am deleted file mode 100644 index 91f05239bdf..00000000000 --- a/mris_diff/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mris_diff -mris_diff_SOURCES=mris_diff.c -mris_diff_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_diff_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_distance_map/Makefile.am b/mris_distance_map/Makefile.am deleted file mode 100644 index 00b68faedc7..00000000000 --- a/mris_distance_map/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_distance_map -mris_distance_map_SOURCES=mris_distance_map.c -mris_distance_map_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_distance_map_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_distance_to_label/Makefile.am b/mris_distance_to_label/Makefile.am deleted file mode 100644 index f1d2383376d..00000000000 --- a/mris_distance_to_label/Makefile.am +++ /dev/null @@ -1,16 +0,0 @@ -## -## Makefile.am -## - -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mris_distance_to_label -mris_distance_to_label_SOURCES=mris_distance_to_label.cpp -mris_distance_to_label_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH) utilscpp/libutilscpp.a ) -mris_distance_to_label_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_distance_transform/Makefile.am b/mris_distance_transform/Makefile.am deleted file mode 100644 index 6c06f583e49..00000000000 --- a/mris_distance_transform/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_distance_transform -mris_distance_transform_SOURCES=mris_distance_transform.c -mris_distance_transform_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_distance_transform_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_divide_parcellation/Makefile.am b/mris_divide_parcellation/Makefile.am deleted file mode 100644 index ea067e9a3ee..00000000000 --- a/mris_divide_parcellation/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_divide_parcellation -mris_divide_parcellation_SOURCES=mris_divide_parcellation.c -mris_divide_parcellation_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_divide_parcellation_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_entropy/Makefile.am b/mris_entropy/Makefile.am deleted file mode 100644 index e47a9606e9a..00000000000 --- a/mris_entropy/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_entropy -mris_entropy_SOURCES=mris_entropy.c -mris_entropy_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_entropy_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_errors/Makefile.am b/mris_errors/Makefile.am deleted file mode 100644 index 4f4eb08bc0f..00000000000 --- a/mris_errors/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_errors -mris_errors_SOURCES=mris_errors.c -mris_errors_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_errors_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_euler_number/Makefile.am b/mris_euler_number/Makefile.am deleted file mode 100644 index a5693b6c433..00000000000 --- a/mris_euler_number/Makefile.am +++ /dev/null @@ -1,33 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mris_euler_number - -mris_euler_number_SOURCES=mris_euler_number.c mris_euler_number.help.xml.h -mris_euler_number_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_euler_number_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mris_euler_number.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mris_euler_number.help.xml.html - -TESTS=$(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=$(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mris_euler_number.help.xml.h mris_euler_number.help.xml.html - diff --git a/mris_expand/Makefile.am b/mris_expand/Makefile.am deleted file mode 100644 index 213c08c9bbc..00000000000 --- a/mris_expand/Makefile.am +++ /dev/null @@ -1,29 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_expand -mris_expand_SOURCES=mris_expand.c -mris_expand_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_expand_LDFLAGS=$(OS_LDFLAGS) - -# trick to get test data into the build directory -foo_SOURCES= -foo: - if ! test -f "$(top_builddir)/mris_expand/testdata.tar.gz"; then \ - cp -v $(top_srcdir)/mris_expand/testdata.tar.gz \ - $(top_builddir)/mris_expand/; fi; - -check_PROGRAMS=foo - -TESTS=test_mris_expand - -EXTRA_DIST=testdata.tar.gz test_mris_expand - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_extract_patches/Makefile.am b/mris_extract_patches/Makefile.am deleted file mode 100644 index 281cb7eea16..00000000000 --- a/mris_extract_patches/Makefile.am +++ /dev/null @@ -1,16 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_extract_patches -mris_extract_patches_SOURCES=mris_extract_patches.c -mris_extract_patches_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_extract_patches_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_fbirn_annot/Makefile.am b/mris_fbirn_annot/Makefile.am deleted file mode 100644 index c18bfab85c8..00000000000 --- a/mris_fbirn_annot/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_fbirn_annot -mris_fbirn_annot_SOURCES=mris_fbirn_annot.c -mris_fbirn_annot_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_fbirn_annot_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_fill/Makefile.am b/mris_fill/Makefile.am deleted file mode 100644 index 5437ac6db52..00000000000 --- a/mris_fill/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_fill -mris_fill_SOURCES=mris_fill.c -mris_fill_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_fill_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_find_flat_regions/Makefile.am b/mris_find_flat_regions/Makefile.am deleted file mode 100644 index faa81c98073..00000000000 --- a/mris_find_flat_regions/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_find_flat_regions -mris_find_flat_regions_SOURCES=mris_find_flat_regions.c -mris_find_flat_regions_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_find_flat_regions_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_fix_topology/Makefile.am b/mris_fix_topology/Makefile.am deleted file mode 100644 index 4284b6cf722..00000000000 --- a/mris_fix_topology/Makefile.am +++ /dev/null @@ -1,62 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mris_fix_topology mris_remove_intersection - -mris_fix_topology_SOURCES=mris_fix_topology.c -mris_fix_topology_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_fix_topology_LDFLAGS=$(OS_LDFLAGS) - -mris_remove_intersection_SOURCES=mris_remove_intersection.c -mris_remove_intersection_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_remove_intersection_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mris_fix_topology.help.xml mris_remove_intersection.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mris_fix_topology.help.xml.html mris_remove_intersection.help.xml.html - -## ---- -## CUDA -## ---- - -# BUILDCUDA is defined if configure.in finds CUDA -if BUILDCUDA - -NVCCFLAGS += -g -arch sm_13 --ptxas-options=-v - -# rules for building cuda files -.cu.o: - $(NVCC) -o $@ -c $< $(NVCCFLAGS) $(CUDA_CFLAGS) -I$(top_srcdir)/include - -bin_PROGRAMS += mris_fix_topology_cuda -mris_fix_topology_cuda_SOURCES = mris_fix_topology.c -mris_fix_topology_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -mris_fix_topology_cuda_CXXFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -mris_fix_topology_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) -mris_fix_topology_cuda_LDFLAGS = $(OS_LDFLAGS) -mris_fix_topology_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(mris_fix_topology_cuda_CFLAGS) \ - $(CFLAGS) $(mris_fix_topology_cuda_LDFLAGS) $(LDFLAGS) -o $@ - -endif - -TESTS=test_mris_fix_topology $(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=test_mris_fix_topology testdata.tar.gz $(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mris_fix_topology.help.xml.h mris_remove_intersection.help.xml.h \ - mris_fix_topology.help.xml.html mris_remove_intersection.help.xml.html diff --git a/mris_flatten/Makefile.am b/mris_flatten/Makefile.am deleted file mode 100644 index 9fa7456395e..00000000000 --- a/mris_flatten/Makefile.am +++ /dev/null @@ -1,44 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mris_flatten -mris_flatten_SOURCES=mris_flatten.c -mris_flatten_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_flatten_LDFLAGS=$(OS_LDFLAGS) - -## ---- -## CUDA -## ---- - -# BUILDCUDA is defined if configure.in finds CUDA -if BUILDCUDA - -NVCCFLAGS += -g -arch sm_13 --ptxas-options=-v - -# rules for building cuda files -.cu.o: - $(NVCC) -o $@ -c $< $(NVCCFLAGS) $(CUDA_CFLAGS) -I$(top_srcdir)/include - -bin_PROGRAMS += mris_flatten_cuda -mris_flatten_cuda_SOURCES = mris_flatten.c -mris_flatten_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -mris_flatten_cuda_CXXFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -mris_flatten_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) -mris_flatten_cuda_LDFLAGS = $(OS_LDFLAGS) -mris_flatten_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(mris_flatten_cuda_CFLAGS) \ - $(CFLAGS) $(mris_flatten_cuda_LDFLAGS) $(LDFLAGS) -o $@ - -endif - -EXTRA_DIST = make_mris_flatten_movie.tcl - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_fwhm/Makefile.am b/mris_fwhm/Makefile.am deleted file mode 100644 index a34104b80a6..00000000000 --- a/mris_fwhm/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_fwhm -mris_fwhm_SOURCES=mris_fwhm.c -mris_fwhm_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_fwhm_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_glm/Makefile.am b/mris_glm/Makefile.am deleted file mode 100644 index a5830ca0e41..00000000000 --- a/mris_glm/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mris_glm -mris_glm_SOURCES=mris_glm.c $(top_srcdir)/fsgdf/fsgdf.c -mris_glm_LDADD=$(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_glm_LDFLAGS= - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_hausdorff_dist/Makefile.am b/mris_hausdorff_dist/Makefile.am deleted file mode 100644 index 54b7d32eae9..00000000000 --- a/mris_hausdorff_dist/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_hausdorff_dist -mris_hausdorff_dist_SOURCES=mris_hausdorff_dist.c -mris_hausdorff_dist_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_hausdorff_dist_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_inflate/Makefile.am b/mris_inflate/Makefile.am deleted file mode 100644 index 06776f28b7c..00000000000 --- a/mris_inflate/Makefile.am +++ /dev/null @@ -1,65 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mris_inflate - -mris_inflate_SOURCES=mris_inflate.c mris_inflate.help.xml.h -mris_inflate_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_inflate_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mris_inflate.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mris_inflate.help.xml.html - -## ---- -## CUDA -## ---- - -# BUILDCUDA is defined if configure.in finds CUDA -if BUILDCUDA - -NVCCFLAGS += -g -arch sm_13 --ptxas-options=-v - -# rules for building cuda files -.cu.o: - $(NVCC) -o $@ -c $< $(NVCCFLAGS) $(CUDA_CFLAGS) -I$(top_srcdir)/include - -bin_PROGRAMS += mris_inflate_cuda -mris_inflate_cuda_SOURCES = mris_inflate.c -mris_inflate_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -mris_inflate_cuda_CXXFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -mris_inflate_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) -mris_inflate_cuda_LDFLAGS = $(OS_LDFLAGS) -mris_inflate_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(mris_inflate_cuda_CFLAGS) \ - $(CFLAGS) $(mris_inflate_cuda_LDFLAGS) $(LDFLAGS) -o $@ - -endif - -# trick to get test data into the build directory -foo_SOURCES= -foo: - if ! test -f "$(top_builddir)/mris_inflate/testdata.tar.gz"; then \ - cp -v $(top_srcdir)/mris_inflate/testdata.tar.gz \ - $(top_builddir)/mris_inflate/; fi; - -TESTS=$(top_builddir)/scripts/help_xml_validate test_fs_posix - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=$(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mris_inflate.help.xml.h mris_inflate.help.xml.html - diff --git a/mris_info/Makefile.am b/mris_info/Makefile.am deleted file mode 100644 index ae6710e39f5..00000000000 --- a/mris_info/Makefile.am +++ /dev/null @@ -1,23 +0,0 @@ -## -## Makefile.am -## - -if USE_LOCAL_EXPAT -EXPAT_THINGS=-I$(top_srcdir)/expat -else -EXPAT_THINGS= -endif - -AM_CXXFLAGS=-I$(top_srcdir)/include $(EXPAT_THINGS) -AM_LDFLAGS= - -bin_PROGRAMS = mris_info -mris_info_SOURCES=mris_info.cpp -mris_info_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_info_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_init_global_tractography/Makefile.am b/mris_init_global_tractography/Makefile.am deleted file mode 100644 index b3b68d7fb8f..00000000000 --- a/mris_init_global_tractography/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_init_global_tractography -mris_init_global_tractography_SOURCES=mris_init_global_tractography.c -mris_init_global_tractography_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_init_global_tractography_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_interpolate_warp/Makefile.am b/mris_interpolate_warp/Makefile.am deleted file mode 100644 index 92557f3eafa..00000000000 --- a/mris_interpolate_warp/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_interpolate_warp -mris_interpolate_warp_SOURCES=mris_interpolate_warp.c -mris_interpolate_warp_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_interpolate_warp_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_jacobian/Makefile.am b/mris_jacobian/Makefile.am deleted file mode 100644 index 8f8aed65d08..00000000000 --- a/mris_jacobian/Makefile.am +++ /dev/null @@ -1,40 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mris_jacobian - -mris_jacobian_SOURCES=mris_jacobian.c mris_jacobian.help.xml.h -mris_jacobian_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_jacobian_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mris_jacobian.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mris_jacobian.help.xml.html - -# trick to get test data into the build directory -foo_SOURCES= -foo: - if ! test -f "$(top_builddir)/mris_jacobian/testdata.tar.gz"; then \ - cp -v $(top_srcdir)/mris_jacobian/testdata.tar.gz \ - $(top_builddir)/mris_jacobian/; fi; - -TESTS=$(top_builddir)/scripts/help_xml_validate test_fs_posix - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=$(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mris_jacobian.help.xml.h mris_jacobian.help.xml.html - diff --git a/mris_label2annot/Makefile.am b/mris_label2annot/Makefile.am deleted file mode 100644 index 10d3cfceb39..00000000000 --- a/mris_label2annot/Makefile.am +++ /dev/null @@ -1,19 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_label2annot -mris_label2annot_SOURCES=mris_label2annot.c -mris_label2annot_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_label2annot_LDFLAGS=$(OS_LDFLAGS) - -EXTRA_DIST = runit - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_label_area/Makefile.am b/mris_label_area/Makefile.am deleted file mode 100644 index db40411b644..00000000000 --- a/mris_label_area/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_label_area -mris_label_area_SOURCES=mris_label_area.c -mris_label_area_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_label_area_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_label_calc/Makefile.am b/mris_label_calc/Makefile.am deleted file mode 100644 index db4d993235a..00000000000 --- a/mris_label_calc/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_label_calc -mris_label_calc_SOURCES=mris_label_calc.cpp -mris_label_calc_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_label_calc_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_label_mode/Makefile.am b/mris_label_mode/Makefile.am deleted file mode 100644 index f70efc9c0ba..00000000000 --- a/mris_label_mode/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_label_mode -mris_label_mode_SOURCES=mris_label_mode.c -mris_label_mode_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_label_mode_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_left_right_register/Makefile.am b/mris_left_right_register/Makefile.am deleted file mode 100644 index cc3f75ab970..00000000000 --- a/mris_left_right_register/Makefile.am +++ /dev/null @@ -1,54 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include $(PETSC_CFLAGS) -AM_LDFLAGS=$(PETSC_LIBS) - -# if there is a need to activate petsc support, delete the #PETSC text - -#PETSC if HAVE_PETSC_LIBS -#PETSC LIBS_PETSC=-lpetsc -lmpiuni -#PETSC else -LIBS_PETSC= -#PETSC endif - -bin_PROGRAMS = mris_left_right_register -mris_left_right_register_SOURCES=mris_left_right_register.c -mris_left_right_register_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_left_right_register_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA= -#foo_DATA=mris_left_right_register.help.xml - - -#PETSC if HAVE_PETSC_LIBS -#PETSC install-exec-hook: -#PETSC # put a wrapper around the bin, used to setup Petsc enviro vars -#PETSC cp $(srcdir)/mris_left_right_register $(DESTDIR)$(bindir)/mris_left_right_register.bin -#PETSC echo "#!/bin/tcsh -ef" > $(DESTDIR)$(bindir)/mris_left_right_register -#PETSC echo "source \$$FREESURFER_HOME/bin/petsc_setup" \ -#PETSC >> $(DESTDIR)$(bindir)/mris_left_right_register -#PETSC echo "mris_left_right_register.bin \$$argv" >> $(DESTDIR)$(bindir)/mris_left_right_register -#PETSC chmod a+x $(DESTDIR)$(bindir)/mris_left_right_register -#PETSC uninstall-hook: -#PETSC rm -f $(DESTDIR)$(bindir)/mris_left_right_register.bin -#PETSC else -#PETSC install-exec-hook: -#PETSC endif - -#TESTS=$(top_builddir)/scripts/help_xml_validate -TESTS= - -EXTRA_DIST=make_mris_register_movie.tcl $(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES= -#BUILT_SOURCES=mris_left_right_register.help.xml.h - diff --git a/mris_longitudinal_surfaces/Makefile.am b/mris_longitudinal_surfaces/Makefile.am deleted file mode 100644 index 1b94f5047b0..00000000000 --- a/mris_longitudinal_surfaces/Makefile.am +++ /dev/null @@ -1,16 +0,0 @@ -## -## Makefile.am -## -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mris_longitudinal_surfaces -mris_longitudinal_surfaces_SOURCES=mris_longitudinal_surfaces.c -mris_longitudinal_surfaces_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_longitudinal_surfaces_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_make_average_surface/Makefile.am b/mris_make_average_surface/Makefile.am deleted file mode 100644 index bba1db5e2b3..00000000000 --- a/mris_make_average_surface/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_make_average_surface -mris_make_average_surface_SOURCES=mris_make_average_surface.c -mris_make_average_surface_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_make_average_surface_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_make_face_parcellation/Makefile.am b/mris_make_face_parcellation/Makefile.am deleted file mode 100644 index 0176e19d885..00000000000 --- a/mris_make_face_parcellation/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_make_face_parcellation -mris_make_face_parcellation_SOURCES=mris_make_face_parcellation.c -mris_make_face_parcellation_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_make_face_parcellation_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_make_map_surfaces/Makefile.am b/mris_make_map_surfaces/Makefile.am deleted file mode 100644 index 9db194a51ab..00000000000 --- a/mris_make_map_surfaces/Makefile.am +++ /dev/null @@ -1,32 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_make_map_surfaces -mris_make_map_surfaces_SOURCES=mris_make_map_surfaces.c -mris_make_map_surfaces_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_make_map_surfaces_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mris_make_map_surfaces.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mris_make_map_surfaces.help.xml.html - -TESTS=$(top_builddir)/scripts/help_xml_validate - -EXTRA_DIST=$(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mris_make_map_surfaces.help.xml.h \ - mris_make_map_surfaces.help.xml.html - -clean-local: - rm -f $(BUILT_SOURCES) diff --git a/mris_make_surfaces/Makefile.am b/mris_make_surfaces/Makefile.am deleted file mode 100644 index a5d7a955c54..00000000000 --- a/mris_make_surfaces/Makefile.am +++ /dev/null @@ -1,47 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mris_make_surfaces \ - mris_refine_surfaces \ - mris_mef_surfaces \ - mris_exvivo_surfaces - -mris_make_surfaces_SOURCES=mris_make_surfaces.c mris_make_surfaces.help.xml.h -mris_make_surfaces_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_make_surfaces_LDFLAGS= $(OS_LDFLAGS) - -mris_refine_surfaces_SOURCES=mris_refine_surfaces.c -mris_refine_surfaces_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_refine_surfaces_LDFLAGS= $(OS_LDFLAGS) - -mris_mef_surfaces_SOURCES=mris_mef_surfaces.c -mris_mef_surfaces_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_mef_surfaces_LDFLAGS= $(OS_LDFLAGS) - -mris_exvivo_surfaces_SOURCES=mris_exvivo_surfaces.c -mris_exvivo_surfaces_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_exvivo_surfaces_LDFLAGS= $(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mris_make_surfaces.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mris_make_surfaces.help.xml.html - -TESTS=test_mris_make_surfaces $(top_builddir)/scripts/help_xml_validate - -EXTRA_DIST=test_mris_make_surfaces testdata.tar.gz $(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mris_make_surfaces.help.xml.h mris_make_surfaces.help.xml.html - -clean-local: - rm -f $(BUILT_SOURCES) diff --git a/mris_make_template/Makefile.am b/mris_make_template/Makefile.am deleted file mode 100644 index 2fd9f2690bb..00000000000 --- a/mris_make_template/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_make_template -mris_make_template_SOURCES=mris_make_template.c -mris_make_template_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_make_template_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_map_cuts/Makefile.am b/mris_map_cuts/Makefile.am deleted file mode 100644 index a45ce1f3359..00000000000 --- a/mris_map_cuts/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_map_cuts -mris_map_cuts_SOURCES=mris_map_cuts.c -mris_map_cuts_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_map_cuts_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_merge_parcellations/Makefile.am b/mris_merge_parcellations/Makefile.am deleted file mode 100644 index 44cef32efad..00000000000 --- a/mris_merge_parcellations/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_merge_parcellations -mris_merge_parcellations_SOURCES=mris_merge_parcellations.c -mris_merge_parcellations_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_merge_parcellations_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_mesh_subdivide/Makefile.am b/mris_mesh_subdivide/Makefile.am deleted file mode 100644 index 919a559a347..00000000000 --- a/mris_mesh_subdivide/Makefile.am +++ /dev/null @@ -1,65 +0,0 @@ - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CPPFLAGS=-I$(top_srcdir)/include \ - -I/usr/include/libxml2 -AM_CXXFLAGS=-Wno-deprecated -I$(top_srcdir)/include \ - -I$(top_srcdir)/vtkfsio \ - -I$(top_srcdir)/vtkutils \ - $(VTK_CXXFLAGS) - -# vtkutils does not build if KWWIDGETS is not enabled. -# Therefore do not build mris_mesh_subdivide either because -# mris_mesh_subdivide depends upon libvtkutils. -if ENABLE_KWWIDGETS_APPS -bin_PROGRAMS = mris_mesh_subdivide -mris_mesh_subdivide_SOURCES=mris_mesh_subdivide.cxx -mris_mesh_subdivide_LDADD= \ - $(top_builddir)/vtkfsio/libvtkfsio.a \ - $(top_builddir)/vtkutils/libvtkutils.a \ - $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(VTK_LIBS) $(VTK_VERDICT_LIB) -lvtkGraphics \ - $(VTK_EXPAT_LIB) $(VTK_FREETYPE_LIB) \ - $(VTK_TIFF_LIB) $(VTK_JPEG_LIB) \ - $(VTK_METAIO_LIB) $(VTK_PNG_LIB) $(VTK_Z_LIB) $(VTK_SQLITE_LIB) \ - -lvtkImaging -lvtkFiltering \ - -lvtkCommon -lvtksys \ - -lvtkexoIIc -lvtkNetCDF $(VTK_NETCDFCXX_LIB) \ - -lvtkRendering -lvtkftgl \ - -lvtkHybrid $(VTK_HDF5_LIB) \ - -lvtkIO $(VTK_LSDYNA_LIB) -lvtkDICOMParser $(VTK_MPEG2ENCODE_LIB) -mris_mesh_subdivide_LDFLAGS=$(OS_LDFLAGS) - -# put a script wrapper around the binary, to set up VTK environment (from QDEC example) -install-exec-hook:mris_mesh_subdivide - cp $(top_builddir)/mris_mesh_subdivide/mris_mesh_subdivide $(DESTDIR)$(bindir)/mris_mesh_subdivide.bin - echo "#!/bin/tcsh -ef" > $(DESTDIR)$(bindir)/mris_mesh_subdivide - echo "source \$$FREESURFER_HOME/bin/vtk_setup" \ - >> $(DESTDIR)$(bindir)/mris_mesh_subdivide - echo "if (-e /bin/pwd) then" >> $(DESTDIR)$(bindir)/mris_mesh_subdivide - echo " setenv HOME \`cd \$$HOME; /bin/pwd\`" \ - >> $(DESTDIR)$(bindir)/mris_mesh_subdivide - echo " setenv SUBJECTS_DIR \`cd \$$SUBJECTS_DIR; /bin/pwd\`" \ - >> $(DESTDIR)$(bindir)/mris_mesh_subdivide - echo "endif" >> $(DESTDIR)$(bindir)/mris_mesh_subdivide - echo "mris_mesh_subdivide.bin \$$argv" >> $(DESTDIR)$(bindir)/mris_mesh_subdivide - chmod a+x $(DESTDIR)$(bindir)/mris_mesh_subdivide - if [[ -f /usr/pubsw/bin/chrpath ]]; then \ - /usr/pubsw/bin/chrpath -d $(DESTDIR)$(bindir)/mris_mesh_subdivide.bin; fi - -uninstall-hook: - rm -f $(DESTDIR)$(bindir)/mris_mesh_subdivide.bin - - -else -bin_PROGRAMS = - -all: - @echo "Building KWWidgets apps not enabled." - @echo "Run configure with either --enable-kww-apps or --with-kwwidgets-dir=DIR" -endif - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_morph_stats/Makefile.am b/mris_morph_stats/Makefile.am deleted file mode 100644 index 82fb34ebe5f..00000000000 --- a/mris_morph_stats/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_morph_stats -mris_morph_stats_SOURCES=mris_morph_stats.c -mris_morph_stats_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_morph_stats_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_ms_refine/Makefile.am b/mris_ms_refine/Makefile.am deleted file mode 100644 index 02150f19dee..00000000000 --- a/mris_ms_refine/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_ms_refine -mris_ms_refine_SOURCES=mris_ms_refine.c -mris_ms_refine_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_ms_refine_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_ms_surface_CNR/Makefile.am b/mris_ms_surface_CNR/Makefile.am deleted file mode 100644 index 08dc4188573..00000000000 --- a/mris_ms_surface_CNR/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mris_ms_surface_CNR -mris_ms_surface_CNR_SOURCES=mris_ms_surface_CNR.c -mris_ms_surface_CNR_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_ms_surface_CNR_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_multiscale_stats/Makefile.am b/mris_multiscale_stats/Makefile.am deleted file mode 100644 index afd78388b42..00000000000 --- a/mris_multiscale_stats/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_multiscale_stats -mris_multiscale_stats_SOURCES=mris_multiscale_stats.c -mris_multiscale_stats_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_multiscale_stats_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_niters2fwhm/Makefile.am b/mris_niters2fwhm/Makefile.am deleted file mode 100644 index fab7e4291d9..00000000000 --- a/mris_niters2fwhm/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_niters2fwhm -mris_niters2fwhm_SOURCES=mris_niters2fwhm.c -mris_niters2fwhm_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_niters2fwhm_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_parcellate_connectivity/Makefile.am b/mris_parcellate_connectivity/Makefile.am deleted file mode 100644 index b17e31e998d..00000000000 --- a/mris_parcellate_connectivity/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_parcellate_connectivity -mris_parcellate_connectivity_SOURCES=mris_parcellate_connectivity.c -mris_parcellate_connectivity_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_parcellate_connectivity_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_pmake/Makefile.am b/mris_pmake/Makefile.am deleted file mode 100644 index b4655d61547..00000000000 --- a/mris_pmake/Makefile.am +++ /dev/null @@ -1,63 +0,0 @@ -## -## Makefile.am -## - -foodir=$(prefix)/docs/xml -foo_DATA=mris_pmake.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mris_pmake.help.xml.html - -bin_PROGRAMS = mris_pmake -mris_pmake_SOURCES = \ - abs2rel.c \ - asynch.cpp \ - c_label.cpp \ - C_mpmProg.cpp \ - c_SMessage.cpp \ - c_SSocket.cpp \ - c_surface.cpp \ - c_vertex.cpp \ - dijkstra.cpp \ - env.cpp \ - general.cpp \ - help.cpp \ - mris_pmake.cpp \ - rel2abs.c \ - scanopt.cpp \ - surface.cpp \ - C_mpmOverlay.cpp \ - C_mpmOverlay.h \ - legacy.cpp \ - legacy.h - -if BUILDOPENCL # Include OpenCL version of algorithms - AM_CFLAGS=-I$(top_srcdir)/include - AM_CXXFLAGS=-I$(top_srcdir)/include \ - -I$(top_srcdir)/opencl_algorithms/ $(OPENCL_CFLAGS) - mris_pmake_LDADD = $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - ../opencl_algorithms/libopencl_algorithms.a $(OPENCL_LIBS) - mris_pmake_LDFLAGS = $(OS_LDFLAGS) -else # No OpenCL present - AM_CFLAGS=-I$(top_srcdir)/include - AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/opencl_algorithms/ - mris_pmake_LDADD = $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - ../opencl_algorithms/libopencl_algorithms.a - mris_pmake_LDFLAGS = $(OS_LDFLAGS) -endif - -TESTS=$(top_builddir)/scripts/help_xml_validate test_mris_pmake - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=asynch.h c_label.h C_mpmProg.h c_SMessage.h c_SSocket.h \ - c_surface.h c_vertex.h dijkstra.h env.h general.h help.h pathconvert.h \ - pstream.h scanopt.h surface.h $(foo_DATA) $(BUILT_SOURCES) test_mris_pmake - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mris_pmake.help.xml.h mris_pmake.help.xml.html diff --git a/mris_register/Makefile.am b/mris_register/Makefile.am deleted file mode 100644 index 3997c908275..00000000000 --- a/mris_register/Makefile.am +++ /dev/null @@ -1,55 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include $(PETSC_CFLAGS) -AM_LDFLAGS=$(PETSC_LIBS) - -# if there is a need to activate petsc support, delete the #PETSC text - -#PETSC if HAVE_PETSC_LIBS -#PETSC LIBS_PETSC=-lpetsc -lmpiuni -#PETSC else -LIBS_PETSC= -#PETSC endif - -bin_PROGRAMS = mris_register -mris_register_SOURCES=mris_register.c mris_register.help.xml.h -mris_register_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_register_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mris_register.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mris_register.help.xml.html - - -#PETSC if HAVE_PETSC_LIBS -#PETSC install-exec-hook: -#PETSC # put a wrapper around the bin, used to setup Petsc enviro vars -#PETSC cp $(srcdir)/mris_register $(DESTDIR)$(bindir)/mris_register.bin -#PETSC echo "#!/bin/tcsh -ef" > $(DESTDIR)$(bindir)/mris_register -#PETSC echo "source \$$FREESURFER_HOME/bin/petsc_setup" \ -#PETSC >> $(DESTDIR)$(bindir)/mris_register -#PETSC echo "mris_register.bin \$$argv" >> $(DESTDIR)$(bindir)/mris_register -#PETSC chmod a+x $(DESTDIR)$(bindir)/mris_register -#PETSC uninstall-hook: -#PETSC rm -f $(DESTDIR)$(bindir)/mris_register.bin -#PETSC else -#PETSC install-exec-hook: -#PETSC endif - -TESTS=test_mris_register $(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=make_mris_register_movie.tcl $(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mris_register.help.xml.h mris_register.help.xml.html diff --git a/mris_register_label_map/Makefile.am b/mris_register_label_map/Makefile.am deleted file mode 100644 index d94368f7c6e..00000000000 --- a/mris_register_label_map/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_register_label_map -mris_register_label_map_SOURCES=mris_register_label_map.c -mris_register_label_map_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_register_label_map_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_register_to_volume/Makefile.am b/mris_register_to_volume/Makefile.am deleted file mode 100644 index 4e86ef90324..00000000000 --- a/mris_register_to_volume/Makefile.am +++ /dev/null @@ -1,20 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_register_to_volume mris_register_to_label -mris_register_to_volume_SOURCES=mris_register_to_volume.c -mris_register_to_volume_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_register_to_volume_LDFLAGS=$(OS_LDFLAGS) - -mris_register_to_label_SOURCES=mris_register_to_label.c -mris_register_to_label_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_register_to_label_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_remove_variance/Makefile.am b/mris_remove_variance/Makefile.am deleted file mode 100644 index c7e8dc90cf5..00000000000 --- a/mris_remove_variance/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_remove_variance -mris_remove_variance_SOURCES=mris_remove_variance.c -mris_remove_variance_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_remove_variance_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_resample/Makefile.am b/mris_resample/Makefile.am deleted file mode 100644 index e5f41fdd76e..00000000000 --- a/mris_resample/Makefile.am +++ /dev/null @@ -1,23 +0,0 @@ -## -## Makefile.am -## - -if HAVE_ANN_LIBS -if HAVE_BOOST_LIBS - -AM_CXXFLAGS=-I$(top_srcdir)/include $(ANN_CFLAGS) $(BOOST_CFLAGS) - -bin_PROGRAMS = mris_resample -mris_resample_SOURCES=mris_resample.cpp -mris_resample_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(BOOST_PO_LIB) $(ANN_LIBS) -lANN -mris_resample_LDFLAGS=$(OS_LDFLAGS) - -endif -endif - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_rescale/Makefile.am b/mris_rescale/Makefile.am deleted file mode 100644 index e8a62e14c4f..00000000000 --- a/mris_rescale/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_rescale -mris_rescale_SOURCES=mris_rescale.c -mris_rescale_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_rescale_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_reverse/Makefile.am b/mris_reverse/Makefile.am deleted file mode 100644 index b4ad9a6c268..00000000000 --- a/mris_reverse/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_reverse -mris_reverse_SOURCES=mris_reverse.c -mris_reverse_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_reverse_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_rf_label/Makefile.am b/mris_rf_label/Makefile.am deleted file mode 100644 index 0ce22cc3365..00000000000 --- a/mris_rf_label/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_rf_label -mris_rf_label_SOURCES=mris_rf_label.c -mris_rf_label_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_rf_label_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_rf_train/Makefile.am b/mris_rf_train/Makefile.am deleted file mode 100644 index 1e0680b6831..00000000000 --- a/mris_rf_train/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_rf_train -mris_rf_train_SOURCES=mris_rf_train.c -mris_rf_train_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_rf_train_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_rotate/Makefile.am b/mris_rotate/Makefile.am deleted file mode 100644 index 8e52fc9bfa5..00000000000 --- a/mris_rotate/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_rotate -mris_rotate_SOURCES=mris_rotate.c -mris_rotate_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_rotate_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_sample_label/Makefile.am b/mris_sample_label/Makefile.am deleted file mode 100644 index d540d070195..00000000000 --- a/mris_sample_label/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_sample_label -mris_sample_label_SOURCES=mris_sample_label.c -mris_sample_label_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_sample_label_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_sample_parc/Makefile.am b/mris_sample_parc/Makefile.am deleted file mode 100644 index 14dba856712..00000000000 --- a/mris_sample_parc/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_sample_parc -mris_sample_parc_SOURCES=mris_sample_parc.c -mris_sample_parc_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_sample_parc_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_seg2annot/Makefile.am b/mris_seg2annot/Makefile.am deleted file mode 100644 index 81da1957581..00000000000 --- a/mris_seg2annot/Makefile.am +++ /dev/null @@ -1,14 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mris_seg2annot -mris_seg2annot_SOURCES=mris_seg2annot.c -mris_seg2annot_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_seg2annot_LDFLAGS=$(OS_LDFLAGS) - -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_segment/Makefile.am b/mris_segment/Makefile.am deleted file mode 100644 index 278f2617883..00000000000 --- a/mris_segment/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_segment -mris_segment_SOURCES=mris_segment.c -mris_segment_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_segment_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_segment_vals/Makefile.am b/mris_segment_vals/Makefile.am deleted file mode 100644 index 32c50891e51..00000000000 --- a/mris_segment_vals/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_segment_vals -mris_segment_vals_SOURCES=mris_segment_vals.c -mris_segment_vals_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_segment_vals_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_segmentation_stats/Makefile.am b/mris_segmentation_stats/Makefile.am deleted file mode 100644 index 465c9572aae..00000000000 --- a/mris_segmentation_stats/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_segmentation_stats -mris_segmentation_stats_SOURCES=mris_segmentation_stats.c -mris_segmentation_stats_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_segmentation_stats_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_shrinkwrap/Makefile.am b/mris_shrinkwrap/Makefile.am deleted file mode 100644 index 05c5b566cd0..00000000000 --- a/mris_shrinkwrap/Makefile.am +++ /dev/null @@ -1,21 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mris_shrinkwrap mris_AA_shrinkwrap -mris_AA_shrinkwrap_SOURCES=mris_AA_shrinkwrap.c -mris_AA_shrinkwrap_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_AA_shrinkwrap_LDFLAGS=$(OS_LDFLAGS) - -mris_shrinkwrap_SOURCES=mris_shrinkwrap.c -mris_shrinkwrap_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_shrinkwrap_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_simulate_atrophy/Makefile.am b/mris_simulate_atrophy/Makefile.am deleted file mode 100644 index 6dc56146211..00000000000 --- a/mris_simulate_atrophy/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_simulate_atrophy -mris_simulate_atrophy_SOURCES=mris_simulate_atrophy.c -mris_simulate_atrophy_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_simulate_atrophy_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_smooth/Makefile.am b/mris_smooth/Makefile.am deleted file mode 100644 index 4654b62251a..00000000000 --- a/mris_smooth/Makefile.am +++ /dev/null @@ -1,39 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mris_smooth - -mris_smooth_SOURCES=mris_smooth.c -mris_smooth_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_smooth_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mris_smooth.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mris_smooth.help.xml.html - -# trick to get test data into the build directory -foo_SOURCES= -foo: - if ! test -f "$(top_builddir)/mris_registetr/testdata.tar.gz"; then \ - cp -v $(top_srcdir)/mris_registetr/testdata.tar.gz \ - $(top_builddir)/mris_registetr/; fi; - -TESTS=$(top_builddir)/scripts/help_xml_validate test_fs_posix - -EXTRA_DIST=$(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mris_smooth.help.xml.h - -clean-local: - -rm *.help.xml.h *.help.xml.html diff --git a/mris_sphere/Makefile.am b/mris_sphere/Makefile.am deleted file mode 100644 index 7aa589a8c59..00000000000 --- a/mris_sphere/Makefile.am +++ /dev/null @@ -1,72 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mris_sphere mris_remove_negative_vertices - -mris_sphere_SOURCES=mris_sphere.c mris_sphere.help.xml.h -mris_sphere_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_sphere_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mris_sphere.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mris_sphere.help.xml.html - -mris_remove_negative_vertices_SOURCES=mris_remove_negative_vertices.c -mris_remove_negative_vertices_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_remove_negative_vertices_LDFLAGS=$(OS_LDFLAGS) - -## ---- -## CUDA -## ---- - -# BUILDCUDA is defined if configure.in finds CUDA -if BUILDCUDA - -NVCCFLAGS += -g -arch sm_13 --ptxas-options=-v - -# rules for building cuda files -.cu.o: - $(NVCC) -o $@ -c $< $(NVCCFLAGS) $(CUDA_CFLAGS) -I$(top_srcdir)/include - -bin_PROGRAMS += mris_sphere_cuda -mris_sphere_cuda_SOURCES = mris_sphere.c -mris_sphere_cuda_CFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -mris_sphere_cuda_CXXFLAGS = $(CUDA_CFLAGS) $(AM_CFLAGS) -DFS_CUDA -mris_sphere_cuda_LDADD = $(addprefix $(top_builddir)/, $(LIBS_CUDA_MGH)) $(CUDA_LIBS) -mris_sphere_cuda_LDFLAGS = $(OS_LDFLAGS) -mris_sphere_cuda_LINK = $(LIBTOOL) --tag=CC $(AM_LIBTOOLFLAGS) \ - $(LIBTOOLFLAGS) --mode=link $(CCLD) $(mris_sphere_cuda_CFLAGteS) \ - $(CFLAGS) $(mris_sphere_cuda_LDFLAGS) $(LDFLAGS) -o $@ - -endif - -# trick to get test data into the build directory -foo_SOURCES= -foo: - if ! test -f "$(top_builddir)/mris_sphere/testdata.tar.gz"; then \ - cp -v $(top_srcdir)/mris_sphere/testdata.tar.gz \ - $(top_builddir)/mris_sphere/; fi; - -check_PROGRAMS=foo - -TESTS=test.py test_fs_posix $(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=$(foo_DATA) $(BUILT_SOURCES) \ - make_mris_sphere_movie.tcl test.py - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mris_sphere.help.xml.h mris_sphere.help.xml.html - diff --git a/mris_spherical_average/Makefile.am b/mris_spherical_average/Makefile.am deleted file mode 100644 index 7812a800242..00000000000 --- a/mris_spherical_average/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_spherical_average -mris_spherical_average_SOURCES=mris_spherical_average.c -mris_spherical_average_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_spherical_average_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_surface_change/Makefile.am b/mris_surface_change/Makefile.am deleted file mode 100644 index 5c104226031..00000000000 --- a/mris_surface_change/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_surface_change -mris_surface_change_SOURCES=mris_surface_change.c -mris_surface_change_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_surface_change_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_surface_stats/Makefile.am b/mris_surface_stats/Makefile.am deleted file mode 100644 index 18a11ab5fb5..00000000000 --- a/mris_surface_stats/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = mris_surface_stats -mris_surface_stats_SOURCES=mris_surface_stats.c -mris_surface_stats_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_surface_stats_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_surface_to_vol_distances/Makefile.am b/mris_surface_to_vol_distances/Makefile.am deleted file mode 100644 index 23c53b28197..00000000000 --- a/mris_surface_to_vol_distances/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_surface_to_vol_distances -mris_surface_to_vol_distances_SOURCES=mris_surface_to_vol_distances.c -mris_surface_to_vol_distances_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_surface_to_vol_distances_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_svm_classify/Makefile.am b/mris_svm_classify/Makefile.am deleted file mode 100644 index 1bca86319c3..00000000000 --- a/mris_svm_classify/Makefile.am +++ /dev/null @@ -1,18 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS=mris_svm_classify -mris_svm_classify_SOURCES=mris_svm_classify.c -mris_svm_classify_LDADD=\ - $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(addprefix $(top_builddir)/, svm-lib/libsvm.a) -mris_svm_classify_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_svm_train/Makefile.am b/mris_svm_train/Makefile.am deleted file mode 100644 index 6e1a3b3e6da..00000000000 --- a/mris_svm_train/Makefile.am +++ /dev/null @@ -1,18 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_svm_train -mris_svm_train_SOURCES=mris_svm_train.c -mris_svm_train_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - ../svm-lib/libsvm.a -mris_svm_train_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_talairach/Makefile.am b/mris_talairach/Makefile.am deleted file mode 100644 index 58ede9c0cce..00000000000 --- a/mris_talairach/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_talairach -mris_talairach_SOURCES=mris_talairach.c -mris_talairach_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_talairach_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_thickness/Makefile.am b/mris_thickness/Makefile.am deleted file mode 100644 index 5e0a23d9bb8..00000000000 --- a/mris_thickness/Makefile.am +++ /dev/null @@ -1,28 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mris_thickness mris_intensity_profile mris_gradient -mris_thickness_SOURCES=mris_thickness.c -mris_thickness_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_thickness_LDFLAGS=$(OS_LDFLAGS) - -mris_intensity_profile_SOURCES=mris_intensity_profile.c -mris_intensity_profile_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_intensity_profile_LDFLAGS=$(OS_LDFLAGS) - - -mris_gradient_SOURCES=mris_gradient.c -mris_gradient_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_gradient_LDFLAGS=$(OS_LDFLAGS) - -EXTRA_DIST = mris_cluster_profiles.c - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_thickness_comparison/Makefile.am b/mris_thickness_comparison/Makefile.am deleted file mode 100644 index 024296768fc..00000000000 --- a/mris_thickness_comparison/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_thickness_comparison -mris_thickness_comparison_SOURCES=mris_thickness_comparison.c -mris_thickness_comparison_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_thickness_comparison_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_thickness_diff/Makefile.am b/mris_thickness_diff/Makefile.am deleted file mode 100644 index 5ad18749a68..00000000000 --- a/mris_thickness_diff/Makefile.am +++ /dev/null @@ -1,16 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_thickness_diff -mris_thickness_diff_SOURCES=mris_thickness_diff.c -mris_thickness_diff_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_thickness_diff_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_topo_fixer/Makefile.am b/mris_topo_fixer/Makefile.am deleted file mode 100644 index e93bbcc7e3e..00000000000 --- a/mris_topo_fixer/Makefile.am +++ /dev/null @@ -1,18 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_topo_fixer -mris_topo_fixer_SOURCES=mris_topo_fixer.cpp -mris_topo_fixer_LDADD= $(addprefix $(top_builddir)/, \ - $(LIBS_MGH) utilscpp/libutilscpp.a ) -mris_topo_fixer_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_transform/Makefile.am b/mris_transform/Makefile.am deleted file mode 100644 index 3ab311dda65..00000000000 --- a/mris_transform/Makefile.am +++ /dev/null @@ -1,18 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_transform -mris_transform_SOURCES=mris_transform.c -mris_transform_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_transform_LDFLAGS=$(OS_LDFLAGS) - -TESTS=test - -EXTRA_DIST=test testdata.tar.gz $(foo_DATA) $(BUILT_SOURCES) - -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_translate_annotation/Makefile.am b/mris_translate_annotation/Makefile.am deleted file mode 100644 index 83ed85b46e6..00000000000 --- a/mris_translate_annotation/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_translate_annotation -mris_translate_annotation_SOURCES=mris_translate_annotation.c -mris_translate_annotation_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_translate_annotation_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_transmantle_dysplasia_paths/Makefile.am b/mris_transmantle_dysplasia_paths/Makefile.am deleted file mode 100644 index 86d0d2007be..00000000000 --- a/mris_transmantle_dysplasia_paths/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_transmantle_dysplasia_paths -mris_transmantle_dysplasia_paths_SOURCES=mris_transmantle_dysplasia_paths.c -mris_transmantle_dysplasia_paths_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_transmantle_dysplasia_paths_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_twoclass/Makefile.am b/mris_twoclass/Makefile.am deleted file mode 100644 index 343ef81a54a..00000000000 --- a/mris_twoclass/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mris_twoclass -mris_twoclass_SOURCES=mris_twoclass.c -mris_twoclass_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_twoclass_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_volmask/Makefile.am b/mris_volmask/Makefile.am deleted file mode 100644 index f17c6fd5598..00000000000 --- a/mris_volmask/Makefile.am +++ /dev/null @@ -1,89 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include $(VTK_CXXFLAGS) -Wno-deprecated - -bin_PROGRAMS=mris_volmask mris_volmask_novtk - -foodir=$(prefix)/docs/xml -foo_DATA=mris_volmask.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mris_volmask.help.xml.html - -if HAVE_VTK_LIBS -bin_PROGRAMS += mris_volmask_vtk -mris_volmask_vtk_SOURCES=mris_volmask_old.cpp cmd_line_interface.cpp -mris_volmask_vtk_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ -$(X_LIBS) \ --ldl -lpthread \ -$(VTK_LIBS) \ -$(VTK_FREETYPE_LIB) $(VTK_PNG_LIB) \ -$(VTK_TIFF_LIB) $(VTK_JPEG_LIB) $(VTK_SQLITE_LIB) \ -$(VTK_Z_LIB) $(VTK_EXPAT_LIB) $(VTK_METAIO_LIB) \ --lvtkFiltering $(VTK_VERDICT_LIB) -lvtkHybrid $(VTK_HDF5_LIB) \ --lvtkRendering -lvtkGraphics \ --lvtkImaging -lvtkftgl \ --lvtkIO $(VTK_LSDYNA_LIB) -lvtkFiltering -lvtkCommon -lvtkDICOMParser \ --lvtksys \ -$(VTK_MPEG2ENCODE_LIB) -lvtkexoIIc -lvtkNetCDF $(VTK_NETCDFCXX_LIB) -endif - -mris_volmask_novtk_SOURCES=mris_volmask_old.cpp cmd_line_interface.cpp -mris_volmask_novtk_CPPFLAGS=-DNO_VTK -mris_volmask_novtk_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) - -mris_volmask_SOURCES=mris_volmask.cpp cmd_line_interface.cpp \ - mris_volmask.help.xml.h -mris_volmask_CPPFLAGS=-DNO_VTK -mris_volmask_CXXFLAGS=$(AM_CFLAGS) $(VXL_CFLAGS) -Wno-non-virtual-dtor -mris_volmask_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) - -TESTS=test_mris_volmask $(top_builddir)/scripts/help_xml_validate - -# CPPUNIT tests -if HAVE_CPPUNIT - -#check_PROGRAMS = TestMRISOBBTree TestMRISDistanceField - -#TESTS = TestMRISOBBTree TestMRISDistanceField - -#TestMRISOBBTree_SOURCES = TestMRISOBBTree.cpp -#TestMRISOBBTree_CXXFLAGS=$(AM_CFLAGS) $(CPPUNIT_CFLAGS) $(VXL_CFLAGS) -Wno-non-virtual-dtor -#TestMRISOBBTree_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(CPPUNIT_LIBS) -lcppunit - -#TestMRISDistanceField_SOURCES = TestMRISDistanceField.cpp -#TestMRISDistanceField_CXXFLAGS=$(AM_CFLAGS) $(CPPUNIT_CFLAGS) $(VXL_CFLAGS) -Wno-non-virtual-dtor -#TestMRISDistanceField_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(CPPUNIT_LIBS) -lcppunit -endif - -# put a wrapper around the bin, used to setup VTK enviro vars -if HAVE_VTK_LIBS -install-exec-hook: - cp $(top_builddir)/mris_volmask/mris_volmask_vtk \ - $(DESTDIR)$(bindir)/mris_volmask_vtk.bin - echo "#!/bin/tcsh -ef" > $(DESTDIR)$(bindir)/mris_volmask_vtk - echo "source \$$FREESURFER_HOME/bin/vtk_setup" \ - >> $(DESTDIR)$(bindir)/mris_volmask_vtk - echo "mris_volmask_vtk.bin \$$argv" >> $(DESTDIR)$(bindir)/mris_volmask_vtk - chmod a+x $(DESTDIR)$(bindir)/mris_volmask_vtk - -uninstall-hook: - rm -f $(DESTDIR)$(bindir)/mris_volmask_vtk.bin -endif - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=cmd_line_interface.h test_mris_volmask $(foo_DATA) \ - TestMRISOBBTree.cpp TestMRISDistanceField.cpp $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mris_volmask.help.xml.h mris_volmask.help.xml.html - diff --git a/mris_volume/Makefile.am b/mris_volume/Makefile.am deleted file mode 100644 index 11121462e6f..00000000000 --- a/mris_volume/Makefile.am +++ /dev/null @@ -1,21 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_volume mris_wm_volume -mris_volume_SOURCES=mris_volume.c -mris_volume_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_volume_LDFLAGS=$(OS_LDFLAGS) - -mris_wm_volume_SOURCES=mris_wm_volume.c -mris_wm_volume_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_wm_volume_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_w_to_curv/Makefile.am b/mris_w_to_curv/Makefile.am deleted file mode 100644 index 63bd3bab8a8..00000000000 --- a/mris_w_to_curv/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = mris_w_to_curv -mris_w_to_curv_SOURCES=mris_w_to_curv.c -mris_w_to_curv_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_w_to_curv_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/mris_warp/Makefile.am b/mris_warp/Makefile.am deleted file mode 100644 index d2a6d934de1..00000000000 --- a/mris_warp/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = mris_warp -mris_warp_SOURCES=mris_warp.c -mris_warp_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_warp_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/mris_watershed/Makefile.am b/mris_watershed/Makefile.am deleted file mode 100644 index 41dcb6b5515..00000000000 --- a/mris_watershed/Makefile.am +++ /dev/null @@ -1,27 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -BUILT_SOURCES=mris_watershed.help.xml.h mris_watershed.help.xml.html - -foodir=$(prefix)/docs/xml -foo_DATA=mris_watershed.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mris_watershed.help.xml.html - -bin_PROGRAMS = mris_watershed -mris_watershed_SOURCES=mris_watershed.c -mris_watershed_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mris_watershed_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -clean-local: - rm -f $(BUILT_SOURCES) diff --git a/mrisp_paint/Makefile.am b/mrisp_paint/Makefile.am deleted file mode 100644 index 89757e14246..00000000000 --- a/mrisp_paint/Makefile.am +++ /dev/null @@ -1,33 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mrisp_paint - -mrisp_paint_SOURCES=mrisp_paint.c mrisp_paint.help.xml.h -mrisp_paint_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mrisp_paint_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mrisp_paint.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mrisp_paint.help.xml.html - -TESTS=$(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=$(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mrisp_paint.help.xml.h mrisp_paint.help.xml.html - diff --git a/mrisp_write/Makefile.am b/mrisp_write/Makefile.am deleted file mode 100644 index 6543b4f8b94..00000000000 --- a/mrisp_write/Makefile.am +++ /dev/null @@ -1,33 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = mrisp_write - -mrisp_write_SOURCES=mrisp_write.c mrisp_write.help.xml.h -mrisp_write_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mrisp_write_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=mrisp_write.help.xml -foo2dir=$(prefix)/docs/html -foo2_DATA=mrisp_write.help.xml.html - -TESTS=$(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=$(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=mrisp_write.help.xml.h mrisp_write.help.xml.html - diff --git a/nmovie/Makefile.am b/nmovie/Makefile.am deleted file mode 100644 index 2a907458822..00000000000 --- a/nmovie/Makefile.am +++ /dev/null @@ -1,42 +0,0 @@ -## -# Makefile.am -## - -if ENABLE_XAWPLUS_APPS -AM_CPPFLAGS=\ - -DHAVE_XAWPLUS $(XAWPLUS_CFLAGS) \ - -DHAVE_OPENGL $(GL_CFLAGS) \ - -I$(top_srcdir)/include \ - -I$(top_srcdir)/unix \ - -I$(top_srcdir)/glut -else -AM_CPPFLAGS=\ - -DHAVE_OPENGL $(GL_CFLAGS) \ - -I$(top_srcdir)/include \ - -I$(top_srcdir)/unix \ - -I$(top_srcdir)/glut -endif -AM_LDFLAGS= - -if HAVE_OPENGL_LIBS -bin_PROGRAMS = nmovie -nmovie_SOURCES=nmovie.c -if ENABLE_XAWPLUS_APPS -nmovie_LDADD= $(addprefix $(top_builddir)/,$(LIBS_MGH)) \ - $(LIBS_OPENGL) $(XAWPLUS_LIBS) $(LIBS_XAWPLUS) -lXext \ - $(top_builddir)/glut/libglut.a -else -nmovie_LDADD= $(addprefix $(top_builddir)/,$(LIBS_MGH)) \ - $(LIBS_OPENGL) -lXt -lXext -lXaw \ - $(top_builddir)/glut/libglut.a -endif -nmovie_LDFLAGS=$(X_LIBS) -else -bin_PROGRAMS= -endif - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/nmovie_qt/Makefile.am b/nmovie_qt/Makefile.am deleted file mode 100644 index 039dcf23204..00000000000 --- a/nmovie_qt/Makefile.am +++ /dev/null @@ -1,92 +0,0 @@ -if ENABLE_QT_APPS - -include $(top_srcdir)/build-aux/autotroll.mk - -bin_PROGRAMS = nmovie_qt - -BUILT_SOURCES = ui_MainWindow.h \ - moc_MainWindow.cpp \ - moc_RenderWidget.cpp - -nmovie_qt_SOURCES = $(BUILT_SOURCES) \ - MainWindow.cpp \ - RenderWidget.cpp \ - main.cpp - -#qrc_nmovie_qt.cpp: nmovie_qt.qrc -# $(RCC) $< -o $@ - -if HAVE_MAC_OSX -AM_CXXFLAGS=\ - -fno-strict-aliasing \ - -Wno-deprecated \ - -Wno-unused \ - -Wno-uninitialized \ - -Wno-return-type \ - -Wno-reorder \ - -Wno-sign-compare \ - -I$(top_srcdir)/include \ - $(GL_CFLAGS) - - -nmovie_qt_CXXFLAGS = $(QT_CXXFLAGS) $(AM_CXXFLAGS) -nmovie_qt_CPPFLAGS = $(QT_CPPFLAGS) $(AM_CPPFLAGS) -nmovie_qt_LDFLAGS = $(QT_LDFLAGS) $(OS_LDFLAGS) -framework Cocoa -framework IOKit -nmovie_qt_LDADD = $(QT_LIBS) \ - $(addprefix $(top_builddir)/, $(LIBS_MGH)) - -uninstall-hook: - rm -f $(DESTDIR)$(bindir)/nmovie_qt - -else - -AM_CXXFLAGS=\ - -fno-strict-aliasing \ - -Wno-deprecated \ - -Wno-unused \ - -Wno-uninitialized \ - -Wno-return-type \ - -Wno-reorder \ - -Wno-sign-compare \ - -I$(top_srcdir)/include \ - $(GL_CFLAGS) - - -nmovie_qt_CXXFLAGS = $(QT_CXXFLAGS) $(AM_CXXFLAGS) -nmovie_qt_CPPFLAGS = $(QT_CPPFLAGS) $(AM_CPPFLAGS) -nmovie_qt_LDFLAGS = $(QT_LDFLAGS) $(OS_LDFLAGS) -nmovie_qt_LDADD = $(QT_LIBS) \ - $(addprefix $(top_builddir)/, $(LIBS_MGH)) - -# put a wrapper around the bin, used to setup tcltktixblt,vtk,kww enviro vars -# and if the OS is MACOSX have a different install-hook to create a bundle -install-exec-hook:nmovie_qt - cp $(top_builddir)/nmovie_qt/nmovie_qt $(DESTDIR)$(bindir)/nmovie_qt.bin - echo "#!/bin/tcsh -ef" > $(DESTDIR)$(bindir)/nmovie_qt - echo "source \$$FREESURFER_HOME/bin/tcl_setup" \ - >> $(DESTDIR)$(bindir)/nmovie_qt - echo "source \$$FREESURFER_HOME/bin/vtk_setup" \ - >> $(DESTDIR)$(bindir)/nmovie_qt - echo "source \$$FREESURFER_HOME/bin/qt_setup" \ - >> $(DESTDIR)$(bindir)/nmovie_qt - echo "nmovie_qt.bin \$$argv" >> $(DESTDIR)$(bindir)/nmovie_qt - chmod a+x $(DESTDIR)$(bindir)/nmovie_qt - if [[ -f /usr/pubsw/bin/chrpath ]]; then \ - /usr/pubsw/bin/chrpath -d $(DESTDIR)$(bindir)/nmovie_qt.bin; fi - -uninstall-hook: - rm -f $(DESTDIR)$(bindir)/nmovie_qt.bin -endif -endif - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=MainWindow.ui MainWindow.h nmovie.pro - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - diff --git a/oct_register_mosaic/Makefile.am b/oct_register_mosaic/Makefile.am deleted file mode 100644 index 1a997c851b8..00000000000 --- a/oct_register_mosaic/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = oct_register_mosaic -oct_register_mosaic_SOURCES=oct_register_mosaic.c -oct_register_mosaic_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -oct_register_mosaic_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/oct_train/Makefile.am b/oct_train/Makefile.am deleted file mode 100644 index ecb59350040..00000000000 --- a/oct_train/Makefile.am +++ /dev/null @@ -1,21 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = oct_train oct_rf_train -oct_train_SOURCES=oct_train.c -oct_train_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -oct_train_LDFLAGS=$(OS_LDFLAGS) - -oct_rf_train_SOURCES=oct_rf_train.c -oct_rf_train_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -oct_rf_train_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/opencl_algorithms/Makefile.am b/opencl_algorithms/Makefile.am deleted file mode 100644 index 2e611339ae8..00000000000 --- a/opencl_algorithms/Makefile.am +++ /dev/null @@ -1,24 +0,0 @@ -# -# Makefile.am for libopencl_algorithms.a -# - -noinst_LIBRARIES=libopencl_algorithms.a - -if BUILDOPENCL -# If OpenCL was detected on the system, include all of the OpenCL code. -# Otherwise, just build versions of the code that do not require -# OpenCL (reference algorithms). -libopencl_algorithms_a_SOURCES = oclDijkstraKernel.cpp oclDijkstraKernel.h \ - oclCommon.cpp oclCommon.h -libopencl_algorithms_a_CXXFLAGS = $(AM_CXXFLAGS) $(OPENCL_CFLAGS) -else -libopencl_algorithms_a_SOURCES = oclDijkstraKernel.cpp -endif - -EXTRA_DIST = dijkstra.cl dijkstra.cl.h make_cl_header.sh - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/optseq2/Makefile.am b/optseq2/Makefile.am deleted file mode 100644 index 9da3eebe946..00000000000 --- a/optseq2/Makefile.am +++ /dev/null @@ -1,30 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = optseq2 -optseq2_SOURCES=optseq2.c -optseq2_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -optseq2_LDFLAGS=$(OS_LDFLAGS) - -# trick to get test data into the build directory -foo_SOURCES= -foo: - if ! test -f "$(top_builddir)/optseq2/test_data.tar.gz"; then \ - cp -v $(top_srcdir)/optseq2/test_data.tar.gz \ - $(top_builddir)/optseq2/; fi; - -check_PROGRAMS=foo - -TESTS=test_optseq2.csh - -EXTRA_DIST=test_optseq2.csh test_data.tar.gz - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/python/freesurfer/__init__.py b/python/freesurfer/__init__.py index 23ac63dbdee..f332129400c 100644 --- a/python/freesurfer/__init__.py +++ b/python/freesurfer/__init__.py @@ -1,11 +1,12 @@ -from .util import * -from .log import * -from .geometry import * -from ._surface import * -from ._normalize import * -from .freeview import * -from . import metrics +# first import basic IO tools +from . import term +from .logging import * +from .parser import ArgParser + +# primary utilities +from .utility import * +# c bindings try: from . import bindings except ImportError: @@ -21,3 +22,9 @@ from .surface import * from .volume import * + +from .geometry import * +from ._surface import * +from ._normalize import * +from .freeview import * +from . import metrics diff --git a/python/freesurfer/_normalize.py b/python/freesurfer/_normalize.py index 739142ad4ea..6a67f9f3578 100644 --- a/python/freesurfer/_normalize.py +++ b/python/freesurfer/_normalize.py @@ -1,8 +1,8 @@ import numpy as np -from sklearn import mixture + def piecewise_linear_normalize(in_img_data, ref_img_data): - """Function to piecewise linearly scale image intensities to training data landmarks""" + '''Function to piecewise linearly scale image intensities to training data landmarks.''' import sklearn.mixture in_img_flat = np.ravel(in_img_data, 'C') in_img_fg = in_img_flat[in_img_flat > 0].reshape(-1, 1) @@ -39,7 +39,7 @@ def piecewise_linear_normalize(in_img_data, ref_img_data): def wm_peak_normalize(in_img_data): - """Function to scale image intensities by setting wm peak to 200""" + '''Function to scale image intensities by setting wm peak to 200.''' import sklearn.mixture in_img_flat = np.ravel(in_img_data, 'C') in_img_fg = in_img_flat[in_img_flat > 0].reshape(-1, 1) @@ -66,9 +66,8 @@ def robust_normalize(in_img_data): return out_img_data def wm_peak_normalize_t2w(in_img_data): - """Function to scale image intensities by setting wm peak to 200""" - - + '''Function to scale image intensities by setting wm peak to 200.''' + import sklearn.mixture in_img_flat = np.ravel(in_img_data, 'C') in_img_fg = in_img_flat[in_img_flat > 0].reshape(-1, 1) @@ -79,20 +78,18 @@ def wm_peak_normalize_t2w(in_img_data): in_img_fg = in_img_fg.reshape(-1,1) # clf = mixture.GMM(n_components=3, covariance_type='full') - # clf = mixture.GaussianMixture(n_components=2, covariance_type='full') clf.fit(in_img_fg) print('GMM centroids are ') print(sorted(clf.means_)) wm_peak_intensity = sorted(clf.means_)[0] - # - # + # h, bin_edges = np.histogram(in_img_fg, 500) # max_bin = np.argmax(h) # mode_h = max_bin * (bin_edges[1] - bin_edges[0]) -# max of means is the wm centroid for t1w images -# wm_peak_intensity = mode_h + # max of means is the wm centroid for t1w images + # wm_peak_intensity = mode_h wm_scaling = 0.3 / wm_peak_intensity print(wm_peak_intensity) @@ -114,10 +111,9 @@ def wm_peak_normalize_t2w(in_img_data): in_img_fg = in_img_fg.reshape(-1,1) # clf = mixture.GMM(n_components=3, covariance_type='full') - # clf = mixture.GaussianMixture(n_components=2, covariance_type='full') clf.fit(in_img_fg) - print('GMM centroids are ') + print('GMM centroids are:') print(sorted(clf.means_)) wm_peak_intensity = sorted(clf.means_)[0] # @@ -156,8 +152,6 @@ def histmatch(in_img_data, ref_img_data): ref_img_data_flat = ref_img_data.flatten() ref_img_fg = ref_img_data_flat[ref_img_data_flat > 0] # foreground is > 0 - # plot histograms - # plt.figure() bins_in = np.linspace(0, 1, 255 / 1) bins_ref = np.linspace(0, 1, 255 / 1) @@ -182,4 +176,4 @@ def histmatch(in_img_data, ref_img_data): for i in range(1, len(bins_in)): out_img_data[(in_img_data > bins_in_z[i - 1]) & (in_img_data <= bins_in_z[i])] = interp_ref_values[i - 1] - return out_img_data, bins_in_z, interp_ref_values \ No newline at end of file + return out_img_data, bins_in_z, interp_ref_values diff --git a/python/freesurfer/_surface.py b/python/freesurfer/_surface.py index ef071bc23d0..5ebb37f5e47 100644 --- a/python/freesurfer/_surface.py +++ b/python/freesurfer/_surface.py @@ -3,7 +3,7 @@ import nibabel as nib import math -from . import errorExit, sample_patch +from . import sample_patch def MRISP(scale, nfuncs): @@ -17,7 +17,7 @@ def averageRadius(surface): xhi = yhi = zhi = -10000.0 xlo = ylo = zlo = 10000.0 - + for (x, y, z) in surface[0]: if x > xhi: xhi = x if x < xlo: xlo = x @@ -121,8 +121,10 @@ def parameterizeSurface(surface, overlay, fno=0, mrisp=None, scale=1.0): fillstatus[fillstatus == filling] = filled mrisp[:] = tmpimage npasses += 1 - if npasses > 1000: errorExit('could not fill parameterization') - if num_unfilled == 0: break + if npasses > 1000: + raise RuntimeError('could not fill parameterization') + if num_unfilled == 0: + break return mrisp diff --git a/python/freesurfer/deeplearn/_deepnet.py b/python/freesurfer/deeplearn/_deepnet.py index 013d84a749f..046c4cfe5b9 100644 --- a/python/freesurfer/deeplearn/_deepnet.py +++ b/python/freesurfer/deeplearn/_deepnet.py @@ -2849,4 +2849,4 @@ def validation_label_generator(self, batch_size): y_list.append(self.data_storage.root.trg_validation[index]) x_list = np.asarray(x_list) y_list = np.asarray(y_list) - yield x_list, y_list \ No newline at end of file + yield x_list, y_list diff --git a/python/freesurfer/deeplearn/_utility.py b/python/freesurfer/deeplearn/_utility.py index 85ddf3b7177..86a4404521b 100644 --- a/python/freesurfer/deeplearn/_utility.py +++ b/python/freesurfer/deeplearn/_utility.py @@ -260,7 +260,7 @@ def build_image_from_patches(in_patches, patch_size, idx_x, idx_y, idx_z, padded count_img_data = count_img_data[patch_size[0]:patch_size[0] + unpadded_img_size[0], patch_size[1]:patch_size[1] + unpadded_img_size[1], patch_size[2]:patch_size[2] + unpadded_img_size[2]] - + return out_img_data, count_img_data diff --git a/python/freesurfer/freeview.py b/python/freesurfer/freeview.py index 5cc1ff24761..7a756c2d248 100644 --- a/python/freesurfer/freeview.py +++ b/python/freesurfer/freeview.py @@ -16,7 +16,6 @@ class Freeview: fv.show() For a quicker but more limited way to view volumes or overlays, see `fv()` and `fvoverlay()`. - ''' def __init__(self): self._tempdir = None diff --git a/python/freesurfer/gems/io.py b/python/freesurfer/gems/io.py index 3ec0ea18a0a..b20eb9ffba1 100644 --- a/python/freesurfer/gems/io.py +++ b/python/freesurfer/gems/io.py @@ -43,4 +43,4 @@ def kvlReadCompressionLookupTable(fileName): # Sort output according to compressedLabel table = sorted(table, key=itemgetter('compressedLabel')) FreeSurferLabels, names, colors = [[entry[key] for entry in table] for key in ['FreeSurferLabel', 'name', 'color']] - return FreeSurferLabels, names, colors \ No newline at end of file + return FreeSurferLabels, names, colors diff --git a/python/freesurfer/gems/merge_alphas.py b/python/freesurfer/gems/merge_alphas.py index 2e0a74ac928..bb784df3b1f 100644 --- a/python/freesurfer/gems/merge_alphas.py +++ b/python/freesurfer/gems/merge_alphas.py @@ -3,11 +3,6 @@ import numpy as np import colorsys -from freesurfer import errorExit - - -logger = logging.getLogger(__name__) - def meshValidityTest(alphas, name): probability_discrepancy = np.max(np.abs(np.sum(alphas, axis=1) - 1)) @@ -17,10 +12,8 @@ def meshValidityTest(alphas, name): def kvlMergeAlphas(alphas, names, mergeOptions, FreeSurferLabels=None, colors=None): - # - # Creates a 'mergedAlphas' matrix where one or more columns of the 'alphas' - # matrix have been "merged" (i.e., added together) - # + '''Creates a 'mergedAlphas' matrix where one or more columns of the 'alphas' + matrix have been "merged" (i.e., added together).''' alpha_count, label_count = alphas.shape if FreeSurferLabels is None: @@ -39,13 +32,14 @@ def kvlMergeAlphas(alphas, names, mergeOptions, FreeSurferLabels=None, colors=No mergedNames.append(mergeOption.mergedName.strip()) for searchString in mergeOption.searchStrings: for structureNumber, name in enumerate(names): - if searchString in name: translationTable[classNumber, structureNumber] = 1.0 - + if searchString in name: + translationTable[classNumber, structureNumber] = 1.0 + if not translationTable.any(): - errorExit('some structures are not associated with any super-structures') - - translationTable = translationTable / np.sum(translationTable, 0) - + raise ValueError('some structures are not associated with any super-structures') + + translationTable = translationTable / np.sum(translationTable, 0) + mergedAlphas = np.dot(alphas, translationTable.T) meshValidityTest(mergedAlphas, 'mergedAlphas') @@ -58,10 +52,10 @@ def kvlMergeAlphas(alphas, names, mergeOptions, FreeSurferLabels=None, colors=No # Print out merge info for classNumber in range(numberOfClasses): - print(mergedNames[classNumber]) - for structureNumber in range(len(names)): - percentage = int(translationTable[classNumber, structureNumber] * 100) - if percentage > 0: - print(' %s (%d%%)' % (names[structureNumber].ljust(len(max(names, key=len))), percentage)) + print(mergedNames[classNumber]) + for structureNumber in range(len(names)): + percentage = int(translationTable[classNumber, structureNumber] * 100) + if percentage > 0: + print(' %s (%d%%)' % (names[structureNumber].ljust(len(max(names, key=len))), percentage)) return mergedAlphas, mergedNames, mergedFreeSurferLabels, mergedColors, translationTable diff --git a/python/freesurfer/logging.py b/python/freesurfer/logging.py new file mode 100644 index 00000000000..e086c01d97e --- /dev/null +++ b/python/freesurfer/logging.py @@ -0,0 +1,136 @@ +import sys +import re +import datetime as dt + +from . import term + + +def log(message): + '''Prints a timestamped message.''' + print(term.cyan(dt.datetime.now().strftime('%H:%M:%S') + ' | ') + message) + + +def warning(message): + '''Prints a warning message.''' + print(term.yellow('warning: ') + message) + + +def error(message): + '''Prints an error message.''' + print(term.red('error: ') + message) + + +def errorExit(message, retcode=1): + '''Prints an error message then calls `sys.exit`. + + Args: + message (str): Message to print. + retcode (int): Exit code. Defaults to 1. + ''' + error(message) + sys.exit(retcode) + + +class Logger(object): + '''A base logging class that writes to a file and stdout (if tee'ing is turned on). + + Note: + To automatically direct all standard output to a `Logger`, + use the `RedirectingLogger` subclass. + + Args: + filename (str): Path to log file. + tee (bool): Write to stdout as well. Defaults to True. + mode (str): File opening mode. Overwrites by default. + ''' + def __init__(self, filename, tee=True, mode='w'): + self.tee = tee + self.filename = filename + self.file = open(self.filename, mode) + self.stdout = sys.stdout + + def __del__(self): + self.close() # be sure to close the file upon deletion + + def write(self, string): + '''Writes a string to the log file and, if tee'd, to the system stdout.''' + if term.istty: + if self.tee: + # write to stdout + self.stdout.write(string) + # write to file + string = term.removecolor(string) + self.file.write(string) + + def flush(self): + '''Flushes the file and, if tee'd, stdout.''' + if self.tee: + self.stdout.flush() + self.file.flush() + + def close(self): + '''Closes the log file.''' + self.file.close() + + +class RedirectingLogger(Logger): + '''A `Logger` that will redirect stdout and stderr to itself after + initialization. Make sure to call `close` when you would no longer like to + redirect the output. + ''' + def __init__(self, *args, **kwargs): + super(RedirectingLogger, self).__init__(*args, **kwargs) + sys.stdout = sys.stderr = self + + def close(self): + '''Closes the log file and resets stdout and stderr to the system defaults.''' + sys.stdout = sys.__stdout__ + sys.stderr = sys.__stderr__ + super(RedirectingLogger, self).close() + + +class Table: + '''Facilitates simple table formatting. + + Args: + columns: List of column header names. + ''' + def __init__(self, columns, precision=2): + self.rows = [] + self.columns = columns + self.precision = precision + + def addRow(self, cells): + '''Adds a row of cells to the table. The number of cells provided must match the + table's number of columns.''' + if len(cells) != len(self.columns): + raise ValueError('number of input cells does not match number of columns') + self.rows.append([self._format(cell) for cell in cells]) + + def getColumn(self, idx): + '''Returns a list of cells for a given column index.''' + return [self.columns[idx]] + [row[idx] for row in self.rows] + + def _format(self, element): + if isinstance(element, float): + return '%.*f' % (self.precision, n) + return str(element) + + def _pad(self, string, width): + # width should never be smaller than the length of the string + return string + ' ' * (width - len(term.removecolor(string))) + + def __str__(self): + # compute column widths + widths = [] + for col in range(len(self.columns)): + colorless = [term.removecolor(cell) for cell in self.getColumn(col)] + widths.append(len(max(colorless, key=len))) + strings = [] + # format header + header = ' '.join([self._pad(name, widths[n]) for n, name in enumerate(self.columns)]) + strings.append(term.bold(header)) + # format rows + for row in self.rows: + strings.append(' '.join([self._pad(cell, widths[n]) for n, cell in enumerate(row)])) + return '\n'.join(strings) diff --git a/python/freesurfer/metrics.py b/python/freesurfer/metrics.py index 14d50a5995b..e15af758290 100644 --- a/python/freesurfer/metrics.py +++ b/python/freesurfer/metrics.py @@ -1,10 +1,8 @@ import numpy as np -from . import error def hausdorffDistance(vol1, vol2, thresh=0.01, measure=np.max): - """ - The Hausdorff distance between two volumes. Computes the max of + """The Hausdorff distance between two volumes. Computes the max of the minimum euclidian distances between bordering voxels of the two input volumes. The mean minimum distance can be reported instead of the max minimum distance by setting the `measure` function @@ -16,18 +14,14 @@ def hausdorffDistance(vol1, vol2, thresh=0.01, measure=np.max): thresh (optional): Input volume threshold. Defaults to 0.01. measure (optional): Function used to calculate the final distance reported. Defaults to `np.max`. - Returns: The Hausdorff distance. - """ - # temporarily import these within the function from scipy.ndimage.morphology import binary_erosion from scipy.spatial.distance import cdist - # make sure inputs are the same shape + # make sure inputs have the same shape if vol1.shape != vol2.shape: - error('hausdorffDistance - inputs must have the same shape') - return np.NaN + raise ValueError('inputs must have the same shape') # find borders by eroding binary masks mask1 = vol1 >= thresh mask2 = vol2 >= thresh diff --git a/python/freesurfer/log.py b/python/freesurfer/parser.py similarity index 63% rename from python/freesurfer/log.py rename to python/freesurfer/parser.py index aa2ff11f89a..e35bea13ef1 100644 --- a/python/freesurfer/log.py +++ b/python/freesurfer/parser.py @@ -1,88 +1,17 @@ import sys -import re -import platform import argparse import textwrap - -def istty(): - """Checks if file descriptor is a terminal device.""" - return hasattr(sys.stdout, 'isatty') and sys.stdout.isatty() - - -class _TerminalColors(dict): - """A class for colorful terminal output.""" - - - def __init__(self): - self.black = self._setCode('\033[30m') - self.red = self._setCode('\033[31m') - self.green = self._setCode('\033[32m') - self.yellow = self._setCode('\033[33m') - self.blue = self._setCode('\033[34m') - self.magenta = self._setCode('\033[35m') - self.cyan = self._setCode('\033[36m') - self.white = self._setCode('\033[37m') - self.underline = self._setCode('\033[4m') - self.bold = self._setCode('\033[1m') - self.dim = self._setCode('\033[2m') - self.end = self._setCode('\033[0m') - - - def _setCode(self, code): - if istty() and platform.system() in ("Darwin", "Linux"): return code - else: return '' - - -# create a global, preinitialized TerminalColors -term = _TerminalColors() - - -def warning(message): - """Prints a warning message.""" - print(term.yellow + 'warning: '+ term.end + message) - - -def error(message): - """Prints an error message.""" - print(term.red + 'error: ' + term.end + message) - - -def errorExit(message, ret=1): - """Prints an error message and exits with specified return code.""" - error(message) - sys.exit(ret) - - -# global verbosity levels -_verbosity = 0 - - -def setVerbosity(level): - """Sets the global verbosity level.""" - global _verbosity - _verbosity = level - - -def verbose(message, level=1): - """Prints message dependent on the global verbosity level.""" - if _verbosity >= level: - print(message) - - -# ----------------- Argument Parsing and Help Formatting ----------------- +from . import term class _HelpFormatter(argparse.HelpFormatter): - """HelpFormatter subclass used to format the help output to the freesurfer standard.""" - - # Set default indent to 4 spaces + # set default indent to 4 spaces def __init__(self, indent_increment=4, *args, **kwargs): super(_HelpFormatter, self).__init__(indent_increment=indent_increment, *args, **kwargs) - - # Format each argument + # format each argument def _format_action(self, action): parts = [self._current_indent * ' ' + self._format_action_invocation(action)] if action.help: @@ -93,47 +22,45 @@ def _format_action(self, action): self._dedent() return '\n'.join(parts) + '\n\n' - - # Format the argument invocation syntax + # format the argument invocation syntax def _format_action_invocation(self, action): if not action.option_strings: metavar, = self._metavar_formatter(action, action.dest)(1) - return term.bold + metavar + term.end + return term.bold(metavar) else: - msg = ', '.join([term.bold + opt + term.end for opt in action.option_strings]) + msg = ', '.join([term.bold(opt) for opt in action.option_strings]) if action.nargs != 0: default = self._get_default_metavar_for_optional(action) - msg += ' ' + term.blue + self._format_args(action, default) + term.end + msg += ' ' + term.blue(self._format_args(action, default).upper()) return msg - - # Format the usage string + # format the usage string def _format_usage(self, usage, actions, groups, prefix): if prefix is None: prefix = 'usage: ' - # If usage is specified, use that + # if usage is specified, use that if usage is not None: usage = usage % dict(prog=self._prog) - # If no optionals or positionals are available, usage is just prog + # if no optionals or positionals are available, usage is just prog elif usage is None and not actions: usage = '%(prog)s' % dict(prog=self._prog) - # If optionals and positionals are available, calculate usage + # if optionals and positionals are available, calculate usage elif usage is None: prog = '%(prog)s' % dict(prog=self._prog) - # Split flags from positionals + # split flags from positionals positionals = [action for action in actions if not action.option_strings] flags = [action for action in actions if action.option_strings] - # Build full usage string + # build full usage string format = self._format_actions_usage action_usage = format(positionals + flags, groups) usage = ' '.join([s for s in [prog, action_usage] if s]) - # Wrap the usage parts if it's too long + # wrap the usage parts if it's too long text_width = self._width - self._current_indent if action_usage and len(prefix) + len(usage) > text_width: usage = prog + ' ' @@ -145,7 +72,6 @@ def _format_usage(self, usage, actions, groups, prefix): return self._current_indent * ' ' + prefix + usage + '\n\n' - # Format the usage string arguments def _format_actions_usage(self, actions, groups): parts = [] @@ -162,21 +88,18 @@ def _format_actions_usage(self, actions, groups): parts.append('[options]') return ' '.join(parts) - - # Use type for flagged argument metavar + # use type for flagged argument metavar def _get_default_metavar_for_optional(self, action): if action.type: return action.type.__name__ else: return action.dest - - # Don't remove newlines when adding text + # don't remove newlines when adding text def _fill_text(self, text, width, indent): return '\n'.join([textwrap.fill(line, width, initial_indent=indent, subsequent_indent=indent) for line in text.strip().splitlines()]) - - # Don't remove newlines when adding help text to arguments + # don't remove newlines when adding help text to arguments def _split_lines(self, text, width): lines = [] for line in text.strip().splitlines(): @@ -186,10 +109,9 @@ def _split_lines(self, text, width): class _Section(argparse.HelpFormatter._Section): - - # Reformat each section's header + # reformat each section's header def format_help(self): - # Format the indented section + # format the indented section if self.parent is not None: self.formatter._indent() join = self.formatter._join_parts @@ -197,53 +119,49 @@ def format_help(self): if self.parent is not None: self.formatter._dedent() - # Return nothing if the section was empty + # return nothing if the section was empty if not item_help: return '' - # Add the heading if the section was non-empty + # add the heading if the section was non-empty if self.heading is not argparse.SUPPRESS and self.heading is not None: indent = self.formatter._current_indent * ' ' - heading = indent + term.bold + self.heading + term.end + '\n' + heading = indent + term.bold(self.heading) + '\n' else: heading = '' - # Join the section-initial newline, the heading and the help + # join the section-initial newline, the heading and the help return join(['\n', heading, item_help, '\n']) class ArgParser(argparse.ArgumentParser): """ArgumentParser subclass to format the help interface to the freesurfer standard.""" - - # Use the custom freesurfer help formatter by default + # use the custom freesurfer help formatter by default def __init__(self, add_help=True, allow_abbrev=False, formatter_class=_HelpFormatter, *args, **kwargs): super(ArgParser, self).__init__(allow_abbrev=allow_abbrev, formatter_class=formatter_class, add_help=False, *args, **kwargs) - # Let's organize default arguments by required/optional status instead of positional/flagged + # let's organize default arguments by required/optional status instead of positional/flagged self._action_groups.clear() self._required = self.add_argument_group('REQUIRED ARGUMENTS') self._optionals = self.add_argument_group('OPTIONAL ARGUMENTS') # _positionals is used as a default group in some places, so we'll remap it to _required self._positionals = self._required # By default, argparse adds the help flag at the beginning of the argument list. To get the help - # flag at the end, we'll add it manually in parse_args(). + # flag at the end, we'll add it manually in parse_args() self.add_help = add_help - - # Wrap the default parse_args + # wrap the default parse_args def parse_args(self, args=None, namespace=None): - # Print usage and exit if no inputs provided. - if not args and len(sys.argv[1:]) == 0: + # print usage and exit if no inputs are provided + if not args and not sys.argv[1:] and self._required._group_actions: self.print_usage() self.exit(2) - # Add help flag (at the end instead of the beginning) + # add help flag (at the end instead of the beginning) if self.add_help: self.add_argument('-h', '--help', action='help', help='Show this help message and exit.') - # Parse return super(ArgParser, self).parse_args(args, namespace) - - # Make sure default args are added to the appropriate custom groups + # make sure default args are added to the appropriate custom groups def _add_action(self, action): if action.required: self._required._add_action(action) @@ -251,31 +169,30 @@ def _add_action(self, action): self._optionals._add_action(action) return action - - # Format the help text layout + # format the help text layout def format_help(self): formatter = self._get_formatter() - # Usage + # usage formatter.start_section('USAGE') formatter.add_usage(self.usage, self._actions, self._mutually_exclusive_groups, prefix='') formatter.end_section() - # Description + # description if self.description: formatter.start_section('DESCRIPTION') formatter.add_text(self.description) formatter.end_section() - # Positionals, optionals and user-defined groups + # positionals, optionals and user-defined groups for action_group in self._action_groups: formatter.start_section(action_group.title) formatter.add_text(action_group.description) formatter.add_arguments(action_group._group_actions) formatter.end_section() - # Epilog + # epilog formatter.add_text(self.epilog) - # Determine help from format above + # determine help from format above return formatter.format_help() diff --git a/python/freesurfer/samseg/color_scheme.py b/python/freesurfer/samseg/color_scheme.py index daa2c1b7cc5..a1df42e928a 100644 --- a/python/freesurfer/samseg/color_scheme.py +++ b/python/freesurfer/samseg/color_scheme.py @@ -115,4 +115,4 @@ def generate_python_code_for_default_palette(palette): if __name__ == '__main__': - generate_python_code_for_default_palette(maximal_distance_palette(metric=perceptual_difference)) \ No newline at end of file + generate_python_code_for_default_palette(maximal_distance_palette(metric=perceptual_difference)) diff --git a/python/freesurfer/samseg/figures.py b/python/freesurfer/samseg/figures.py index 37954b3d5e9..354f31ad69c 100644 --- a/python/freesurfer/samseg/figures.py +++ b/python/freesurfer/samseg/figures.py @@ -1,6 +1,5 @@ import math import numpy as np -from freesurfer import errorExit try: import pyqtgraph as pg @@ -55,8 +54,8 @@ def initVisualizer(showfigs, movie): if showfigs or movie: if not SAMSEG_HAVE_QT_PACKAGES: - errorExit('the samseg visualization tool requires pyqtgraph and pyqt5 - ' - 'please install these python packages to show figures') + raise RuntimeError('the samseg visualization tool requires pyqtgraph and pyqt5 - ' + 'please install these python packages to show figures') else: return ShowFigures(show_flag=showfigs, movie_flag=movie) else: diff --git a/python/freesurfer/samseg/register_atlas.py b/python/freesurfer/samseg/register_atlas.py index 1aefff6edbe..6957327ec29 100644 --- a/python/freesurfer/samseg/register_atlas.py +++ b/python/freesurfer/samseg/register_atlas.py @@ -38,7 +38,7 @@ def registerAtlas( # ------ Register Image ------ if worldToWorldTransformMatrix is not None: - # The world-to-world transfrom is externally given, so let's just compute the corresponding image-to-image + # The world-to-world transfrom is externally given, so let's just compute the corresponding image-to-image # transform (needed for subsequent computations) and be done print('world-to-world transform supplied - skipping registration') imageToImageTransformMatrix = np.linalg.inv(imageToWorldTransformMatrix) @ worldToWorldTransformMatrix @ templateImageToWorldTransformMatrix @@ -54,7 +54,7 @@ def registerAtlas( K = 1e-7 maximalDeformationStopCriterion = 0.005 lineSearchMaximalDeformationIntervalStopCriterion = maximalDeformationStopCriterion # Doesn't seem to matter very much - + # Initialization if initLTAFile is None: initialWorldToWorldTransformMatrix = np.identity(4) @@ -81,7 +81,7 @@ def registerAtlas( rotationMatrix[2, 1] = sin_theta rotationMatrix[2, 2] = cos_theta initialWorldToWorldTransformMatrix = rotationMatrix @ initialWorldToWorldTransformMatrix - + # Isotropic scaling scaling = 0.9 scalingMatrix = np.diag([scaling, scaling, scaling, 1.0]) @@ -95,7 +95,7 @@ def registerAtlas( voxelSpacing = np.sum(imageToWorldTransformMatrix[0:3, 0:3] ** 2, axis=0) ** (1 / 2) downSamplingFactors = np.round(targetDownsampledVoxelSpacing / voxelSpacing) downSamplingFactors[downSamplingFactors < 1] = 1 - + # Use initial transform to define the reference (rest) position of the mesh (i.e. the one # where the log-prior term is zero) mesh_collection = gems.KvlMeshCollection() @@ -103,7 +103,7 @@ def registerAtlas( mesh_collection.k = K * np.prod(downSamplingFactors) mesh_collection.transform(gems.KvlTransform(requireNumpyArray(initialImageToImageTransformMatrix))) mesh = mesh_collection.reference_mesh - + # Get image data imageBuffer = image.getImageBuffer() visualizer.show(images=imageBuffer, window_id='atlas initial', title='Initial Atlas Registration') diff --git a/python/freesurfer/samseg/samsegment.py b/python/freesurfer/samseg/samsegment.py index 228cd7c14c0..0cc4f9289fc 100644 --- a/python/freesurfer/samseg/samsegment.py +++ b/python/freesurfer/samseg/samsegment.py @@ -229,7 +229,7 @@ def samsegment( if saveHistory: history['historyWithinEachMultiResolutionLevel'] = [] - print('samsegment Starting Resolution Loop VmPeak', fs.GetVmPeak()) + fs.printPeakMemory('samsegment starting resolution loop') numberOfMultiResolutionLevels = len(optimizationOptions.multiResolutionSpecification) for multiResolutionLevel in range(numberOfMultiResolutionLevels): @@ -344,7 +344,7 @@ def samsegment( # Main iteration loop over both EM and deformation for iterationNumber in range(maximumNumberOfIterations): logger.debug('iterationNumber=%d', iterationNumber) - print('samsegment Resolution %d Iter %d VmPeak' % (multiResolutionLevel, iterationNumber), fs.GetVmPeak()) + fs.printPeakMemory('samsegment resolution %d iteration %d' % (multiResolutionLevel, iterationNumber)) # Part I: estimate Gaussian mixture model parameters, as well as bias field parameters using EM. @@ -620,12 +620,11 @@ def samsegment( # Get the final node positions finalNodePositions = mesh.points - # Transform back in template space (i.e., undoing the affine registration - # that we applied), and save for later usage + # Transform back in template space (i.e., undoing the affine registration that we applied), and save for later usage tmp = np.linalg.solve(totalTransformationMatrix, np.pad(finalNodePositions, ((0, 0), (0, 1)), 'constant', constant_values=1).T).T finalNodePositionsInTemplateSpace = tmp[:, 0: 3] - + # Record deformation delta here in lieu of maintaining history nodeDeformationInTemplateSpaceAtPreviousMultiResolutionLevel = finalNodePositionsInTemplateSpace - initialNodePositionsInTemplateSpace @@ -653,7 +652,7 @@ def samsegment( # OK, now that all the parameters have been estimated, try to segment the original, full resolution image # with all the original labels (instead of the reduced "super"-structure labels we created) - print('samsegment starting sementation VmPeak', fs.GetVmPeak()) + fs.printPeakMemory('samsegment starting segmentation') # Get bias field corrected images biasCorrectedImageBuffers = np.zeros((imageSize[0], imageSize[1], imageSize[2], numberOfContrasts)) @@ -677,7 +676,7 @@ def samsegment( transformMatrix = transform.as_numpy_array tmp = np.linalg.solve(transformMatrix, np.pad(nodePositions, ((0, 0), (0, 1)), mode='constant', constant_values=1).T).T nodePositionsInTemplateSpace = tmp[:, 0: 3] - + # Get the estimated warp in template space [estimatedNodeDeformationInTemplateSpace, estimated_averageDistance, estimated_maximumDistance] = gems.kvlWarpMesh( optimizationOptions.multiResolutionSpecification[-1].atlasFileName, @@ -764,9 +763,9 @@ def samsegment( for contrastNumber, imageFileName in enumerate(imageFileNames): image_base_path, ext = os.path.splitext(imageFileName) data_path, scanName = os.path.split(image_base_path) - + # First bias field - we're computing it also outside of the mask, but clip the - # intensities there to the range observed inside the mask (with some margin) to + # intensities there to the range observed inside the mask (with some margin) to # avoid crazy extrapolation values logBiasField = biasFields[:, :, :, contrastNumber] clippingMargin = np.log(2) @@ -785,7 +784,7 @@ def samsegment( outputFileName, gems.KvlTransform(requireNumpyArray(imageToWorldTransformMatrix)) ) - + # Then bias field corrected data biasCorrected = np.zeros(nonCroppedImageSize, dtype=np.float32) biasCorrected[ diff --git a/python/freesurfer/samseg/utilities.py b/python/freesurfer/samseg/utilities.py index e33d296ccf7..fbca07ceb40 100644 --- a/python/freesurfer/samseg/utilities.py +++ b/python/freesurfer/samseg/utilities.py @@ -67,7 +67,7 @@ def ensureDims(np_array, dims): def icv(structures, includeStructures=None): if not includeStructures: print("using default intracranial structures to compute sbtiv measure") - includeStructures = [ + includeStructures = [ 'Brain-Stem', 'CSF', 'Left-Cerebellum-Cortex', @@ -109,4 +109,4 @@ def icv(structures, includeStructures=None): 'non-WM-hypointensities', '5th-Ventricle' ] - return sum(structure[1] for structure in structures if structure[0] in includeStructures) \ No newline at end of file + return sum(structure[1] for structure in structures if structure[0] in includeStructures) diff --git a/python/freesurfer/term.py b/python/freesurfer/term.py new file mode 100644 index 00000000000..bbe97ccaaf1 --- /dev/null +++ b/python/freesurfer/term.py @@ -0,0 +1,74 @@ +import sys +import re +import shutil +import platform + + +# terminal color codes +colors = { + 'black': '\033[30m', + 'red': '\033[31m', + 'green': '\033[32m', + 'yellow': '\033[33m', + 'blue': '\033[34m', + 'magenta': '\033[35m', + 'cyan': '\033[36m', + 'white': '\033[37m', + 'underline': '\033[4m', + 'dim': '\033[2m', + 'bold': '\033[1m', + 'end': '\033[0m', +} + +# check if tty allows colors +istty = hasattr(sys.stdout, 'isatty') and sys.stdout.isatty() +colorsEnabled = istty and platform.system() in ("Darwin", "Linux") +# clear all color codes if they're not enabled +if not colorsEnabled: + colors = dict.fromkeys(colors, '') + +# temporary function to dynamically create string-wrapping methods +def mkmethod(name, code): + def wrapstring(string): + return ''.join((str(code), string, colors['end'])) + return wrapstring + +# create the color methods and remove the temporary variables +for color, code in colors.items(): + vars()[color] = mkmethod(color, code) +del color, code, mkmethod + + +def colorformat(string): + '''Formats a string with the text formatting options available in `colors`. + + Args: + string (str): String to format. + Returns: + The formatted string. + ''' + return string.format(**colors) + + +def removecolor(string): + '''Removes color codes from a string. + + Args: + string (str): String to reformat. + Returns: + The string with color codes removed. + ''' + colorless = re.sub('\\033\[\d\dm', '', string) + colorless = re.sub('\\033\[\dm', '', colorless) + return colorless + + +def width(fallback=60): + '''Gets the current terminal width. + + Args: + fallback (int): Default width if none is found. Defaults to 60. + Returns: + Terminal width. + ''' + return shutil.get_terminal_size((fallback, 20)).columns diff --git a/python/freesurfer/test.py b/python/freesurfer/test.py index 3ca995de0c0..ceb7f35a4a8 100644 --- a/python/freesurfer/test.py +++ b/python/freesurfer/test.py @@ -1,189 +1,180 @@ -import os -import os.path as op +import os, os.path as op import sys -import argparse -from .util import run, rmdir, rmext -from .log import term, errorExit - - -# This class is built specifically for configuring regression tests on -# freesurfer binaries within the main source tree. This assumes all test data is -# stored as a 'testdata.tar.gz' tarball in the directory where the test script -# lives. Commands should be tested using run(), and outputs should be compared -# against reference data by using the diff(), mridiff, or surfdiff() functions. -# Example: -# -# rt = fst.RegressionTest() -# -# rt.run('mri_normalize -mprage nu.mgz T1.mgz') -# rt.mridiff('T1.mgz', 'T1.ref.mgz') -# -# rt.run('mri_normalize -gentle orig.mgz gentle.mgz') -# rt.mridiff('gentle.mgz', 'gentle.ref.mgz') -# -# rt.cleanup() -# -# The initialization of a RegressionTest object will parse the command line args and -# look for the --regenerate flag, which will overwrite the reference data with any -# produced outputs specified in the diff functions. +import shutil + +from . import run, term, errorExit, ArgParser + class RegressionTest: - def __init__(self): - # parse command line arguments - parser = argparse.ArgumentParser() - parser.add_argument('--regenerate', action='store_true', help='regenerate the reference data') - parser.add_argument('--keep-data', action='store_true', help='keep the testdata dir even after success') - args = parser.parse_args() - self.keepdata = args.keep_data - # get directory of the test script - self.testdir = os.getcwd() - self.testdatadir = op.join(self.testdir, 'testdata') - self.scriptdir = op.dirname(op.realpath(sys.argv[0])) - self.testdatatar = op.join(self.scriptdir, 'testdata.tar.gz') - self.fs_home = self.findPath(self.scriptdir, 'distribution') - self.setEnvironment() - # if regenerating testdata... - self.regenerate = args.regenerate - if self.regenerate: - print('regenerating %s testdata' % op.basename(self.scriptdir)) - # make the tmp generation directory - self.regeneration_dir = op.join(self.testdir, 'testdata_regeneration') - rmdir(self.regeneration_dir) - os.makedirs(self.regeneration_dir) - os.chdir(self.regeneration_dir) - # extract the original testdata to get replaced later - self.runcmd('tar -xzvf ' + self.testdatatar) - os.chdir(self.testdir) - - - # set default testing environment - def setEnvironment(self): - os.environ['FREESURFER_HOME'] = self.fs_home - os.environ['SUBJECTS_DIR'] = self.testdatadir - os.environ['FSLOUTPUTTYPE'] = 'NIFTI_GZ' - # set up martinos license if needed - have_license = os.environ.get('FS_LICENSE') or \ - op.exists(op.join(self.fs_home, '.license')) or \ - op.exists(op.join(self.fs_home, 'license.txt')) - if not have_license and op.exists('/space/freesurfer/.license'): - os.environ["FS_LICENSE"] = '/space/freesurfer/.license' - - - # recursively search upwards for a given target - # this is used to locate the 'distribution' folder or the compiled 'mri_diff' - # in the build directory - def findPath(self, startpath, target): - distpath = op.join(startpath, target) - if not op.exists(distpath): - parent = op.abspath(op.join(startpath, '..')) - if parent == '/': errorExit("max recursion reached - could not locate '%s'" % target) - return self.findPath(parent, target) - return distpath - - - # print and run a command, and exit if it fails - def runcmd(self, cmd, fatal=True): - print(term.bold + '>> ' + cmd + term.end) - ret = run(cmd) - if fatal and ret != 0: - errorExit('"%s" failed' % cmd) - return ret - - - # a fatal cd - def cd(self, dirname): - if not op.isdir(dirname): errorExit('directory "%s" does not exist' % dirname) - os.chdir(dirname) - - - # run a test command (this is what should be called from the actual test script) - def run(self, cmd, threads=None, allow_failure=False, expect_failure=False): - self.cd(self.testdir) - # extract the testdata - rmdir(self.testdatadir) - # self.runcmd('tar -xzvf ' + self.testdatatar) - self.runcmd('tar -xzvf ' + '"' + self.testdatatar + '"') - self.cd(self.testdatadir) - # set number of OMP threads if necessary - if threads is not None: - os.environ['OMP_NUM_THREADS'] = str(threads) - print('setting OMP_NUM_THREADS = %s' % os.environ['OMP_NUM_THREADS']) - # run the test command - assumes the command is located in the testdir (above testdatadir) - ret = self.runcmd('../' + cmd, fatal=False) - if expect_failure: - if ret == 0: errorExit('test command "%s" returned 0, but expected a failure') - elif ret != 0 and not allow_failure: errorExit('test command "%s" failed' % cmd) - - - # a simple diff using the standard unix diff command - def diff(self, orig, ref, ignore_comments=False): - if self.regenerate: - self._regen(orig, ref) - else: - self.cd(self.testdatadir) - cmd = 'diff %s %s' % (orig, ref) - if ignore_comments: - cmd += " -I '#'" - if self.runcmd(cmd, fatal=False) != 0: - errorExit('diff of %s and %s failed' % (orig, ref)) - - - # run a diff on two volumes (calls mri_diff, which must be already - # built in the source directory) - def mridiff(self, orig, ref, thresh=0.0, res_thresh=1e-6, geo_thresh=8e-6, flags=""): - if self.regenerate: - self._regen(orig, ref) - else: - self.cd(self.testdatadir) - diffcmd = op.relpath(self.findPath(self.testdatadir, 'mri_diff/mri_diff')) - cmd = '%s %s %s' % (diffcmd, orig, ref) - origname = rmext(op.basename(orig)) - cmd += ' --debug --diff diff-%s.mgz --log diff-%s.log' % (origname, origname) - cmd += ' --thresh %f --res-thresh %f --geo-thresh %f %s' % (thresh, res_thresh, geo_thresh, flags) - if self.runcmd(cmd, fatal=False) != 0: - errorExit('mri_diff of %s and %s failed' % (orig, ref)) - - - # run a diff on two surfs (calls mris_diff, which must be already - # built in the source directory) - def surfdiff(self, orig, ref, flags=""): - if self.regenerate: - self._regen(orig, ref) - else: - self.cd(self.testdatadir) - diffcmd = op.relpath(self.findPath(self.testdatadir, 'mris_diff/mris_diff')) - cmd = '%s %s %s --debug %s' % (diffcmd, orig, ref, flags) - if self.runcmd(cmd, fatal=False) != 0: - errorExit('mris_diff of %s and %s failed' % (orig, ref)) - self.cd(self.testdir) # return to testdir - - - # overwrite a reference file with the observed output - # this will re-tar and overwrite the primary testdata.tar.gz - def _regen(self, orig, ref): - os.chdir(self.regeneration_dir) - # replace the old with the new - self.runcmd('mv -f %s %s' % (op.join(op.relpath(self.testdatadir), orig), op.join('testdata', ref))) - self.cd(self.testdatadir) - - - # delete the testdata directory and output any final messages - # this should only get called when the whole test finishes successfully - def cleanup(self): - self.cd(self.testdir) - if not self.keepdata: rmdir('testdata') - # tar the regenerated data - if self.regenerate: - # tar up the testdata - self.cd(self.regeneration_dir) - self.runcmd('tar -czvf testdata.tar.gz testdata') - # make sure the annex file is unlocked before replacing it - os.chdir(self.scriptdir) - self.runcmd('git annex unlock testdata.tar.gz') - self.runcmd('mv -f %s .' % op.join(self.regeneration_dir, 'testdata.tar.gz')) - rmdir(self.regeneration_dir) - print('testdata has been regenerated') - print('make sure to run "git annex add testdata.tar.gz" to rehash before committing') - self.cd(self.testdir) - else: - print('%s[success]%s %s test has passed' % (term.green, term.end, op.basename(self.scriptdir))) + ''' + This class is built specifically for configuring regression tests for + freesurfer binaries in the main source tree. This assumes all test data is + stored as a 'testdata.tar.gz' tarball in the directory where the test script + lives. Commands should be tested using run(), and outputs should be compared + against reference data by using the diff(), mridiff, or surfdiff() functions. + Example: + + rt = fst.RegressionTest() + + rt.run('mri_normalize -mprage nu.mgz T1.mgz') + rt.mridiff('T1.mgz', 'T1.ref.mgz') + + rt.run('mri_normalize -gentle orig.mgz gentle.mgz') + rt.mridiff('gentle.mgz', 'gentle.ref.mgz') + + rt.cleanup() + + The initialization of a RegressionTest object will parse the command line and + look for the --regenerate flag, which will overwrite the reference data with any + produced outputs specified in the diff functions. + ''' + + def __init__(self): + # parse command line arguments + parser = ArgParser() + parser.add_argument('--regenerate', action='store_true', help='Regenerate the reference data.') + parser.add_argument('--keep-data', action='store_true', help='Keep the testdata dir even after success.') + args = parser.parse_args() + + # get directory of the test script + self.keepdata = args.keep_data + self.testdir = os.getcwd() + self.testdatadir = op.join(self.testdir, 'testdata') + self.scriptdir = op.dirname(op.realpath(sys.argv[0])) + self.testdatatar = op.join(self.scriptdir, 'testdata.tar.gz') + self.fshome = self._findPath(self.scriptdir, 'distribution') + self._setEnvironment() + + # if regenerating testdata... + self.regenerate = args.regenerate + if self.regenerate: + print('regenerating %s testdata' % op.basename(self.scriptdir)) + # make the tmp generation directory + self.regeneration_dir = op.join(self.testdir, 'testdata_regeneration') + shutil.rmtree(self.regeneration_dir, ignore_errors=True) + os.makedirs(self.regeneration_dir) + os.chdir(self.regeneration_dir) + # extract the original testdata to get replaced later + self._runcmd('tar -xzvf "%s"' % self.testdatatar) + os.chdir(self.testdir) + + def _setEnvironment(self): + # setup the default testing environment + os.environ['FREESURFER_HOME'] = self.fshome + os.environ['SUBJECTS_DIR'] = self.testdatadir + os.environ['FSLOUTPUTTYPE'] = 'NIFTI_GZ' + # setup martinos license if needed + haveLicense = os.environ.get('FS_LICENSE') or \ + op.exists(op.join(self.fshome, '.license')) or \ + op.exists(op.join(self.fshome, 'license.txt')) + if not haveLicense and op.exists('/space/freesurfer/.license'): + os.environ["FS_LICENSE"] = '/space/freesurfer/.license' + + # recursively search upwards for a target + # this is used to locate the 'distribution' folder or the compiled 'mri_diff' + # in the build directory + def _findPath(self, startpath, target): + distpath = op.join(startpath, target) + if not op.exists(distpath): + parent = op.abspath(op.join(startpath, '..')) + if parent == '/': + errorExit("max recursion reached - could not locate '%s'" % target) + return self._findPath(parent, target) + return distpath + + # print and run a command, and exit if it fails + def _runcmd(self, cmd, fatal=True): + print(term.bold('>> ' + cmd)) + ret = run(cmd) + if fatal and ret != 0: + errorExit('"%s" failed' % cmd) + return ret + + def run(self, cmd, threads=None, allow_failure=False, expect_failure=False): + '''Runs a command (this is what should be called from the actual test script).''' + os.chdir(self.testdir) + # extract the testdata + shutil.rmtree(self.testdatadir, ignore_errors=True) + self._runcmd('tar -xzvf "%s"' % self.testdatatar) + os.chdir(self.testdatadir) + # set number of OMP threads if necessary + if threads is not None: + os.environ['OMP_NUM_THREADS'] = str(threads) + print('setting OMP_NUM_THREADS = %s' % os.environ['OMP_NUM_THREADS']) + # run the test command - assumes the command is located in the testdir (above testdatadir) + ret = self._runcmd('../' + cmd, fatal=False) + if expect_failure: + if ret == 0: + errorExit('test command "%s" returned 0, but expected a failure') + elif ret != 0 and not allow_failure: + errorExit('test command "%s" failed' % cmd) + + def diff(self, orig, ref, ignore_comments=False): + '''Runs the standard unix diff command.''' + if self.regenerate: + self._regen(orig, ref) + else: + os.chdir(self.testdatadir) + cmd = 'diff %s %s' % (orig, ref) + if ignore_comments: + cmd += " -I '#'" + if self._runcmd(cmd, fatal=False) != 0: + errorExit('diff of %s and %s failed' % (orig, ref)) + + def mridiff(self, orig, ref, thresh=0.0, res_thresh=1e-6, geo_thresh=8e-6, flags=""): + '''Runs a diff on two volumes (calls mri_diff, which must be already built in the source directory).''' + if self.regenerate: + self._regen(orig, ref) + else: + os.chdir(self.testdatadir) + diffcmd = op.relpath(self._findPath(self.testdatadir, 'mri_diff/mri_diff')) + cmd = '%s %s %s' % (diffcmd, orig, ref) + origname = op.basename(orig) + for ext in ('.mgh', '.mgz', '.nii', '.nii.gz'): + if orig.endswith(ext): + origname = origname[:-len(ext)] + cmd += ' --debug --diff diff-%s.mgz --log diff-%s.log' % (origname, origname) + cmd += ' --thresh %f --res-thresh %f --geo-thresh %f %s' % (thresh, res_thresh, geo_thresh, flags) + if self._runcmd(cmd, fatal=False) != 0: + errorExit('mri_diff of %s and %s failed' % (orig, ref)) + + def surfdiff(self, orig, ref, flags=""): + '''Runs a diff on two surfs (calls `mris_diff`, which must be already built in the source directory).''' + if self.regenerate: + self._regen(orig, ref) + else: + os.chdir(self.testdatadir) + diffcmd = op.relpath(self._findPath(self.testdatadir, 'mris_diff/mris_diff')) + cmd = '%s %s %s --debug %s' % (diffcmd, orig, ref, flags) + if self._runcmd(cmd, fatal=False) != 0: + errorExit('mris_diff of %s and %s failed' % (orig, ref)) + os.chdir(self.testdir) # return to testdir + + def _regen(self, orig, ref): + # overwrites a reference file with the observed output + # this will re-tar and overwrite the primary testdata.tar.gz + os.chdir(self.regeneration_dir) + # replace the old with the new + self._runcmd('mv -f %s %s' % (op.join(op.relpath(self.testdatadir), orig), op.join('testdata', ref))) + os.chdir(self.testdatadir) + + def cleanup(self): + '''Deletes the testdata directory and outputs any final messages. This should only get called when the + whole test finishes successfully.''' + os.chdir(self.testdir) + if not self.keepdata: + shutil.rmtree('testdata', ignore_errors=True) + if self.regenerate: + # tar the regenerated data + os.chdir(self.regeneration_dir) + self._runcmd('tar -czvf testdata.tar.gz testdata') + # make sure the annex file is unlocked before replacing it + os.chdir(self.scriptdir) + self._runcmd('git annex unlock testdata.tar.gz') + self._runcmd('mv -f %s .' % op.join(self.regeneration_dir, 'testdata.tar.gz')) + shutil.rmtree(self.regeneration_dir) + print('testdata has been regenerated') + print('make sure to run "git annex add testdata.tar.gz" to rehash before committing') + os.chdir(self.testdir) + else: + print('%s %s test has passed' % (term.green('[success]'), op.basename(self.scriptdir))) diff --git a/python/freesurfer/util.py b/python/freesurfer/util.py deleted file mode 100644 index 21dd47769e4..00000000000 --- a/python/freesurfer/util.py +++ /dev/null @@ -1,103 +0,0 @@ -import sys -import os -import shutil -import select -import datetime as dt -import subprocess as sp -from .log import error - - -# run a shell command and return the exit code -def run(cmd, silent=False, executable='/bin/bash', background=False): - if background: - cmd = '( %s ) &' % cmd - if silent: - return sp.call(cmd, stdout=sp.DEVNULL, stderr=sp.DEVNULL, shell=True, executable=executable) - else: - return sp.call(cmd, shell=True, executable=executable) - - -# returns the output of a subprocess along with the exit code -def getoutput(cmd): - result = sp.run(cmd, stdout=sp.PIPE, stderr=sp.STDOUT, shell=True, executable='/bin/bash') - return result.stdout.decode('utf-8'), result.returncode - - -# removes a directory if it exists -def rmdir(dirpath): - if os.path.exists(dirpath) and os.path.isdir(dirpath): - shutil.rmtree(dirpath) - - -# remove extensions from a volume filename -def rmext(filename): - for ext in ('.mgh', '.mgz', '.nii', '.nii.gz'): - if filename.endswith(ext): return filename[:-len(ext)] - - -# custom pythonic source function -def source(filename): - # source the file and return the resulting env - output, ret = getoutput('. {0} 2>&1 /dev/null ; env'.format(filename)) - # parse the env output to a dict of env variables - varlist = [] - for line in output.splitlines(): - pair = line.split('=', 1) - if len(pair) == 1: varlist[-1][1] += '\n' + line - else: varlist.append(pair) - # update the python environ - os.environ.update(dict(varlist)) - - -# source a freesurfer environment -def sourceFS(fspath): - os.environ['FREESURFER_HOME'] = fspath - setup_script = os.path.join(fspath, 'SetUpFreeSurfer.sh') - if not os.path.isfile(setup_script): return False - source(setup_script) - return True - - -# get freesurfer home -def fshome(): - return os.environ.get('FREESURFER_HOME') - - -# make sure freesurfer has been sourced -def checkfs(): - if not fshome(): - errorExit('freesurfer has not been sourced') - - -# print an error message and exit -def errorExit(message, ret=1): - error(message) - exit(ret) - - -# simple timer class -class Timer: - def __init__(self, message=None): - if message: print(message) - self.start_time = dt.datetime.now() - - @property - def elapsed(self): - return dt.datetime.now() - self.start_time - - def mark(self, message): - print('%s: %s' % (message, str(self.elapsed))) - -# Return the peak memory in kb for calling process -def GetVmPeak(): - fp = open('/proc/self/status','r'); - for line in fp: - ind = line.rfind('VmPeak:'); - if(ind != -1): - tmp = line.split(); - return tmp[1]; - #endif - #endfor -#endfunc - - diff --git a/python/freesurfer/utility.py b/python/freesurfer/utility.py new file mode 100644 index 00000000000..fffe329003d --- /dev/null +++ b/python/freesurfer/utility.py @@ -0,0 +1,135 @@ +import os +import sys +import re +import platform +import datetime as dt +import subprocess as sp + + +def run(command, silent=False, background=False, executable='/bin/bash'): + '''Runs a shell command and returns the exit code. + + Note: + A command run in the background will always return `None`. + Args: + command (str): Command to run. + silent (bool): Send output to devnull. Defaults to False. + background (bool): Run command as a background process. Defaults to False. + executable (str): Shell executable. Defaults to `/bin/bash`. + Returns: + Command exit code. + ''' + # redirect the standard output appropriately + if silent: + std = {'stdout': sp.DEVNULL, 'stderr': sp.DEVNULL} + elif not background: + std = {'stdout': sp.PIPE, 'stderr': sp.STDOUT} + else: + std = {} # do not redirect + # run the command + process = sp.Popen(command, **std, shell=True, executable=executable) + if not background: + # write the standard output stream + if process.stdout: + for line in process.stdout: + sys.stdout.write(line.decode('utf-8')) + # wait for process to finish + process.wait() + return process.returncode + + +def collectOutput(command, executable='/bin/bash'): + '''Collects the output of a shell command. + + Args: + command (str): Command to run. + executable (str): Shell executable. Defaults to `/bin/bash`. + Returns: + Tuple containing the command output and its exit code. + ''' + result = sp.run(command, stdout=sp.PIPE, stderr=sp.STDOUT, shell=True, executable=executable) + return result.stdout.decode('utf-8'), result.returncode + + +def source(filename): + '''Sources a bash file and updates the current environment. + + Args: + filename: Bash script to source. + Raises: + IOError: If file does not exist. + RuntimeError: If sourcing fails. + ''' + if not os.path.isfile(filename): + raise IOError('%s is not a valid file' % filename) + # source the file and return the resulting environment + output, retcode = collectOutput('. %s && env' % filename) + if retcode != 0: + raise RuntimeError('could not source %s' % filename) + # parse the env output into a list of pairs + env = {} + for line in output.splitlines(): + pair = line.split('=', 1) + if len(pair) == 1: + # this line is just a continuation of the previous variable + env[previous] += '\n' + line + else: + key, value = pair + env[key] = value + previous = key + # update the environment + os.environ.update(env) + + +def hostname(short=True): + '''Gets the system hostname. + + Args: + short (bool): Provide the short hostname. Defaults to True. + Returns: + Hostname string. + ''' + node = platform.node() + if short: + return node.split('.')[0] + return node + + +def fshome(): + '''Returns the freesurfer home directory.''' + return os.environ.get('FREESURFER_HOME') + + +def vmpeak(): + '''Returns the peak memory usage of the process in kilobytes. This only works + on linux machines because it requires `/proc/self/status`.''' + procstatus = '/proc/self/status' + if os.path.exists(procstatus): + with open(procstatus, 'r') as file: + for line in file: + if 'VmPeak' in line: + return int(line.split()[1]) + return None + + +def printPeakMemory(prefix=''): + '''Prints the peak memory usage of the process if available.''' + peak = vmpeak() + if peak is not None: + if prefix: + prefix += ' ' + print('%sVmPeak: %d kB' % (prefix, peak)) + + +class Timer: + '''A simple timer class to track process speed.''' + def __init__(self, message=None): + if message: print(message) + self.start_time = dt.datetime.now() + + @property + def elapsed(self): + return dt.datetime.now() - self.start_time + + def mark(self, message): + print('%s: %s' % (message, str(self.elapsed))) diff --git a/python/setup.py b/python/setup.py index 298d2e3d0c6..3256b3bf638 100644 --- a/python/setup.py +++ b/python/setup.py @@ -1,10 +1,10 @@ #!/usr/bin/env python -import os import sys import glob import platform import operator +import os.path as path from setuptools import setup, find_packages, Distribution @@ -16,11 +16,8 @@ ] # get required dependencies from requirements.txt -base_dir = os.path.abspath(os.path.dirname(__file__)) -with open(os.path.join(base_dir, 'requirements.txt')) as requirements_file: - requirements = [line for line in requirements_file.read().splitlines() - if not line.startswith('#')] - +with open(path.join(path.dirname(path.realpath(__file__)), 'requirements.txt')) as file: + requirements = [line for line in file.read().splitlines() if not line.startswith('#')] # ---- run the setup ---- @@ -38,7 +35,7 @@ def find_libs(libname, required=True): if required and not libraries: print('error: could not find %s library that matches the current python version' % libname) sys.exit(1) - return [os.path.basename(filename) for filename in libraries] + return [path.basename(filename) for filename in libraries] setup( distclass=BinaryDistribution, diff --git a/qdec/CMakeLists.txt b/qdec/CMakeLists.txt deleted file mode 100644 index f127e3eaf67..00000000000 --- a/qdec/CMakeLists.txt +++ /dev/null @@ -1,77 +0,0 @@ -project(qdec) - -if(BUILD_QDEC - AND BUILD_GUIS - AND OPENGL_FOUND - AND TCLTKTIXBLT_FOUND - AND VTK_FOUND - AND KWWidgets_FOUND) - - if(APPLE AND NOT BUILD_OSX_TK_GUIS) - - install_symlinks(${CMAKE_SOURCE_DIR}/distribution/osx32b/qdec TYPE programs DESTINATION bin) - - else() - - include_directories( - ${CMAKE_CURRENT_SOURCE_DIR} - ${FS_INCLUDE_DIRS} - ${CMAKE_SOURCE_DIR}/fsgdf - ${CMAKE_SOURCE_DIR}/vtkfsio - ${CMAKE_SOURCE_DIR}/vtkutils - ${CMAKE_SOURCE_DIR}/qdecproject - ${TCLTKTIXBLT_INCLUDE_DIR} - ${X11_INCLUDE_DIR} - ${VTK_INCLUDE_DIRS} - ${KWWidgets_INCLUDE_DIR} - ) - - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-deprecated") - - # use vtkWrapTcl to create the tcl-wrapped code for these objects - vtk_wrap_tcl(vtkKWQdecApp.h vtkKWQdecAppTcl.cxx) - vtk_wrap_tcl(vtkKWQdecWindow.h vtkKWQdecWindowTcl.cxx) - vtk_wrap_tcl(vtkKWQdecView.h vtkKWQdecViewTcl.cxx) - vtk_wrap_tcl_init(QdecLibInit.data QdecLibInit.cxx) - - set(SOURCES - QdecMain.cxx - vtkKWQdecApp.cxx - vtkKWQdecAppTcl.cxx - vtkKWQdecWindow.cxx - vtkKWQdecWindowTcl.cxx - vtkKWQdecView.cxx - vtkKWQdecViewTcl.cxx - QdecUtilities.cxx - QdecLibInit.cxx - ) - - if(APPLE) - set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -framework Cocoa -framework Carbon -framework IOKit") - endif() - - add_executable(qdec ${SOURCES}) - target_link_libraries(qdec - utils - fsgdf - vtkfsio - vtkutils - qdecproject - ${OPENGL_LIBRARIES} - ${TCLTKTIXBLT_LIBRARIES} - ${X11_LIBRARIES} - ${VTK_LIBRARIES} - ${VTK_TCL_LIBRARIES} - ${KWWidgets_LIBRARIES} - ) - - install(TARGETS qdec DESTINATION bin) - - endif() - - install_symlinks(qdec_splash.png TYPE files DESTINATION lib/images) - install_symlinks(QdecIcons.txt TYPE files DESTINATION lib/resource) - -endif() - -install(PROGRAMS run_mris_preproc DESTINATION bin) diff --git a/qdec/Makefile.am b/qdec/Makefile.am deleted file mode 100644 index 886b9ab0db7..00000000000 --- a/qdec/Makefile.am +++ /dev/null @@ -1,186 +0,0 @@ -foodir=$(prefix)/lib/images - -foo_datafiles=qdec_splash.png - -AM_CPPFLAGS=-I$(top_srcdir)/include $(TCL_CFLAGS) \ - -I/usr/include/libxml2 - -AM_CXXFLAGS=-Wno-deprecated -I$(top_srcdir)/include \ - -I$(top_srcdir)/vtkfsio \ - -I$(top_srcdir)/vtkutils \ - -I$(top_srcdir)/qdecproject \ - $(VTK_CXXFLAGS) $(KWWIDGETS_CXXFLAGS) $(TCL_CFLAGS) - -dist_bin_SCRIPTS=run_mris_preproc - -if ENABLE_TCLTK_APPS -bin_PROGRAMS = qdec -qdec_SOURCES= \ - QdecMain.cxx \ - vtkKWQdecApp.cxx vtkKWQdecApp.h vtkKWQdecAppTcl.cxx \ - vtkKWQdecWindow.cxx vtkKWQdecWindow.h vtkKWQdecWindowTcl.cxx \ - vtkKWQdecView.cxx vtkKWQdecView.h vtkKWQdecViewTcl.cxx \ - QdecUtilities.cxx QdecLibInit.cxx \ - QdecEvents.h QdecVertexAnnotationLookup.h -qdec_LDADD= \ - $(top_builddir)/fsgdf/libfsgdf.a \ - $(top_builddir)/vtkfsio/libvtkfsio.a \ - $(top_builddir)/vtkutils/libvtkutils.a \ - $(top_builddir)/qdecproject/libqdecproject.a \ - $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(LIBS_TCL_OPENGL) \ - $(VTK_LIBS) $(VTK_VERDICT_LIB) -lvtkGraphics \ - $(VTK_EXPAT_LIB) $(VTK_FREETYPE_LIB) \ - $(VTK_TIFF_LIB) $(VTK_JPEG_LIB) \ - $(VTK_METAIO_LIB) $(VTK_PNG_LIB) $(VTK_Z_LIB) \ - $(VTK_SQLITE_LIB) \ - -lvtkImaging -lvtkFiltering \ - -lvtkCommon -lvtksys \ - -lvtkexoIIc -lvtkNetCDF $(VTK_NETCDFCXX_LIB) \ - -lvtkVolumeRendering -lvtkRendering -lvtkftgl \ - -lvtkWidgets -lvtkHybrid $(VTK_HDF5_LIB) \ - -lvtkIO $(VTK_LSDYNA_LIB) -lvtkDICOMParser $(VTK_MPEG2ENCODE_LIB) \ - -lvtkImagingTCL -lvtkVolumeRenderingTCL -lvtkRenderingTCL \ - -lvtkFilteringTCL -lvtkWidgetsTCL \ - -lvtkHybridTCL -lvtkGraphicsTCL -lvtkImagingTCL -lvtkIOTCL \ - -lvtkCommonTCL \ - $(KWWIDGETS_LIBS) -lKWWidgets -qdec_LDFLAGS=$(OS_LDFLAGS) $(LDFLAGS_TCL) - -qdecdir=$(prefix)/lib/resource -qdec_DATA=QdecIcons.txt - -vtkKWQdecAppTcl.cxx: vtkKWQdecApp.h - ${VTK_DIR}/bin/vtkWrapTcl vtkKWQdecApp.h \ - ${VTK_LIB_VTK}/hints 1 vtkKWQdecAppTcl.cxx - -vtkKWQdecWindowTcl.cxx: vtkKWQdecWindow.h - ${VTK_DIR}/bin/vtkWrapTcl vtkKWQdecWindow.h \ - ${VTK_LIB_VTK}/hints 1 vtkKWQdecWindowTcl.cxx - -vtkKWQdecViewTcl.cxx: vtkKWQdecView.h - ${VTK_DIR}/bin/vtkWrapTcl vtkKWQdecView.h \ - ${VTK_LIB_VTK}/hints 1 vtkKWQdecViewTcl.cxx - -QdecLibInit.cxx: QdecLibInit.data - ${VTK_DIR}/bin/vtkWrapTclInit QdecLibInit.data QdecLibInit.cxx - -# put a wrapper around the bin, used to setup tcltktixblt,vtk,kww enviro vars -install-exec-hook:qdec - cp $(top_builddir)/qdec/qdec $(DESTDIR)$(bindir)/qdec.bin - echo "#!/bin/tcsh -ef" > $(DESTDIR)$(bindir)/qdec - echo "source \$$FREESURFER_HOME/bin/tcl_setup" \ - >> $(DESTDIR)$(bindir)/qdec - echo "source \$$FREESURFER_HOME/bin/vtk_setup" \ - >> $(DESTDIR)$(bindir)/qdec - echo "source \$$FREESURFER_HOME/bin/kww_setup" \ - >> $(DESTDIR)$(bindir)/qdec - echo "if (-e /bin/pwd) then" >> $(DESTDIR)$(bindir)/qdec - echo " setenv HOME \`cd \$$HOME; /bin/pwd\`" \ - >> $(DESTDIR)$(bindir)/qdec - echo " setenv SUBJECTS_DIR \`cd \$$SUBJECTS_DIR; /bin/pwd\`" \ - >> $(DESTDIR)$(bindir)/qdec - echo "endif" >> $(DESTDIR)$(bindir)/qdec - echo "qdec.bin \$$argv" >> $(DESTDIR)$(bindir)/qdec - chmod a+x $(DESTDIR)$(bindir)/qdec - if [[ -f /usr/pubsw/bin/chrpath ]]; then \ - /usr/pubsw/bin/chrpath -d $(DESTDIR)$(bindir)/qdec.bin; fi - -install-data-local: - test -z $(DESTDIR)$(foodir) || $(mkdir_p) $(DESTDIR)$(foodir) - $(INSTALL_DATA) $(foo_datafiles) $(DESTDIR)$(foodir) - -uninstall-hook: - rm -f $(DESTDIR)$(bindir)/qdec.bin - -clean-local: - -rm *Tcl.cxx QdecLibInit.cxx - -else -bin_PROGRAMS = - -all: - @echo "Building KWWidgets apps not enabled." - @echo "Run configure with either --enable-kww-apps or --with-kwwidgets-dir=DIR" - -install-exec-hook: - -# these are created on-th-fly (see above), but make dist complains if they -# don't exist, so create some empty files for packaging purposes: -dist-exec-hook: - @touch vtkKWQdecAppTcl.cxx - @touch vtkKWQdecWindowTcl.cxx - @touch vtkKWQdecViewTcl.cxx - @touch QdecLibInit.cxx - @sleep 2 - @touch vtkKWQdecApp.h - @touch vtkKWQdecWindow.h - @touch vtkKWQdecView.h - @touch QdecLibInit.data - -vtkKWQdecAppTcl.cxx: -vtkKWQdecWindowTcl.cxx: -vtkKWQdecViewTcl.cxx: -QdecLibInit.cxx: -endif - -# Copy over precompiled 32-bit versions until we get 64-bit builds working. -if INSTALL_MAC32_GUIS - -qdecdir=$(prefix)/lib/resource -qdec_DATA=QdecIcons.txt - -install-exec-hook: - rm -vf $(DESTDIR)$(bindir)/qdec.bin - cp $(top_builddir)/distribution/Mac_32b/qdec.bin $(DESTDIR)$(bindir)/qdec.bin - echo "#!/bin/tcsh -ef" > $(DESTDIR)$(bindir)/qdec - echo "source \$$FREESURFER_HOME/bin/tcl_setup" \ - >> $(DESTDIR)$(bindir)/qdec - echo "source \$$FREESURFER_HOME/bin/vtk_setup" \ - >> $(DESTDIR)$(bindir)/qdec - echo "source \$$FREESURFER_HOME/bin/kww_setup" \ - >> $(DESTDIR)$(bindir)/qdec - echo "if (-e /bin/pwd) then" >> $(DESTDIR)$(bindir)/qdec - echo " setenv HOME \`cd \$$HOME; /bin/pwd\`" \ - >> $(DESTDIR)$(bindir)/qdec - echo " setenv SUBJECTS_DIR \`cd \$$SUBJECTS_DIR; /bin/pwd\`" \ - >> $(DESTDIR)$(bindir)/qdec - echo "endif" >> $(DESTDIR)$(bindir)/qdec - echo "qdec.bin \$$argv" >> $(DESTDIR)$(bindir)/qdec - chmod a+x $(DESTDIR)$(bindir)/qdec - if [[ -f /usr/pubsw/bin/chrpath ]]; then \ - /usr/pubsw/bin/chrpath -d $(DESTDIR)$(bindir)/qdec.bin; fi - -install-data-local: - test -z $(DESTDIR)$(foodir) || $(mkdir_p) $(DESTDIR)$(foodir) - $(INSTALL_DATA) $(foo_datafiles) $(DESTDIR)$(foodir) - -uninstall-hook: - rm -f $(DESTDIR)$(bindir)/qdec.bin -endif - -EXTRA_DIST=QdecIcons.txt $(foo_DATA) \ -qdec2.table.dat $(dist_bin_SCRIPTS) \ -QdecEvents.h \ -QdecLibInit.cxx \ -QdecLibInit.data \ -QdecMain.cxx \ -QdecUtilities.cxx \ -QdecUtilities.h \ -QdecVertexAnnotationLookup.h \ -vtkKWQdecApp.cxx \ -vtkKWQdecApp.h \ -vtkKWQdecAppTcl.cxx \ -vtkKWQdecView.cxx \ -vtkKWQdecView.h \ -vtkKWQdecViewTcl.cxx \ -vtkKWQdecWindow.cxx \ -vtkKWQdecWindow.h \ -vtkKWQdecWindowTcl.cxx \ -development_notes.txt \ -qdec.ppt - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/qdec_glmfit/Makefile.am b/qdec_glmfit/Makefile.am deleted file mode 100644 index 14d5abb2ee2..00000000000 --- a/qdec_glmfit/Makefile.am +++ /dev/null @@ -1,12 +0,0 @@ -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-Wno-deprecated -I$(top_srcdir)/include \ - -I$(top_srcdir)/qdecproject - -bin_PROGRAMS = qdec_glmfit -qdec_glmfit_SOURCES=qdec_glmfit.cxx -qdec_glmfit_LDADD= $(top_builddir)/qdecproject/libqdecproject.a \ - $(addprefix $(top_builddir)/, $(LIBS_MGH)) -qdec_glmfit_LDFLAGS=$(OS_LDFLAGS) - -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/qdecproject/Makefile.am b/qdecproject/Makefile.am deleted file mode 100644 index a969e9be09b..00000000000 --- a/qdecproject/Makefile.am +++ /dev/null @@ -1,28 +0,0 @@ -# -# Makefile.am for libqdecproject.a -# - -AM_CPPFLAGS= -Wno-deprecated \ - $(X_CFLAGS) \ - $(VXL_CFLAGS) \ - -I$(top_srcdir)/include - -AM_LDFLAGS= - -noinst_LIBRARIES= libqdecproject.a - -libqdecproject_a_SOURCES= QdecContrast.cxx QdecDataTable.cxx \ - QdecFactor.cxx QdecGlmDesign.cxx QdecGlmFit.cxx QdecGlmFitResults.cxx \ - QdecProject.cxx QdecSubject.cxx - -am_libqdecprojet_a_OBJECTS=$(libqdecproject_a_SOURCES:%.cxx=%.o) - -EXTRA_DIST= ProgressUpdateGUI.h QdecContrast.h QdecDataTable.h \ - QdecFactor.h QdecGlmDesign.h QdecGlmFit.h QdecGlmFitResults.h \ - QdecProject.h QdecSubject.h umbrello.xmi - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/rbftest/Makefile.am b/rbftest/Makefile.am deleted file mode 100644 index 891625ef934..00000000000 --- a/rbftest/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -# Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = rbftest -rbftest_SOURCES=rbftest.c -rbftest_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -rbftest_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/regdat2xfm/Makefile.am b/regdat2xfm/Makefile.am deleted file mode 100644 index 06b4cb6f8dd..00000000000 --- a/regdat2xfm/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = regdat2xfm -regdat2xfm_SOURCES=regdat2xfm.cpp -regdat2xfm_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -regdat2xfm_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/repair_siemens_file/Makefile.am b/repair_siemens_file/Makefile.am deleted file mode 100644 index a0eddf8b10a..00000000000 --- a/repair_siemens_file/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = repair_siemens_file -repair_siemens_file_SOURCES=repair_siemens_file.c -repair_siemens_file_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -repair_siemens_file_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/rgb/Makefile.am b/rgb/Makefile.am deleted file mode 100644 index 087960e080a..00000000000 --- a/rgb/Makefile.am +++ /dev/null @@ -1,16 +0,0 @@ -# -# Makefile.am for libutils.a -# - -AM_CPPFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -noinst_LIBRARIES= librgb.a -librgb_a_SOURCES = close.c name.c rdwr.c row.c \ - filbuf.c open.c rgbutils.c flsbuf.c pix.c rle.c - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/run_selected_tests b/run_selected_tests deleted file mode 100755 index fe27a103ae9..00000000000 --- a/run_selected_tests +++ /dev/null @@ -1,43 +0,0 @@ -#!/bin/bash -# -# Tests runner for a selection of tests as specified by TESTS env -# variable which should contain space separated collection of entries of -# syntax -# DIRECTORYGLOB[:test1[,test2,...]] -# e.g. smth as simple as -# TESTS="expat mri_*" -# or -# TESTS="expat:runtestspp tiff" -# etc -# -# Directories which have no 'make check' available would be skipped - -set -eu -failed=0; - -# Skip some tests that wont pass on travis platform -# but should pass on Martinos build machine. -export SKIP_LIBG2C_TEST=1 - -# Should come from env var -TESTS=${TESTS:-} -outfile=$(mktemp) - -for TEST in ${TESTS}; do - tests=$(echo "$TEST" | sed -n -e 's,^[^:]*\(:\(.*\)\)$,\2,gp' | sed -e 's/,/ /g'); - testdir=${TEST#:*}; - [ -z "$tests" ] && testsstr='' || testsstr="TESTS=\"$tests\"" - # Verify that there is a check rule - make -n -C $testdir -n check >/dev/null 2>&1 || { echo "Not testing $testdir -- no check rule"; continue; } - echo -n "Testing $testdir/ $testsstr: "; - t0=$(date -u +%s) - make -C $testdir check -j4 $testsstr 1>|$outfile 2>&1 && ok=1 || ok=0 - t1=$(date -u +%s) - tdiff=$(($t1-$t0)) - diff=$(date -u -d @"$tdiff" +'[%-Hh %-Mm %-Ss] ') - [ $ok = 1 ] && echo -e "\rPASS in $diff $testdir/ $testsstr" \ - || { echo -e "\rFAIL in $diff $testdir/ $testsstr"; cat $outfile; failed=1; } -done - -exit $failed - diff --git a/samseg/run_samseg b/samseg/run_samseg index bec0191ee0a..12cef776b45 100755 --- a/samseg/run_samseg +++ b/samseg/run_samseg @@ -2,7 +2,6 @@ import os import sys -import argparse import numpy as np import json import scipy.io @@ -13,38 +12,39 @@ from freesurfer.samseg import Specification, registerAtlas, samsegment, initVisu # ------ Parse Command Line Arguments ------ -parser = argparse.ArgumentParser() +parser = fs.ArgParser() # required -parser.add_argument('-o', '--output', metavar='FOLDER', dest='outputDirectory', help='output directory', required=True) -parser.add_argument('-i', '--input', action='append', metavar='FILE', dest='inputFileNames', help='input image(s)', required=True) +parser.add_argument('-o', '--output', metavar='DIR', dest='outputDirectory', help='Output directory.', required=True) +parser.add_argument('-i', '--input', action='append', metavar='FILE', dest='inputFileNames', help='Input image(s).', required=True) # optional processing options -parser.add_argument('--threads', type=int, default=os.environ.get('OMP_NUM_THREADS', 1), help='number of threads') -parser.add_argument('--init-lta', metavar='FILE', help='initial registration') -parser.add_argument('--reg-only', action='store_true', default=False, help='only perform registration') -parser.add_argument('-r', '--reg-mat', metavar='FILE', help='skip registration and read transform from file') +parser.add_argument('--threads', type=int, default=os.environ.get('OMP_NUM_THREADS', 1), help='Number of threads to use. Defaults to current OMP_NUM_THREADS or 1.') +parser.add_argument('--reg-only', action='store_true', default=False, help='Only perform initial affine registration.') +parser.add_argument('-r', '--reg-mat', metavar='FILE', help='Skip initial affine registration and read transform from file.') +parser.add_argument('--init-lta', metavar='FILE', help='Initial affine registration.') parser.add_argument('-a', '--atlas', metavar='DIR', help='Point to an alternative atlas directory.') -parser.add_argument('--no-brainmask', action='store_true', default=False, help='no initial brain masking based on affine atlas registration') -parser.add_argument('--diag-covs', action='store_true', default=False, help='use diagonal covariance matrices (only affect multi-contrast case)') -parser.add_argument('--stiffness', type=float, default=0.1, help='stiffness of the mesh (default is 0.1)') -parser.add_argument('--max-iters', type=int, default=100, help='maximum number of iterations') -parser.add_argument('--acpvdsc', type=float, default=1e-4, help='absoluteCostPerVoxelDecreaseStopCriterion') +parser.add_argument('--no-brainmask', action='store_true', default=False, help='Skip the initial brain masking based on the affine atlas registration.') +parser.add_argument('--diag-covs', action='store_true', default=False, help='Use diagonal covariance matrices (only affects multi-contrast case).') +parser.add_argument('--stiffness', type=float, default=0.1, help='Stiffness (K) of the mesh. Defaults to 0.1.') +parser.add_argument('--max-iters', type=int, default=100, help='Maximum number of iterations.') +parser.add_argument('--acpvdsc', type=float, default=1e-4, help='Absolute cost-per-voxel-decrease stop criterion. Defaults to 1e-4.') parser.add_argument('--options', metavar='FILE', help='Override advanced options via a json file.') # optional debugging options -parser.add_argument('--history', action='store_true', default=False, help='save history') -parser.add_argument('--showfigs', action='store_true', default=False, help='show figures during run') +parser.add_argument('--history', action='store_true', default=False, help='Save history.') +parser.add_argument('--showfigs', action='store_true', default=False, help='Show figures during run.') parser.add_argument('--save-mesh', action='store_true', help='Save the final mesh in template space.') -parser.add_argument('--movie', action='store_true', default=False, help='show as arrow key controlled time sequence') -parser.add_argument('-v', '--verbose', action='store_true', default=False, help='verbose debug output') +parser.add_argument('--movie', action='store_true', default=False, help='Show history as arrow key controlled time sequence.') +parser.add_argument('-v', '--verbose', action='store_true', default=False, help='Enable verbose debug output.') args = parser.parse_args() -print('run_samseg Init VmPeak', fs.GetVmPeak()) +fs.printPeakMemory('run_samseg init') # ------ Initial Setup ------ # Make sure freesurfer has been sourced -fs.checkfs() +if not fs.fshome(): + fs.errorExit('FREESURFER_HOME must be set') # Start the process timer timer = fs.Timer() @@ -74,7 +74,7 @@ visualizer = initVisualizer(args.showfigs, args.movie) # ------ Perform Affine Registration ------ -print('run_samseg Performing Affine Reg VmPeak ', fs.GetVmPeak()) +fs.printPeakMemory('run_samseg performing affine reg') templateFileName = os.path.join(atlasDir, 'template.nii') affineRegistrationMeshCollectionFileName = os.path.join(atlasDir, 'atlasForAffineRegistration.txt.gz') @@ -175,15 +175,13 @@ optimizationOptions.multiResolutionSpecification = [defaultMultiResolution.merge # ------ Run Samsegment ------ -print('run_samseg Running samsegment VmPeak', fs.GetVmPeak()) +fs.printPeakMemory('run_samseg running samsegment') labels, names, volumes = samsegment(args.inputFileNames, transformedTemplateFileName, modelSpecifications, optimizationOptions, args.outputDirectory, visualizer, saveHistory=args.history, saveMesh=args.save_mesh) # ------ Volumetric Stats ------ -print('run_samseg Running volumetric stats VmPeak', fs.GetVmPeak()) - # Write structural volumes with open(os.path.join(args.outputDirectory, 'samseg.stats'), 'w') as fid: for volume, name in zip(volumes, names): @@ -194,5 +192,5 @@ sbtiv = icv(zip(*[names, volumes])) with open(os.path.join(args.outputDirectory, 'sbtiv.stats'), 'w') as fid: fid.write('# Measure Intra-Cranial, %.6f, mm^3\n' % sbtiv) -print('#VMPC# run_samseg VmPeak', fs.GetVmPeak()) +fs.printPeakMemory('#VMPC# run_samseg') timer.mark('run_samseg complete') diff --git a/samseg/sbtiv b/samseg/sbtiv index ccdf3602bfb..da9c1809d43 100755 --- a/samseg/sbtiv +++ b/samseg/sbtiv @@ -1,20 +1,19 @@ #!/usr/bin/env fspython -import argparse +import freesurfer as fs from freesurfer.samseg import icv - description = ''' -Calculates the total intracranial volume of a subject by summing the individual volumes computed by samseg. -A file containing a list of intracranial label-names can be provided via the '--map' flag, but if omitted, -a default list is used. Label-names must be identical to those defined in the samseg atlas. +Calculates the total intracranial volume of a subject by summing individual volumes computed by samseg. \ +A file containing a list of intracranial labelnames can be provided via the '--labels' flag, but if omitted, \ +a default list is used. Labelnames must be identical to those defined in the samseg atlas. ''' # parse command line args -parser = argparse.ArgumentParser(description=description) -parser.add_argument('-i', '--input', metavar='FILE', help='samseg stats input file', required=True) -parser.add_argument('-o', '--output', metavar='FILE', help='stats output file') -parser.add_argument('-m', '--map', metavar="FILE", help='file containing list of intracranial structure labels') +parser = fs.ArgParser(description=description) +parser.add_argument('stats', metavar='FILE', help='Volume stats input file.') +parser.add_argument('-o', '--out', metavar='FILE', help='Intracranial stats output file.') +parser.add_argument('-l', '--labels', metavar="FILE", help='File containing a list of intracranial structure labelnames to include in the calculation.') args = parser.parse_args() # read in structure names and volumes from samseg stats @@ -36,4 +35,4 @@ sbtiv = icv(structures, includeStructures) # write out and exit print('intracranial volume: %.6f mm^3' % sbtiv) if args.output: - with open(args.output, 'w') as fid: fid.write('# Measure Intra-Cranial, %.6f, mm^3\n' % sbtiv) + with open(args.output, 'w') as fid: fid.write('# Measure Intra-Cranial, %.6f, mm^3\n' % sbtiv) diff --git a/scripts/InfantFS/Makefile.am b/scripts/InfantFS/Makefile.am deleted file mode 100644 index 3b4ff131994..00000000000 --- a/scripts/InfantFS/Makefile.am +++ /dev/null @@ -1,41 +0,0 @@ -# -# Makefile.am for scripts/InfantFS -# - -dist_bin_SCRIPTS = \ -atlassubjects.csh \ -check_infant_recon_success.csh \ -create_pial_surfaces_mprage_subject.csh \ -create_wm_surfaces_mprage_subject.csh \ -find_cerebellar_wm_labels.csh \ -find_cerebral_gm_labels.csh \ -find_cerebral_wm_labels.csh \ -find_neighbors_byAge.csh \ -find_neighbors_byAge_extended.csh \ -find_neighbors_byMI.csh \ -find_neighbors_byMI_extended.csh \ -find_putamen_labels.csh \ -infant_recon_all \ -LabelFusion \ -run_LabelFusion.sh \ -run_LabelFusion_wrapper.csh \ -set_babydev_packages.csh \ -set_infant_recon_params.csh \ -SetLabelFusionParams.csh\ -subjects_example.csh - -xmldir=$(prefix)/docs/xml -xml_DATA= - -install-exec-hook: - $(top_builddir)/utils/fsPrintHelp $(srcdir)/infant_recon_all.help.xml >> $(DESTDIR)$(bindir)/infant_recon_all - -TESTS = - -EXTRA_DIST = - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/scripts/Makefile.am b/scripts/Makefile.am deleted file mode 100644 index fff659611e8..00000000000 --- a/scripts/Makefile.am +++ /dev/null @@ -1,390 +0,0 @@ -# -# Makefile.am for scripts -# - -if INCLUDE_INFANTFS -SUBDIRS = InfantFS -endif - -dist_bin_SCRIPTS = \ -annot2std \ -aparc2feat \ -aseg2feat \ -aparcstats2table \ -asegstats2table \ -aparcstatsdiff \ -asegstatsdiff \ -apas2aseg \ -avi2talxfm \ -reconbatchjobs \ -beta2sxa \ -bblabel \ -bbmask \ -bbregister \ -biasfield \ -bedpostx_mgh \ -bmedits2surf \ -browse-minc-header.tcl \ -bugr \ -build_desikan_killiany_gcs.csh \ -cblumwmgyri \ -check_recons.sh \ -checkMCR.sh \ -check_subject \ -clear_fs_env.csh \ -compute_interrater_variability.csh \ -compute_label_volumes.csh \ -compute_label_vals.csh \ -cor_to_minc \ -cp-dicom \ -cuda_setup \ -datastruct_utils.py \ -dcmdir-info-mgh \ -dcmunpack \ -deface_subject \ -defect-seg \ -dicom-rename \ -dmrirc.example \ -dmrirc.long.example \ -dsh \ -dt_recon \ -easyfv \ -epidewarp.fsl\ -extract_talairach_avi_QA.awk \ -feat2surf \ -feat2segstats \ -findsession \ -fixup_mni_paths \ -fix_subject \ -fix_subject_corrected \ -fix_subject_corrected-lh \ -fix_subject_corrected-rh \ -fix_subject-lh \ -fix_subject_on_seychelles \ -fix_subject-rh \ -fname2ext \ -fname2stem \ -fscalc \ -fscalc.fsl \ -fsdcmdecompress \ -fsgd_parser.py \ -fsl_sub_mgh \ -fsutils.py \ -fvcompare \ -gca-apply \ -gcatrain \ -gcatrainskull \ -jkgcatrain \ -gcaprepone \ -gcainit \ -gtmseg \ -irepifitvol \ -tkmeditfv \ -tksurferfv \ -tkregisterfv \ -stem2fname \ -freesurfer \ -fs_lib_check \ -fs_time \ -fs_tutorial_data \ -fs_update \ -fsl_rigid_register \ -fslregister \ -fsl.5.0.2.xyztrans.sch \ -fsfget \ -getfullpath \ -get_label_thickness \ -grad_unwarp \ -groupstats \ -groupstatsdiff \ -help_xml_validate \ -inflate_subject \ -inflate_subject3 \ -inflate_subject-lh \ -inflate_subject_new \ -inflate_subject_new-lh \ -inflate_subject_new-rh \ -inflate_subject-rh \ -inflate_subject_sc \ -isanalyze \ -IsLTA \ -isnifti \ -is-surface \ -kww_setup \ -label_child \ -label_elderly_subject \ -label_subject \ -label_subject_flash \ -label_subject_mixed \ -labels_union \ -labels_intersect \ -labels_disjoint \ -long_create_base_sigma \ -long_create_orig \ -long_mris_slopes \ -long_stats_slopes \ -long_stats_combine \ -long_stats_tps \ -long_submit_jobs \ -long_submit_postproc \ -long_qdec_table \ -LongQdecTable.py \ -lpcregister \ -make_average_surface \ -make_average_volume \ -make_average_subject \ -make_average_subcort \ -make_cortex_label \ -make_folding_atlas \ -make_upright \ -make_symmetric \ -make_hemi_mask \ -make-segvol-table \ -map_all_labels \ -map_all_labels-lh \ -map_central_sulcus \ -map_to_base \ -mcparams2reg \ -meanval \ -mergeseg \ -merge_stats_tables \ -minc2seqinfo \ -misc.py \ -mkfsdist \ -mkheadsurf \ -mkima_index.tcl \ -mkmnc_index.tcl \ -mksubjdirs \ -mksurfatlas \ -mni152reg \ -morph_only_subject \ -morph_only_subject-lh \ -morph_only_subject-rh \ -morph_rgb-lh \ -morph_rgb-rh \ -morph_subject \ -morph_subject-lh \ -morph_subject_on_seychelles \ -morph_subject-rh \ -morph_tables-lh \ -morph_tables-rh \ -mri_add_new_tp \ -mri_align_long.csh \ -mri_glmfit-sim\ -mri_nu_correct.mni\ -mri-func2sph \ -mri-funcvits \ -mri_create_t2combined \ -mri_mergelabels \ -mri_motion_correct \ -mri_motion_correct2 \ -mri_motion_correct.fsl \ -mri_reorient_LR.csh \ -mri-sph2surf \ -mris_preproc \ -mris_roiCircle \ -mris_volsmooth \ -ms_refine_subject \ -orientLAS \ -fspalm \ -parc_atlas_jackknife_test \ -petsc_setup \ -plot_structure_stats.tcl \ -print_unique_labels.csh \ -process_exvivo_diff_data_bay3.sh \ -progressbar.tcl \ -fsr-checkxopts \ -fsr-getxopts \ -polyorder \ -rbbr \ -rcbf-prep \ -rebuild_gca_atlas.csh \ -recon-all \ -recon-all-exvivo \ -recon-all.makefile \ -reg-feat2anat \ -register_child \ -register.csh \ -register_elderly_subject \ -register_subject \ -register_subject_flash \ -register_subject_mixed \ -reg-mni305.2mm \ -reg2subject \ -reinflate_subject \ -reinflate_subject-lh \ -reinflate_subject-rh \ -remove_talairach \ -renormalize_subject \ -renormalize_subject_keep_editting \ -renormalize_T1_subject \ -reregister_subject_mixed \ -rmcr \ -rtview \ -run-qdec-glm \ -samseg2recon \ -seg2filled \ -segment_monkey \ -segment_subject \ -segment_subject_notal \ -segment_subject_notal2 \ -segment_subject_old_skull_strip \ -segment_subject_sc \ -segment_subject_talmgh \ -segpons \ -setlabelstat\ -sfa2fieldsign \ -show_tal \ -skip_long_make_checks \ -slicedelay \ -sphere_subject \ -sphere_subject-lh \ -sphere_subject-rh \ -spmmat2register \ -spm_t_to_b \ -spmregister \ -sratio \ -stattablediff \ -subject_info.py \ -surfreg \ -pctsurfcon\ -talairach \ -talairach2 \ -talairach_mgh \ -tal_compare \ -talsegprob \ -tcl_setup \ -test_recon-all.csh \ -test_tutorials.sh \ -thickdiffmap \ -trac-all \ -trac-paths \ -trac-preproc \ -tractstats2table \ -unpack_ima1.tcl \ -unpackimadir \ -unpackimadir2 \ -unpack_ima.tcl \ -unpackmincdir \ -unpack_mnc.tcl \ -unpacksdcmdir \ -UpdateNeeded \ -usbtree \ -vno_match_check \ -qt_setup \ -vertexvol \ -vol2segavg \ -vol2symsurf \ -vsm-smooth \ -vtk_setup \ -wfilemask \ -wm-anat-snr \ -wmedits2surf \ -wmsaseg \ -xcerebralseg\ -xcorr\ -xfmrot \ -xhemireg \ -xhemi-tal \ -xsanatreg - -if SMALL_DIST_INSTALL -else -tcldir = $(prefix)/lib/tcl -tcl_SCRIPTS= \ -allisons_surfaces.tcl \ -curv-flat.tcl \ -curv-views.tcl \ -dara_data.tcl \ -dipmovie-flat.tcl \ -eccen-flat.tcl \ -eccen-views.tcl \ -fs-flat.tcl \ -fs-make.tcl \ -fs-views.tcl \ -mk-fieldsign.tcl \ -offsetmovie.tcl \ -phasemovie.tcl \ -polar-flat.tcl \ -polar-views.tcl \ -readenv.tcl \ -real-flat.tcl \ -real-views.tcl \ -saveflat.tcl \ -saveviews.tcl \ -setdefpatchview.tcl \ -solmovie-flat.tcl \ -twocond-flat.tcl \ -twocond-masked-views.tcl \ -twocond-views.tcl \ -wrappers.tcl \ -fsgdfPlot.tcl -endif - -if SMALL_DIST_INSTALL -tktoolsdir = $(prefix)/tktools -tktools_SCRIPTS= \ -tkregister2.tcl -else -tktoolsdir = $(prefix)/tktools -tktools_SCRIPTS= \ -tkanalyse.tcl \ -tkm_common.tcl \ -tkm_dialog.tcl \ -tkmedit.tcl \ -tkm_functional.tcl \ -tkm_graph.tcl \ -tkm_wrappers.tcl \ -tkregister.tcl \ -tkregister2.tcl \ -tksurfer.tcl \ -tkUtils.tcl \ -fsgdfPlot.tcl -endif - -foo_datafiles=fs_spmreg.glnxa64 irepifitvol.glnx64 - -xmldir=$(prefix)/docs/xml -xml_DATA=bbregister.help.xml mri_motion_correct.fsl.help.xml \ - mri_nu_correct.mni.help.xml template.help.xml - -# these utilities should use our local build of tclsh, as that -# has the bug fix to allow usage on 64bit NFS file systems. -# for scripts, append processed .help.xml help text to the end of script -install-exec-hook: - cp $(srcdir)/unpacksdcmdir $(DESTDIR)$(bindir)/unpacksdcmdir.tcl - echo "#!/bin/tcsh -ef" \ - > $(DESTDIR)$(bindir)/unpacksdcmdir - echo "source \$$FREESURFER_HOME/bin/tcl_setup" \ - >> $(DESTDIR)$(bindir)/unpacksdcmdir - echo "\$$FREESURFER_HOME/lib/tcltktixblt/bin/tclsh8.4 \$$FREESURFER_HOME/bin/unpacksdcmdir.tcl \$$argv" \ - >> $(DESTDIR)$(bindir)/unpacksdcmdir - chmod a+x $(DESTDIR)$(bindir)/unpacksdcmdir - cp $(srcdir)/fsfget $(DESTDIR)$(bindir)/fsfget.tcl - echo "#!/bin/tcsh -ef" \ - > $(DESTDIR)$(bindir)/fsfget - echo "source \$$FREESURFER_HOME/bin/tcl_setup" \ - >> $(DESTDIR)$(bindir)/fsfget - echo "\$$FREESURFER_HOME/lib/tcltktixblt/bin/tclsh8.4 \$$FREESURFER_HOME/bin/fsfget.tcl \$$argv" \ - >> $(DESTDIR)$(bindir)/fsfget - chmod a+x $(DESTDIR)$(bindir)/fsfget - $(top_builddir)/utils/fsPrintHelp $(srcdir)/bbregister.help.xml >> $(DESTDIR)$(bindir)/bbregister - -install-data-local: - test -z $(DESTDIR)$(bindir) || $(mkdir_p) $(DESTDIR)$(bindir) - $(INSTALL_SCRIPT) $(foo_datafiles) $(DESTDIR)$(bindir) - -uninstall-hook: - rm -f $(DESTDIR)$(bindir)/unpacksdcmdir.tcl - rm -f $(DESTDIR)$(bindir)/fsfget.tcl - -TESTS = help_xml_validate - -EXTRA_DIST = $(tcl_SCRIPTS) tcl_setup vtk_setup kww_setup qt_setup cuda_setup \ -extract_talairach_avi_QA.awk $(foo_DATA) $(xml_DATA) $(tktools_SCRIPTS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/setup_configure b/setup_configure deleted file mode 100755 index 3a2687d1e3e..00000000000 --- a/setup_configure +++ /dev/null @@ -1,81 +0,0 @@ -#!/bin/tcsh -f - -# For a new dev/ environment, before running configure, -# and anytime after a Makefile.am file has changed, -# the following commands must be executed within the -# dev/ directory: - -set cmd1=(rm -rf autom4te.cache) -set cmd2=(libtoolize --force) -if ( `uname` == "Darwin" ) then - set cmd2=(glibtoolize --force) -endif -set cmd3=(aclocal) -#automake --add-missing is necessary because config.sub -# and config.guess are links, and make not be present, -# so if missing, --add-missing will add them for this -# platform -set cmd4=(automake --add-missing -Wno-portability) -set cmd5=(autoreconf --force -Wno-portability) -#automake Note: autoreconf --force runs automake -set cmd6=(autoconf -Wno-portability) - -echo "";echo "";echo "";echo $cmd1 -$cmd1 -if ($status) then - echo "ERROR: $cmd1" - exit $status -endif - -echo "";echo "";echo "";echo $cmd2 -echo $cmd2 -$cmd2 -if ($status) then - echo "ERROR: $cmd2" - exit $status -endif - -echo "";echo "";echo "";echo $cmd3 -echo $cmd3 -$cmd3 -if ($status) then - echo "ERROR: $cmd3" - exit $status -endif - -echo "";echo "";echo "";echo $cmd4 -echo $cmd4 -$cmd4 -if ($status) then - # seems to always fail, so don't error exit - #echo "ERROR: $cmd4" - #exit $status -endif - -echo "";echo "";echo "";echo $cmd5 -echo $cmd5 -$cmd5 -if ($status) then - echo "ERROR: $cmd5" - exit $status -endif - -echo "";echo "";echo "";echo $cmd6 -echo $cmd6 -$cmd6 -if ($status) then - echo "ERROR: $cmd6" - exit $status -endif - -# The first three commands create the platform specific -# tools needed by configure (on the Mac, symlink glibtoolize -# to libtoolize). These platform specific tools -# are placed in the dev/config directory. -# Autoreconf --force and automake create the Makefile.in -# files from the Makefile.am files in each directory. -# Following successful execution of these commands, the -# configure command can be executed. - -echo -echo "setup_configure complete. now run ./configure" diff --git a/spherical_stats/Makefile.am b/spherical_stats/Makefile.am deleted file mode 100644 index 0b34fcb2be4..00000000000 --- a/spherical_stats/Makefile.am +++ /dev/null @@ -1,13 +0,0 @@ -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = spherical_stats -spherical_stats_SOURCES=spherical_stats.c -spherical_stats_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -spherical_stats_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/spline3/Makefile.am b/spline3/Makefile.am deleted file mode 100644 index 30bb7858365..00000000000 --- a/spline3/Makefile.am +++ /dev/null @@ -1,14 +0,0 @@ -## -## Makefile.am -## - -AM_CXXFLAGS=-I. - -bin_PROGRAMS = Spline3_test -Spline3_test_SOURCES=Spline3_test.cpp - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/stat_normalize/Makefile.am b/stat_normalize/Makefile.am deleted file mode 100644 index 36bf7a6ce92..00000000000 --- a/stat_normalize/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = stat_normalize -stat_normalize_SOURCES=stat_normalize.c -stat_normalize_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -stat_normalize_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/stim_polar/Makefile.am b/stim_polar/Makefile.am deleted file mode 100644 index bf0742d871f..00000000000 --- a/stim_polar/Makefile.am +++ /dev/null @@ -1,24 +0,0 @@ -## -# Makefile.am -## - -AM_CFLAGS=\ - -I$(top_srcdir)/include \ - -I$(top_srcdir)/glut $(GL_CFLAGS) -AM_LDFLAGS= - -if HAVE_OPENGL_LIBS -bin_PROGRAMS = stim_polar -stim_polar_SOURCES=stim_polar.c $(top_srcdir)/utils/machine.c -stim_polar_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(LIBS_OPENGL) $(top_builddir)/glut/libglut.a $(X_LIBS) -stim_polar_LDFLAGS= -else -bin_PROGRAMS= -endif - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/svm-lib/Makefile.am b/svm-lib/Makefile.am deleted file mode 100644 index b724ded0884..00000000000 --- a/svm-lib/Makefile.am +++ /dev/null @@ -1,29 +0,0 @@ -# -# Makefile.am for libsvm.a -# - -AM_CXXFLAGS= -Wno-deprecated -Wno-unused - -AM_LDFLAGS= - -noinst_LIBRARIES= libsvm.a - -libsvm_a_SOURCES=svm-data-param.cpp svm-kernel.cpp svm-lib-c.cpp \ - svm-lib.cpp svm-model.cpp svm-param.cpp svm-similarity.cpp \ - svm-sketch.cpp - -am_libqdecprojet_a_OBJECTS=$(libsvm_a_SOURCES:%.cpp=%.o) - -EXTRA_DIST=svm-data-param.h svm-element-types.h svm-kernel-param.h \ - svm-lib-c.h svm-matrix.h svm-param.h \ - svm-similarity.h svm-vector-types.h \ - svm-element-type.h svm-io-format.h svm-kernel.h \ - svm-lib.h svm-model.h svm-pr-loqo.h svm-sketch.h \ - svm-vector.h svm-pr-loqo.c \ - classification_setup.example INSTALL_README.txt README.txt - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/swi_processing/Makefile.am b/swi_processing/Makefile.am deleted file mode 100644 index a91be66486c..00000000000 --- a/swi_processing/Makefile.am +++ /dev/null @@ -1,21 +0,0 @@ -## -## Makefile.am -## - -AM_CXXFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -bin_PROGRAMS = swi_preprocess swi_process -swi_preprocess_SOURCES=swi_preprocess.cpp cmd_line_interface.cpp -swi_preprocess_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -swi_preprocess_LDFLAGS=$(OS_LDFLAGS) - -swi_process_SOURCES=swi_process.cpp cmd_line_interface.cpp -swi_process_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -swi_process_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/talairach_afd/Makefile.am b/talairach_afd/Makefile.am deleted file mode 100644 index 738bbfe5c52..00000000000 --- a/talairach_afd/Makefile.am +++ /dev/null @@ -1,44 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = talairach_afd -talairach_afd_SOURCES=talairach_afd.c -talairach_afd_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -talairach_afd_LDFLAGS=$(OS_LDFLAGS) - -foodir=$(prefix)/docs/xml -foo_DATA=talairach_afd.help.xml -foo2dir=$(prefix)/docs/xml -foo2_DATA=talairach_afd.help.xml - -# trick to get test data into build dir -foo_SOURCES= -foo: - if ! test -f "$(top_builddir)/talairach_afd/good_tal.txt"; then \ - cp -v $(top_srcdir)/talairach_afd/*tal.* \ - $(top_builddir)/talairach_afd/; fi; - if ! test -f "$(top_builddir)/distribution/fsafd/PonsCutDice.adf"; then \ - cp -v $(top_srcdir)/distribution/fsafd/*.adf \ - $(top_builddir)/distribution/fsafd/; fi; - -check_PROGRAMS=foo - -TESTS=test_tal_afd $(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=test_tal_afd good_tal.xfm good_tal.txt bad_tal.xfm bad_tal.txt \ - $(foo_DATA) $(BUILT_SOURCES) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=talairach_afd.help.xml.h talairach_afd.help.xml.html diff --git a/talairach_avi/Makefile.am b/talairach_avi/Makefile.am deleted file mode 100644 index 5adb5b3fa30..00000000000 --- a/talairach_avi/Makefile.am +++ /dev/null @@ -1,307 +0,0 @@ - - -## -## Makefile.am -## - -# Fortran flags -if HAVE_INTEL_COMPILER -# ifort -AM_FFLAGS=-ax=CORE-AVX512 -qopenmp -132 -nofor_main -else -# gfortran -AM_FFLAGS=-ffixed-line-length-132 -fno-second-underscore -endif - -# LIB_G2C_A is defined to libg2c.a (static lib) if configure find it -AM_LDFLAGS=$(LIB_G2C_A) - -LIBS= - -foodir=$(prefix)/average - -if SMALL_DIST_INSTALL -foo_datafiles= \ - 711-2B_as_mni_average_305_mask.4dfp.ifh \ - 711-2B_as_mni_average_305_mask.4dfp.img \ - 711-2B_as_mni_average_305_mask.4dfp.img.rec \ - 711-2B_as_mni_average_305_mask.4dfp.hdr \ - 711-2C_as_mni_average_305.4dfp.img \ - 711-2C_as_mni_average_305.4dfp.img.rec \ - 711-2C_as_mni_average_305.4dfp.hdr \ - 711-2C_as_mni_average_305.4dfp.ifh \ - 711-2C_as_mni_average_305.4dfp.mat \ - 3T18yoSchwartzReactN32_as_orig.4dfp.hdr \ - 3T18yoSchwartzReactN32_as_orig.4dfp.img \ - 3T18yoSchwartzReactN32_as_orig.4dfp.ifh \ - 3T18yoSchwartzReactN32_as_orig.4dfp.img.rec \ - 3T18yoSchwartzReactN32_as_orig.4dfp.mat \ - 3T18yoSchwartzReactN32_as_orig.lst -else -foo_datafiles= \ - 711-2B_as_mni_average_305.4dfp.hdr \ - 711-2B_as_mni_average_305_mask.4dfp.ifh \ - 711-2C_as_mni_average_305.4dfp.img \ - 711-2B_as_mni_average_305.4dfp.ifh \ - 711-2B_as_mni_average_305_mask.4dfp.img \ - 711-2C_as_mni_average_305.4dfp.img.rec \ - 711-2B_as_mni_average_305.4dfp.img \ - 711-2B_as_mni_average_305_mask.4dfp.img.rec \ - 711-2B_as_mni_average_305.4dfp.img.rec \ - 711-2C_as_mni_average_305.4dfp.hdr \ - 711-2B_as_mni_average_305_mask.4dfp.hdr \ - 711-2C_as_mni_average_305.4dfp.ifh \ - 711-2C_as_mni_average_305.4dfp.mat \ - mni_average_305.4dfp.hdr \ - mni_average_305.4dfp.ifh \ - mni_average_305.4dfp.img \ - mni_average_305.4dfp.img.rec \ - 3T18yoSchwartzReactN32_as_orig.4dfp.hdr \ - 3T18yoSchwartzReactN32_as_orig.4dfp.img \ - 3T18yoSchwartzReactN32_as_orig.4dfp.ifh \ - 3T18yoSchwartzReactN32_as_orig.4dfp.img.rec \ - 3T18yoSchwartzReactN32_as_orig.4dfp.mat \ - 3T18yoSchwartzReactN32_as_orig.lst \ - RLB700_atlas_as_orig.4dfp.hdr \ - RLB700_atlas_as_orig.4dfp.ifh \ - RLB700_atlas_as_orig.4dfp.img \ - RLB700_atlas_as_orig.4dfp.img.rec \ - SVIP_Adult_Comp_N24_as_orig.4dfp.hdr \ - SVIP_Adult_Comp_N24_as_orig.4dfp.ifh \ - SVIP_Adult_Comp_N24_as_orig.4dfp.img \ - SVIP_Adult_Comp_N24_as_orig.4dfp.img.rec \ - SVIP_Adult_Control_N12_as_orig.4dfp.hdr \ - SVIP_Adult_Control_N12_as_orig.4dfp.ifh \ - SVIP_Adult_Control_N12_as_orig.4dfp.img \ - SVIP_Adult_Control_N12_as_orig.4dfp.img.rec \ - SVIP_Adult_Patient_N12_as_orig.4dfp.hdr \ - SVIP_Adult_Patient_N12_as_orig.4dfp.ifh \ - SVIP_Adult_Patient_N12_as_orig.4dfp.img \ - SVIP_Adult_Patient_N12_as_orig.4dfp.img.rec \ - SVIP_Child_Comp_N24_as_orig.4dfp.hdr \ - SVIP_Child_Comp_N24_as_orig.4dfp.ifh \ - SVIP_Child_Comp_N24_as_orig.4dfp.img \ - SVIP_Child_Comp_N24_as_orig.4dfp.img.rec \ - SVIP_Full_Comp_N48_as_orig.4dfp.hdr \ - SVIP_Full_Comp_N48_as_orig.4dfp.ifh \ - SVIP_Full_Comp_N48_as_orig.4dfp.img \ - SVIP_Full_Comp_N48_as_orig.4dfp.img.rec \ - SVIP_Young_Control_N12_as_orig.4dfp.hdr \ - SVIP_Young_Control_N12_as_orig.4dfp.ifh \ - SVIP_Young_Control_N12_as_orig.4dfp.img \ - SVIP_Young_Control_N12_as_orig.4dfp.img.rec \ - SVIP_Young_Patient_N12_as_orig.4dfp.hdr \ - SVIP_Young_Patient_N12_as_orig.4dfp.ifh \ - SVIP_Young_Patient_N12_as_orig.4dfp.img \ - SVIP_Young_Patient_N12_as_orig.4dfp.img.rec -endif - -xmldir=$(prefix)/docs/xml -xml_DATA=talairach_avi.help.xml -htmldir=$(prefix)/docs/html -html_DATA=talairach_avi.help.xml.html - -dist_bin_SCRIPTS = talairach_avi mpr2mni305 brec brec.awk \ - t4img_4dfp tal_QC_AZS - -bin_PROGRAMS= \ - analyzeto4dfp \ - 4dfptoanalyze \ - flip_4dfp \ - gauss_4dfp \ - zero_lt_4dfp \ - imgreg_4dfp \ - t4imgs_4dfp \ - compute_vox2vox \ - ifh2hdr - -TRX_SRCS=rec.c Getifh.c endianio.c - -analyzeto4dfp_SOURCES=analyzeto4dfp.c $(TRX_SRCS) cflip.c -analyzeto4dfp_LDADD=$(LIBS_ICC) $(LIB_G2C_A) - -4dfptoanalyze_SOURCES=4dfptoanalyze.c $(TRX_SRCS) cflip.c Inithdr.c -4dfptoanalyze_LDADD=$(LIBS_ICC) $(LIB_G2C_A) - -flip_4dfp_SOURCES=flip_4dfp.c $(TRX_SRCS) cflip.c -flip_4dfp_LDADD=$(LIBS_ICC) $(LIB_G2C_A) - -RMS_SRCS=cgauss3d.c fftsol.f imgpad.f polfit.f matopr.f eigen.f param6opr.f - -ACT_SRCS=conc.c - -gauss_4dfp_SOURCES=gauss_4dfp.c $(TRX_SRCS) $(RMS_SRCS) $(ACT_SRCS) cgauss3dd.c -gauss_4dfp_LDADD=$(LIBS_ICC) $(FCLIBS) $(LIB_G2C_A) - -zero_lt_4dfp_SOURCES=zero_lt_4dfp.c $(TRX_SRCS) -zero_lt_4dfp_LDADD=$(LIBS_ICC) $(LIB_G2C_A) - -LIN_SRCS=t4_sub.f t4scale.c - -IMG_SRCS=fimgreg.f imgvalm.f imgvalx.f ffind.f - -imgreg_4dfp_SOURCES=imgreg_4dfp.c $(TRX_SRCS) $(RMS_SRCS) \ - $(LIN_SRCS) $(IMG_SRCS) cflip.c -imgreg_4dfp_CFLAGS=-DHAVE_GFORTRAN -imgreg_4dfp_LDADD=$(LIBS_ICC) $(FCLIBS) $(LIB_G2C_A) - -T4IMGS_SRCS=ft4imgo.f to_711-2B.f ft4imgn.f set_rnan.f - -T4A_SRCS=ft4ixyz.f - -t4imgs_4dfp_SOURCES=t4imgs_4dfp.c $(TRX_SRCS) $(RMS_SRCS) $(LIN_SRCS) \ - $(IMG_SRCS) $(T4IMGS_SRCS) $(T4A_SRCS) cflip.c spline3dvgh.f -t4imgs_4dfp_CFLAGS=-DHAVE_GFORTRAN -t4imgs_4dfp_LDADD=$(LIBS_ICC) $(FCLIBS) $(LIB_G2C_A) - -compute_vox2vox_SOURCES=compute_vox2vox.c $(TRX_SRCS) $(RMS_SRCS) $(LIN_SRCS) \ - $(IMG_SRCS) cflip.c set_rnan.f ft4imgo.f -compute_vox2vox_CFLAGS=-DHAVE_GFORTRAN -compute_vox2vox_LDADD=$(LIBS_ICC) $(FCLIBS) $(LIB_G2C_A) - -ifh2hdr_SOURCES=ifh2hdr.c Inithdr.c $(TRX_SRCS) -ifh2hdr_LDADD=$(LIBS_ICC) $(LIB_G2C_A) - -CFILES=\ - 4dfptoanalyze.c \ - analyzeto4dfp.c \ - cflip.c \ - cgauss3d.c \ - cgauss3dd.c \ - compute_vox2vox.c \ - conc.c \ - endianio.c \ - flip_4dfp.c \ - gauss_4dfp.c \ - Getifh.c \ - ifh2hdr.c \ - imgreg_4dfp.c \ - Inithdr.c \ - rec.c \ - t4imgs_4dfp.c \ - t4scale.c \ - zero_lt_4dfp.c - -HFILES=\ - ANALYZE.h \ - conc.h \ - endianio.h \ - Getifh.h \ - ifh.h \ - librms.h \ - rec.h - -FFILES=\ - eigen.f \ - ffind.f \ - fftsol.f \ - fimgreg.f \ - ft4imgn.f \ - ft4imgo.f \ - ft4ixyz.f \ - imgpad.f \ - imgvalm.f \ - imgvalx.f \ - matopr.f \ - param6opr.f \ - polfit.f \ - set_rnan.f \ - spline3dvgh.f \ - t4_sub.f \ - to_711-2B.f - -# trick to get test data and scripts into the build dir (during make distcheck) -foo_SOURCES= -foo: - if ! test -f "$(top_builddir)/distribution/average/mni305.cor.mgz"; \ - then \ - cp -v $(top_srcdir)/distribution/average/mni305.cor.mgz \ - $(top_builddir)/distribution/average/; fi; - if ! test -f "$(top_builddir)/scripts/avi2talxfm"; then \ - cp -v $(top_srcdir)/scripts/avi2talxfm \ - $(top_builddir)/scripts/; fi; - if ! test -f "$(top_builddir)/talairach_avi/nu.mgz"; then \ - cp -v $(top_srcdir)/talairach_avi/nu.mgz \ - $(top_builddir)/talairach_avi/; fi; - if ! test -f "$(top_builddir)/talairach_avi/reference-tal.xfm"; then \ - cp -v $(top_srcdir)/talairach_avi/reference-tal.xfm \ - $(top_builddir)/talairach_avi/; fi; - if ! test -f "$(top_builddir)/talairach_avi/711-2C_as_mni_average_305.4dfp.img"; then \ - cp -v $(top_srcdir)/talairach_avi/711-2* \ - $(top_builddir)/talairach_avi/; fi; - if ! test -f "$(top_builddir)/talairach_avi/3T18yoSchwartzReactN32_as_orig.4dfp.img"; then \ - cp -v $(top_srcdir)/talairach_avi/*_orig* \ - $(top_builddir)/talairach_avi/; fi; - if ! test -f "$(top_builddir)/talairach_avi/talairach_avi"; then \ - list=( $(dist_bin_SCRIPTS) ); \ - for f in $${list[@]}; do \ - cp -v $(top_srcdir)/talairach_avi/$$f $(top_builddir)/talairach_avi/; \ - done; fi; - -check_PROGRAMS=foo - -TESTS=test_libg2c test_talairach_avi $(top_builddir)/scripts/help_xml_validate - -clean-local: - rm -f $(BUILT_SOURCES) - -EXTRA_DIST=$(dist_bin_SCRIPTS) talairach_avi.help.xml.h \ - $(CFILES) \ - $(HFILES) \ - $(FFILES) \ - test_libg2c test_talairach_avi nu.mgz reference-tal.xfm $(xml_DATA) - -listfiles: - @echo $(EXTRA_DIST) Makefile.am - -tarball: - tar cvf talairach_avi.tar $(EXTRA_DIST) Makefile.am - gzip talairach_avi.tar - ls -alF talairach_avi.tar.gz - -# if Avi Snyder needs to supply new source files, then a directory -# called 'src' should be created (presumably from a tarball that he -# supplies), containing his source. then these targets can be used -# to show differences, and copy these files from src - -diff_cfiles_from_src: - list=( $(CFILES) ); for p in $${list[@]}; do \ - find src -follow -type f -name $$p -exec diff $$p {} \;; \ - done; - -diff_hfiles_from_src: - list=( $(HFILES) ); for p in $${list[@]}; do \ - find src -follow -type f -name $$p -exec diff $$p {} \;; \ - done; - -diff_ffiles_from_src: - list=( $(FFILES) ); for p in $${list[@]}; do \ - find src -follow -type f -name $$p -exec diff $$p {} \;; \ - done; - -copy_cfiles_from_src: - list=( $(CFILES) ); for p in $${list[@]}; do \ - find src -follow -type f -name $$p -exec cp -iv {} . \;; \ - done; - -copy_hfiles_from_src: - list=( $(HFILES) ); for p in $${list[@]}; do \ - find src -follow -type f -name $$p -exec cp -iv {} . \;; \ - done; - -copy_ffiles_from_src: - list=( $(FFILES) ); for p in $${list[@]}; do \ - find src -follow -type f -name $$p -exec cp -iv {} . \;; \ - done; - -install-data-local: - test -z $(DESTDIR)$(foodir) || $(mkdir_p) $(DESTDIR)$(foodir) - $(INSTALL_DATA) $(foo_datafiles) $(DESTDIR)$(foodir) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -BUILT_SOURCES=talairach_avi.help.xml.h talairach_avi.help.xml.html diff --git a/template/Makefile.am b/template/Makefile.am deleted file mode 100644 index 46e929e001c..00000000000 --- a/template/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include - -bin_PROGRAMS = template -template_SOURCES=template.c -template_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -template_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/test_exclude_minc/Makefile.am b/test_exclude_minc/Makefile.am deleted file mode 100644 index 8e0cf73ca70..00000000000 --- a/test_exclude_minc/Makefile.am +++ /dev/null @@ -1,20 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_CXXFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom - -bin_PROGRAMS = test_exclude_minc -test_exclude_minc_SOURCES=test_exclude_minc.c -test_exclude_minc_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -test_exclude_minc_LDFLAGS=$(OS_LDFLAGS) - -install-exec-hook: - cp $(top_builddir)/test_exclude_minc/test_exclude_minc $(DESTDIR)$(bindir)/test_exclude_minc.bin - echo "#!/bin/bash" > $(DESTDIR)$(bindir)/test_exclude_minc - echo "source \$$FREESURFER_HOME/sources.sh" >> $(DESTDIR)$(bindir)/test_exclude_minc - echo "test_exclude_minc.bin \"\$$@\"" >> $(DESTDIR)$(bindir)/test_exclude_minc - -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/test_gcamcomputelabels_boost/Makefile.am b/test_gcamcomputelabels_boost/Makefile.am deleted file mode 100644 index 4fc3ffef359..00000000000 --- a/test_gcamcomputelabels_boost/Makefile.am +++ /dev/null @@ -1,51 +0,0 @@ -SUBDIRS = - -AM_CFLAGS=-I$(top_srcdir)/include $(BOOST_CFLAGS) - -AM_CXXFLAGS=-I$(top_srcdir)/include $(BOOST_CFLAGS) -Wall -Wextra - -AM_LDFLAGS= - -## ---- -## CUDA -## ---- - -if HAVE_BOOST_LIBS - -# BUILDCUDA is defined if configure.in finds CUDA -if BUILDCUDA - -if HAVE_FERMI_GPU -NVCCFLAGS += -g -arch sm_20 --ptxas-options=-v - -CUDA_CFLAGS += -DGCAMORPH_ON_GPU -endif - -# rules for building cuda files -.cu.o: - $(NVCC) -o $@ -c $< $(NVCCFLAGS) $(CUDA_CFLAGS) $(AM_CFLAGS) $(MNI_CFLAGS) - - -bin_PROGRAMS = test_gcamcomputelabels_boost - - -test_gcamcomputelabels_boost_SOURCES = test.cpp -test_gcamcomputelabels_boost_CXXFLAGS = -Wno-unused-parameter $(BOOST_CFLAGS) $(AM_CXXFLAGS) -test_gcamcomputelabels_boost_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) $(BOOST_PO_LIB) -test_gcamcomputelabels_boost_LDFLAGS=$(OS_LDFLAGS) - - - -endif -# endif BUILDCUDA - -endif -#endif HAVE_BOOST_LIBS - - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra - diff --git a/test_makevol/Makefile.am b/test_makevol/Makefile.am deleted file mode 100644 index 097307e99aa..00000000000 --- a/test_makevol/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS=makevol -makevol_SOURCES=main.c -makevol_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -makevol_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/tkmedit/CMakeLists.txt b/tkmedit/CMakeLists.txt deleted file mode 100644 index 64f88c5883f..00000000000 --- a/tkmedit/CMakeLists.txt +++ /dev/null @@ -1,40 +0,0 @@ -project(tkmedit) - -if(BUILD_GUIS AND OPENGL_FOUND AND TCLTKTIXBLT_FOUND) - - if(APPLE AND NOT BUILD_OSX_TK_GUIS) - - install_symlinks(${CMAKE_SOURCE_DIR}/distribution/osx32b/tkmedit TYPE programs DESTINATION bin) - - else() - - include_directories( - ${FS_INCLUDE_DIRS} - ${TCLTKTIXBLT_INCLUDE_DIR} - ${CMAKE_SOURCE_DIR}/packages/tiff - ${CMAKE_SOURCE_DIR}/packages/glut - ${X11_INCLUDE_DIR} - ) - - set(SOURCES - tkmDisplayArea.c - tkmedit.c - tkmFunctionalVolume.c - tkmMeditWindow.c - ) - - add_executable(tkmedit ${SOURCES}) - target_link_libraries(tkmedit - utils - fsgdf - ${OPENGL_LIBRARIES} - glut - ${X11_LIBRARIES} - ${TCLTKTIXBLT_LIBRARIES} - ) - - install(TARGETS tkmedit DESTINATION bin) - - endif() - -endif() diff --git a/tkmedit/Makefile.am b/tkmedit/Makefile.am deleted file mode 100644 index d39f04d4036..00000000000 --- a/tkmedit/Makefile.am +++ /dev/null @@ -1,94 +0,0 @@ -## -# Makefile.am -## - -if USE_LOCAL_TIFF -TIFFCFLAGS=-I$(top_srcdir)/tiff -LIBTIFF=$(top_builddir)/tiff/libtiff.a -else -TIFFCFLAGS=$(TIFF_CFLAGS) -LIBTIFF=$(LIB_TIFF) -endif - -AM_CPPFLAGS=\ - $(TCL_CFLAGS) $(TIFFCFLAGS) \ - $(tcl_includes) $(GL_CFLAGS) \ - -I$(top_srcdir)/include \ - -I$(top_srcdir)/glut -AM_LDFLAGS=$(LDFLAGS_TCL) $(TIFF_LIBS) - -if ENABLE_TCLTK_APPS -bin_PROGRAMS=tkmedit -tkmedit_SOURCES=tkmedit.c \ - tkmDisplayArea.c \ - tkmFunctionalVolume.c \ - tkmMeditWindow.c \ - tkmedit.h \ - tkmDisplayArea.h \ - tkmFunctionalVolume.h \ - tkmMeditWindow.h \ - $(top_srcdir)/fsgdf/fsgdf_wrap.c -tkmedit_LDADD= $(top_builddir)/fsgdf/libfsgdf.a \ - $(addprefix $(top_builddir)/,$(LIBS_MGH)) \ - $(LIBS_TCL_OPENGL) \ - $(X_LIBS) $(LIBTIFF) \ - $(top_builddir)/glut/libglut.a -tkmedit_LDFLAGS=$(LDFLAGS_TCL) -else -bin_PROGRAMS= -endif - -if ENABLE_TCLTK_APPS -# put a wrapper around the bin, used to setup tcltktixblt enviro vars -# and install in 'tktools' dir instead of 'bin' (to allow easy deletion -# of all cortech-licensed software) -install-exec-hook: - rm -vf $(DESTDIR)$(bindir)/tkmedit - cp $(top_builddir)/tkmedit/tkmedit $(DESTDIR)$(prefix)/tktools/tkmedit.bin - echo "#!/bin/tcsh -ef" > $(DESTDIR)$(prefix)/tktools/tkmedit - echo "source \$$FREESURFER_HOME/bin/tcl_setup" \ - >> $(DESTDIR)$(prefix)/tktools/tkmedit - echo "exec \$$FREESURFER_HOME/tktools/tkmedit.bin \$$argv" \ - >> $(DESTDIR)$(prefix)/tktools/tkmedit - chmod a+x $(DESTDIR)$(prefix)/tktools/tkmedit - cp $(DESTDIR)$(prefix)/tktools/tkmedit $(DESTDIR)$(bindir)/ - if [[ -f /usr/pubsw/bin/chrpath ]]; then \ - /usr/pubsw/bin/chrpath -d $(DESTDIR)$(prefix)/tktools/tkmedit.bin; fi - -uninstall-hook: - rm -f $(DESTDIR)$(prefix)/tktools/tkmedit* - -else -all: - @echo "Building Tcl/Tk apps not enabled." - @echo "Run configure with either --enable-tcltk-apps or --with-tcl-dir=DIR" -install-exec-hook: -endif - -# Copy over precompiled 32-bit versions until we get 64-bit builds working. -if INSTALL_MAC32_GUIS -install-exec-hook: - rm -vf $(DESTDIR)$(bindir)/tkmedit - rm -vf $(DESTDIR)$(prefix)/tktools/tkmedit.bin - cp $(top_builddir)/distribution/Mac_32b/tkmedit.bin $(DESTDIR)$(prefix)/tktools/tkmedit.bin - echo "#!/bin/tcsh -ef" > $(DESTDIR)$(prefix)/tktools/tkmedit - echo "source \$$FREESURFER_HOME/bin/tcl_setup" \ - >> $(DESTDIR)$(prefix)/tktools/tkmedit - echo "exec \$$FREESURFER_HOME/tktools/tkmedit.bin \$$argv" \ - >> $(DESTDIR)$(prefix)/tktools/tkmedit - chmod a+x $(DESTDIR)$(prefix)/tktools/tkmedit - cp $(DESTDIR)$(prefix)/tktools/tkmedit $(DESTDIR)$(bindir)/ - if [[ -f /usr/pubsw/bin/chrpath ]]; then \ - /usr/pubsw/bin/chrpath -d $(DESTDIR)$(prefix)/tktools/tkmedit.bin; fi - -uninstall-hook: - rm -f $(DESTDIR)$(prefix)/tktools/tkmedit* -endif - -EXTRA_DIST=development_notes.txt - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/tkregister2/CMakeLists.txt b/tkregister2/CMakeLists.txt index 47a249ec60d..053b60b4b78 100644 --- a/tkregister2/CMakeLists.txt +++ b/tkregister2/CMakeLists.txt @@ -2,36 +2,7 @@ project(tkregister2) include_directories(${FS_INCLUDE_DIRS}) -# first build without Tcl/Tk and OpenGL (command-line processing only) add_executable(tkregister2_cmdl tkregister2.c) target_compile_definitions(tkregister2_cmdl PRIVATE -DNO_GUI) target_link_libraries(tkregister2_cmdl utils) install(TARGETS tkregister2_cmdl DESTINATION bin) - -if(NOT MINIMAL AND BUILD_GUIS AND OPENGL_FOUND AND TCLTKTIXBLT_FOUND) - - if(APPLE AND NOT BUILD_OSX_TK_GUIS) - install_symlinks(${CMAKE_SOURCE_DIR}/distribution/osx32b/tkregister2 TYPE programs DESTINATION bin) - else() - - include_directories( - ${CMAKE_SOURCE_DIR}/unix - ${CMAKE_SOURCE_DIR}/packages/glut - ${TCLTKTIXBLT_INCLUDE_DIR} - ${X11_INCLUDE_DIR} - ) - - add_executable(tkregister2 tkregister2.c) - target_link_libraries(tkregister2 - utils - ${OPENGL_LIBRARIES} - glut - ${X11_LIBRARIES} - ${TCLTKTIXBLT_LIBRARIES} - ) - - install(TARGETS tkregister2 DESTINATION bin) - - endif() - -endif() diff --git a/tkregister2/Makefile.am b/tkregister2/Makefile.am deleted file mode 100644 index 92f5eeeae95..00000000000 --- a/tkregister2/Makefile.am +++ /dev/null @@ -1,103 +0,0 @@ -## -# Makefile.am -## - -# also build command-line only version (no gui) -SUBDIRS=cmdl - -if ENABLE_TCLTK_APPS - -AM_CPPFLAGS=$(TCL_CFLAGS) $(tcl_includes) \ - -I$(top_srcdir)/include \ - -I$(top_srcdir)/unix \ - -I$(top_srcdir)/glut \ - $(GL_CFLAGS) -AM_LDFLAGS= $(LDFLAGS_TCL) -bin_PROGRAMS = tkregister2 -tkregister2_SOURCES=tkregister2.c -tkregister2_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(LIBS_TCL_OPENGL) \ - $(X_LIBS) -lGL \ - $(top_builddir)/glut/libglut.a - -else - -bin_PROGRAMS = - -endif - - -if ENABLE_TCLTK_APPS -# put a wrapper around the bin, used to setup tcltktixblt enviro vars -# and install in 'tktools' dir instead of 'bin' (to allow easy deletion -# of all cortech-licensed software) -install-exec-hook: - mv -v $(DESTDIR)$(bindir)/tkregister2_cmdl $(DESTDIR)$(prefix)/tktools/ - rm -vf $(DESTDIR)$(bindir)/tkregister $(DESTDIR)$(bindir)/tkregister2 - cp $(top_builddir)/tkregister2/tkregister2 \ - $(DESTDIR)$(prefix)/tktools/tkregister2.bin - echo "#!/bin/tcsh -ef" > $(DESTDIR)$(prefix)/tktools/tkregister2 - echo "source \$$FREESURFER_HOME/bin/tcl_setup" \ - >> $(DESTDIR)$(prefix)/tktools/tkregister2 - echo "exec \$$FREESURFER_HOME/tktools/tkregister2.bin \$$argv" \ - >> $(DESTDIR)$(prefix)/tktools/tkregister2 - cp $(DESTDIR)$(prefix)/tktools/tkregister2 \ - $(DESTDIR)$(prefix)/tktools/tkregister - chmod a+x $(DESTDIR)$(prefix)/tktools/tkregister - chmod a+x $(DESTDIR)$(prefix)/tktools/tkregister2 - cp $(DESTDIR)$(prefix)/tktools/tkregister $(DESTDIR)$(bindir)/ - cp $(DESTDIR)$(prefix)/tktools/tkregister2 $(DESTDIR)$(bindir)/ - if [[ -f /usr/pubsw/bin/chrpath ]]; then \ - /usr/pubsw/bin/chrpath -d $(DESTDIR)$(prefix)/tktools/tkregister2.bin; fi - -uninstall-hook: - rm -f $(DESTDIR)$(prefix)/tktools/tkregister* - rm -f $(DESTDIR)$(bindir)/tkregister* - -else -if SMALL_DIST -# build/install only tkregister2_cmdl (handled by cmdl/Makefile.am) -else -all: - @echo "" - @echo "Excluding Tcl/Tk and OpenGL elements from this tkregister2 build." - @echo "Run configure with either --enable-tcltk-apps or --with-tcl-dir=DIR" - @echo "" -endif -endif - -# Copy over precompiled 32-bit versions until we get 64-bit builds working. -if INSTALL_MAC32_GUIS -install-exec-hook: - mv -v $(DESTDIR)$(bindir)/tkregister2_cmdl $(DESTDIR)$(prefix)/tktools/ - rm -vf $(DESTDIR)$(bindir)/tkregister $(DESTDIR)$(bindir)/tkregister2 - rm -vf $(DESTDIR)$(bindir)/tkregister2.bin - rm -vf $(DESTDIR)$(prefix)/tktools/tkregister2.bin - cp $(top_builddir)/distribution/Mac_32b/tkregister2.bin \ - $(DESTDIR)$(prefix)/tktools/tkregister2.bin - echo "#!/bin/tcsh -ef" > $(DESTDIR)$(prefix)/tktools/tkregister2 - echo "source \$$FREESURFER_HOME/bin/tcl_setup" \ - >> $(DESTDIR)$(prefix)/tktools/tkregister2 - echo "exec \$$FREESURFER_HOME/tktools/tkregister2.bin \$$argv" \ - >> $(DESTDIR)$(prefix)/tktools/tkregister2 - cp $(DESTDIR)$(prefix)/tktools/tkregister2 \ - $(DESTDIR)$(prefix)/tktools/tkregister - chmod a+x $(DESTDIR)$(prefix)/tktools/tkregister - chmod a+x $(DESTDIR)$(prefix)/tktools/tkregister2 - cp $(DESTDIR)$(prefix)/tktools/tkregister $(DESTDIR)$(bindir)/ - cp $(DESTDIR)$(prefix)/tktools/tkregister2 $(DESTDIR)$(bindir)/ - if [[ -f /usr/pubsw/bin/chrpath ]]; then \ - /usr/pubsw/bin/chrpath -d $(DESTDIR)$(prefix)/tktools/tkregister2.bin; fi - -uninstall-hook: - rm -f $(DESTDIR)$(prefix)/tktools/tkregister* - rm -f $(DESTDIR)$(bindir)/tkregister* -endif - - - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/tkregister2/cmdl/Makefile.am b/tkregister2/cmdl/Makefile.am deleted file mode 100644 index 97be130c2b1..00000000000 --- a/tkregister2/cmdl/Makefile.am +++ /dev/null @@ -1,19 +0,0 @@ -## -# Makefile.am -## - -# build without Tcl/Tk and OpenGL (command-line processing only) -AM_CPPFLAGS=-DNO_GUI -I$(top_srcdir)/include -if USE_LOCAL_MINC -AM_CPPFLAGS+= -I$(top_srcdir)/netcdf_3_6_0_p1 -endif -AM_LDFLAGS= -bin_PROGRAMS = tkregister2_cmdl -tkregister2_cmdl_SOURCES=../tkregister2.c -tkregister2_cmdl_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/tksurfer/CMakeLists.txt b/tksurfer/CMakeLists.txt deleted file mode 100644 index ddb24e4e04f..00000000000 --- a/tksurfer/CMakeLists.txt +++ /dev/null @@ -1,34 +0,0 @@ -project(tksurfer) - -if(BUILD_GUIS AND OPENGL_FOUND AND TCLTKTIXBLT_FOUND) - - if(APPLE AND NOT BUILD_OSX_TK_GUIS) - - install_symlinks(${CMAKE_SOURCE_DIR}/distribution/osx32b/tksurfer TYPE programs DESTINATION bin) - - else() - - include_directories( - ${FS_INCLUDE_DIRS} - ${CMAKE_SOURCE_DIR}/unix - ${CMAKE_SOURCE_DIR}/packages/tiff - ${CMAKE_SOURCE_DIR}/packages/glut - ${TCLTKTIXBLT_INCLUDE_DIR} - ${X11_INCLUDE_DIR} - ) - - add_executable(tksurfer tksurfer.c) - target_link_libraries(tksurfer - utils - fsgdf - ${OPENGL_LIBRARIES} - glut - ${X11_LIBRARIES} - ${TCLTKTIXBLT_LIBRARIES} - ) - - install(TARGETS tksurfer DESTINATION bin) - - endif() - -endif() diff --git a/tksurfer/Makefile.am b/tksurfer/Makefile.am deleted file mode 100644 index b7cc570809e..00000000000 --- a/tksurfer/Makefile.am +++ /dev/null @@ -1,93 +0,0 @@ -## -# Makefile.am -## - -if USE_LOCAL_TIFF -TIFFCFLAGS=-I$(top_srcdir)/tiff -LIBTIFF=$(top_builddir)/tiff/libtiff.a -else -TIFFCFLAGS=$(TIFF_CFLAGS) -LIBTIFF=$(LIB_TIFF) -endif - -AM_CPPFLAGS=\ - $(TCL_CFLAGS) $(GL_CFLAGS) $(TIFFCFLAGS) \ - -I$(top_srcdir)/include \ - -I$(top_srcdir)/dicom \ - -I$(top_srcdir)/glut \ - -I$(top_srcdir)/unix - -AM_LDFLAGS=$(LDFLAGS_TCL) $(TIFF_LIBS) - -if ENABLE_TCLTK_APPS -bin_PROGRAMS=tksurfer -tksurfer_SOURCES=tksurfer.c -tksurfer_LDADD= $(top_builddir)/fsgdf/libfsgdf.a \ - $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(LIBS_TCL_OPENGL) \ - $(X_LIBS) -lGL $(LIBTIFF) \ - $(top_builddir)/glut/libglut.a -tksurfer_LDFLAGS=$(LDFLAGS_TCL) -if HAVE_INTEL_COMPILER -# icc gives 'internal error: 04010026_0' if -O3 is used -tksurfer_CFLAGS=$(CFLAGS) -O2 -endif -else -bin_PROGRAMS= -endif - -if ENABLE_TCLTK_APPS -# put a wrapper around the bin, used to setup tcltktixblt enviro vars -# and install in 'tktools' dir instead of 'bin' (to allow easy deletion -# of all cortech-licensed software) -install-exec-hook: - rm -fv $(DESTDIR)$(bindir)/tksurfer - rm -fv $(DESTDIR)$(prefix)/tktools/tksurfer.bin - cp $(top_builddir)/tksurfer/tksurfer $(DESTDIR)$(prefix)/tktools/tksurfer.bin - echo "#!/bin/tcsh -ef" > $(DESTDIR)$(prefix)/tktools/tksurfer - echo "source \$$FREESURFER_HOME/bin/tcl_setup" \ - >> $(DESTDIR)$(prefix)/tktools/tksurfer - echo "exec \$$FREESURFER_HOME/tktools/tksurfer.bin \$$argv" \ - >> $(DESTDIR)$(prefix)/tktools/tksurfer - chmod a+x $(DESTDIR)$(prefix)/tktools/tksurfer - cp $(DESTDIR)$(prefix)/tktools/tksurfer $(DESTDIR)$(bindir)/ - if [[ -f /usr/pubsw/bin/chrpath ]]; then \ - /usr/pubsw/bin/chrpath -d $(DESTDIR)$(prefix)/tktools/tksurfer.bin; fi - -uninstall-hook: - rm -f $(DESTDIR)$(prefix)/tktools/tksurfer* - -else -all: - @echo "Building Tcl/Tk apps not enabled." - @echo "Run configure with either --enable-tcltk-apps or --with-tcl-dir=DIR" -install-exec-hook: -endif - -# Copy over precompiled 32-bit versions until we get 64-bit builds working. -if INSTALL_MAC32_GUIS -install-exec-hook: - rm -fv $(DESTDIR)$(bindir)/tksurfer - rm -fv $(DESTDIR)$(prefix)/tktools/tksurfer.bin - cp $(top_builddir)/distribution/Mac_32b/tksurfer.bin $(DESTDIR)$(prefix)/tktools/tksurfer.bin - echo "#!/bin/tcsh -ef" > $(DESTDIR)$(prefix)/tktools/tksurfer - echo "source \$$FREESURFER_HOME/bin/tcl_setup" \ - >> $(DESTDIR)$(prefix)/tktools/tksurfer - echo "exec \$$FREESURFER_HOME/tktools/tksurfer.bin \$$argv" \ - >> $(DESTDIR)$(prefix)/tktools/tksurfer - chmod a+x $(DESTDIR)$(prefix)/tktools/tksurfer - cp $(DESTDIR)$(prefix)/tktools/tksurfer $(DESTDIR)$(bindir)/ - if [[ -f /usr/pubsw/bin/chrpath ]]; then \ - /usr/pubsw/bin/chrpath -d $(DESTDIR)$(prefix)/tktools/tksurfer.bin; fi - -uninstall-hook: - rm -f $(DESTDIR)$(prefix)/tktools/surfer* -endif - -EXTRA_DIST=development_notes.txt - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/trc/Makefile.am b/trc/Makefile.am deleted file mode 100644 index ac84d58358d..00000000000 --- a/trc/Makefile.am +++ /dev/null @@ -1,91 +0,0 @@ -## -## Makefile.am -## - -if HAVE_ITK_LIBS -if HAVE_PETSC_LIBS -if HAVE_BOOST_LIBS - -AM_CFLAGS=-I$(top_srcdir)/include -AM_CXXFLAGS=-I$(top_srcdir)/include \ - -I$(top_srcdir)/fem_elastic \ - -I$(top_srcdir)/tetgen \ - $(VXL_CFLAGS) \ - $(ITK_CFLAGS) -DHAVE_ITK_LIBS \ - $(PETSC_CFLAGS) \ - $(BOOST_CFLAGS) - -AM_LDFLAGS=$(OS_LDFLAGS) - -bin_PROGRAMS = dmri_spline dmri_trk2trk dmri_vox2vox \ - dmri_train dmri_paths dmri_pathstats dmri_mergepaths \ - dmri_motion dmri_group dmri_forrest - -dmri_spline_SOURCES=dmri_spline.cxx spline.cxx spline.h -dmri_spline_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -dmri_spline_LDFLAGS=$(OS_LDFLAGS) - -dmri_trk2trk_SOURCES=dmri_trk2trk.cxx vial.cxx vial.h TrackIO.cxx TrackIO.h -dmri_trk2trk_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(top_builddir)/fem_elastic/libfem_elastic.a \ - $(top_builddir)/tetgen/libtetgen.a -dmri_trk2trk_LDFLAGS=$(OS_LDFLAGS) - -dmri_vox2vox_SOURCES=dmri_vox2vox.cxx vial.cxx vial.h -dmri_vox2vox_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(top_builddir)/fem_elastic/libfem_elastic.a \ - $(top_builddir)/tetgen/libtetgen.a -dmri_vox2vox_LDFLAGS=$(OS_LDFLAGS) - -dmri_train_SOURCES=dmri_train.cxx blood.cxx blood.h spline.cxx spline.h \ - vial.cxx vial.h \ - TrackIO.cxx TrackIO.h ByteSwap.h ErrorCode.h -dmri_train_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(top_builddir)/fem_elastic/libfem_elastic.a \ - $(top_builddir)/tetgen/libtetgen.a -dmri_train_LDFLAGS=$(OS_LDFLAGS) - -dmri_paths_SOURCES=dmri_paths.cxx coffin.cxx coffin.h \ - bite.cxx bite.h spline.cxx spline.h vial.cxx vial.h \ - TrackIO.cxx TrackIO.h ByteSwap.h ErrorCode.h -dmri_paths_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(top_builddir)/fem_elastic/libfem_elastic.a \ - $(top_builddir)/tetgen/libtetgen.a -dmri_paths_LDFLAGS=$(OS_LDFLAGS) - -dmri_pathstats_SOURCES=dmri_pathstats.cxx spline.cxx spline.h \ - blood.cxx blood.h \ - vial.cxx vial.h \ - TrackIO.cxx TrackIO.h ByteSwap.h ErrorCode.h -dmri_pathstats_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(top_builddir)/fem_elastic/libfem_elastic.a \ - $(top_builddir)/tetgen/libtetgen.a -dmri_pathstats_LDFLAGS=$(OS_LDFLAGS) - -dmri_mergepaths_SOURCES=dmri_mergepaths.cxx -dmri_mergepaths_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -dmri_mergepaths_LDFLAGS=$(OS_LDFLAGS) - -dmri_motion_SOURCES=dmri_motion.cxx vial.cxx vial.h -dmri_motion_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(top_builddir)/fem_elastic/libfem_elastic.a \ - $(top_builddir)/tetgen/libtetgen.a -dmri_motion_LDFLAGS=$(OS_LDFLAGS) - -dmri_group_SOURCES=dmri_group.cxx vial.cxx vial.h -dmri_group_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(top_builddir)/fem_elastic/libfem_elastic.a \ - $(top_builddir)/tetgen/libtetgen.a -dmri_group_LDFLAGS=$(OS_LDFLAGS) - -dmri_forrest_SOURCES=dmri_forrest.cxx forrest.cxx forrest.h -dmri_forrest_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -dmri_forrest_LDFLAGS=$(OS_LDFLAGS) - -# endif HAVE_ITK_LIBS, HAVE_PETSC_LIBS, HAVE_BOOST_LIBS -endif -endif -endif - -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/tridec/Makefile.am b/tridec/Makefile.am deleted file mode 100644 index 306bdc3d55e..00000000000 --- a/tridec/Makefile.am +++ /dev/null @@ -1,17 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -I$(top_srcdir)/include/dicom -AM_LDFLAGS= - -bin_PROGRAMS = tridec -tridec_SOURCES=tridec.c -tridec_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -tridec_LDFLAGS=$(OS_LDFLAGS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/unix/Makefile.am b/unix/Makefile.am deleted file mode 100644 index d75c49d6edb..00000000000 --- a/unix/Makefile.am +++ /dev/null @@ -1,24 +0,0 @@ -# -# Makefile.am -# - -AM_CPPFLAGS=-I$(top_srcdir)/include \ - $(GL_CFLAGS) \ - $(HAVE_OPENGL) - -AM_LDFLAGS= - -noinst_LIBRARIES=libunix.a - -libunix_a_SOURCES=cuserid.c unix_thread.c xwin.c \ - ftime.c windiag.c xwindow.c \ - oglutil.c xvmri.c texfont.c xvutil.c glStub.c - -EXTRA_DIST=lwpproto.h xvmri.h xwindow.h \ - oglutil.h xvutil.h xwin.h - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/utils/Makefile.am b/utils/Makefile.am deleted file mode 100644 index 6bf25bd76fc..00000000000 --- a/utils/Makefile.am +++ /dev/null @@ -1,468 +0,0 @@ -# -# Makefile.am for libutils.a -# - -NrrdIO_dir = NrrdIO -cephes_dir = cephes -test_dir = test - -SUBDIRS= $(NrrdIO_dir) $(cephes_dir) $(test_dir) - -if HAVE_ITK_LIBS -ITK_THINGS=$(ITK_CFLAGS) -DHAVE_ITK_LIBS -else -ITK_THINGS= -endif - -if HAVE_NIFTI_LIBS -NIFTI_THINGS=$(NIFTI_CFLAGS) -DHAVE_NIFTI_LIBS -else -NIFTI_THINGS= -endif - -if HAVE_OPENGL_LIBS -GLUT_THINGS=-I$(top_srcdir)/glut -DHAVE_GLUT_LIBS -else -GLUT_THINGS= -endif - -if USE_LOCAL_TIFF -TIFF_THINGS=-I$(top_srcdir)/tiff -else -TIFF_THINGS= -endif - -if USE_LOCAL_JPEG -JPEG_THINGS=-I$(top_srcdir)/jpeg -else -JPEG_THINGS= -endif - -if USE_LOCAL_EXPAT -EXPAT_THINGS=-I$(top_srcdir)/expat -else -EXPAT_THINGS= -endif - -NRRDIO_CPPFLAGS=-I$(top_srcdir)/include/NrrdIO \ - -DTEEM_DIO=$(TEEM_DIO) -DTEEM_32BIT=$(TEEM_32BIT) \ - -DTEEM_QNANHIBIT=$(TEEM_QNANHIBIT) -DTEEM_ENDIAN=$(TEEM_ENDIAN) - -AM_CPPFLAGS=\ - -I$(top_srcdir)/include \ - -I$(top_srcdir)/include/dicom \ - -I$(top_srcdir)/xml2 \ - $(NRRDIO_CPPFLAGS) $(JPEG_THINGS) $(TIFF_THINGS) $(EXPAT_THINGS) \ - $(ITK_THINGS) $(NIFTI_THINGS) $(GLUT_THINGS) \ - $(GL_CFLAGS) $(VXL_CFLAGS) $(CUDA_CFLAGS) -DHAVE_ZLIB - -AM_LDFLAGS= - -LIBS= - -noinst_LIBRARIES=libutils.a - -libutils_main_SOURCES=\ - afni.c \ - annotation.c \ - art1.c \ - artmap.c \ - aseg_edit_svm.c \ - autoencoder.c \ - backprop.c \ - bfileio.c \ - box.c \ - Bruker.c \ - chklc.c \ - chronometer.c \ - cluster.c \ - class_array.c \ - cma.c \ - cmat.c \ - cmdargs.c \ - colortab.c \ - connectcomp.c \ - corio.c \ - cpputils.cpp \ - ctrpoints.c \ - cvector.c \ - dcdflib.c \ - dct.c \ - density.c \ - diag.c \ - DICOMRead.c \ - diffuse.c \ - dti.c \ - dtk.fs.c \ - error.c \ - evschutils.c \ - fcd.c \ - fftutils.c \ - field_code.c \ - filter.c \ - fio.c \ - flash.c \ - fmarchmesh.c \ - fmriutils.c \ - fsenv.c \ - fsglm.c \ - fsPrintHelp.c \ - fsinit.c \ - gcaboundary.c \ - gca.c \ - gcamorph.c \ - gcarray.c \ - gclass.c \ - gcsa.c \ - getdelim.c \ - geos.c \ - getline.c \ - geodesics.cpp \ - gifti_io.c \ - gifti_local.c \ - gifti_xml.c \ - gtm.c \ - gw_ic2562.c \ - gw_utils.c \ - handle.c \ - heap.c \ - hippo.c \ - histo.c \ - joint_histo.c \ - ic163842.c \ - ic2562.c \ - ic642.c \ - ic42.c \ - ic12.c \ - icosahedron.c \ - image.c \ - imageio.c \ - imautils.c \ - intensity_eig.c \ - ipmpar.c \ - kernel.c \ - kinput.c \ - label.c \ - lpafile.c \ - machine.c \ - MARS_DT_Boundary.c \ - matfile.c \ - matrix.c \ - dmatrix.c \ - mgh_filter.c \ - mgh_malloc.c \ - mgh_matrix.c \ - min_heap.c \ - mincutils.c \ - minmaxrc.c \ - morph.c \ - mosaic.c \ - mri2.c \ - mri.c \ - mriBSpline.c \ - mriclass.c \ - mri_conform.c \ - mricurv.c \ - mriflood.c \ - mriFunctionalDataAccess.c \ - mriHeadPointList.c \ - mrihisto.c \ - mri_identify.c \ - MRIio_old.c \ - mriio.c \ - mri_level_set.c \ - mrifilter.c \ - mrimorph.c \ - mrinorm.c \ - mripolv.c \ - mriprob.c \ - mrisbiorthogonalwavelets.c \ - mrisegment.c \ - mriset.c \ - mrishash.c \ - mrisp.c \ - mriSurface.c \ - mrisurf.c \ - MRISrigidBodyAlignGlobal.c \ - mrisutils.c \ - mri_tess.c \ - mri_topology.c \ - mri_transform.c \ - mriTransform.c \ - mriVolume.c \ - mrivoxel.c \ - nifti1_io.c \ - offset.c \ - path.c \ - pdf.c \ - pgmstubs.c \ - prime.c \ - Progname.c \ - queue.c \ - randomfields.c \ - rbf.c \ - rbm.c \ - realm.c \ - rec.c \ - region.c \ - registerio.c \ - resample.c \ - rescale.c \ - retinotopy.c \ - rfa.c \ - rfutils.c \ - rforest.c \ - romp_support.c \ - selxavgio.c \ - sig.c \ - signa.c \ - sort.c \ - stats.c \ - stc.c \ - surfcluster.c \ - surfgrad.c \ - svm.c \ - tags.c \ - talairachex.c \ - thread.c \ - timer.c \ - transform.c \ - tritri.c \ - tukey.c \ - utils.c \ - version.c \ - vertexRotator.c \ - vlabels.c \ - volcluster.c \ - voxlist.c \ - x3DList.c \ - xDebug.c \ - xGLutWindow.c \ - xGrowableArray.c \ - xList.c \ - xSparseVolume.c \ - xTypes.c \ - xUndoList.c \ - xUtilities.c \ - xVoxel.c \ - znzlib.c \ - fs_cost_function.cpp \ - fs_lbfgs.cpp \ - fs_lbfgs_observer.cpp \ - fs_lbfgs_subject.cpp \ - fs_powell.cpp \ - mri_fastmarching.cpp \ - mriio_nrrd.c \ - mriio_nrrd_itk.cpp \ - numerics.cpp \ - chronometerpp.cpp\ - gcamorphtestutils.cpp\ - gcautils.cpp\ - gcalinearnode.cpp\ - gcalinearprior.cpp \ - cmat.c \ - mris_compVolFrac.c \ - gcamcomputeLabelsLinearCPU.cpp - -libutils_cephes_SOURCES=\ - $(srcdir)/$(cephes_dir)/bdtr.c \ - $(srcdir)/$(cephes_dir)/chdtr.c \ - $(srcdir)/$(cephes_dir)/const.c \ - $(srcdir)/$(cephes_dir)/fdtr.c \ - $(srcdir)/$(cephes_dir)/gamma.c \ - $(srcdir)/$(cephes_dir)/igam.c \ - $(srcdir)/$(cephes_dir)/igami.c \ - $(srcdir)/$(cephes_dir)/incbet.c \ - $(srcdir)/$(cephes_dir)/incbi.c \ - $(srcdir)/$(cephes_dir)/mtherr.c \ - $(srcdir)/$(cephes_dir)/ndtr.c \ - $(srcdir)/$(cephes_dir)/ndtri.c \ - $(srcdir)/$(cephes_dir)/polevl.c \ - $(srcdir)/$(cephes_dir)/stdtr.c - -libutils_nrrdio_SOURCES=\ - $(srcdir)/$(NrrdIO_dir)/754.c \ - $(srcdir)/$(NrrdIO_dir)/formatPNG.c \ - $(srcdir)/$(NrrdIO_dir)/accessors.c \ - $(srcdir)/$(NrrdIO_dir)/formatPNM.c \ - $(srcdir)/$(NrrdIO_dir)/array.c \ - $(srcdir)/$(NrrdIO_dir)/formatText.c \ - $(srcdir)/$(NrrdIO_dir)/arraysNrrd.c \ - $(srcdir)/$(NrrdIO_dir)/formatVTK.c \ - $(srcdir)/$(NrrdIO_dir)/axis.c \ - $(srcdir)/$(NrrdIO_dir)/gzio.c \ - $(srcdir)/$(NrrdIO_dir)/biffbiff.c \ - $(srcdir)/$(NrrdIO_dir)/keyvalue.c \ - $(srcdir)/$(NrrdIO_dir)/comment.c \ - $(srcdir)/$(NrrdIO_dir)/methodsNrrd.c \ - $(srcdir)/$(NrrdIO_dir)/defaultsNrrd.c \ - $(srcdir)/$(NrrdIO_dir)/miscAir.c \ - $(srcdir)/$(NrrdIO_dir)/dio.c \ - $(srcdir)/$(NrrdIO_dir)/mop.c \ - $(srcdir)/$(NrrdIO_dir)/encodingAscii.c \ - $(srcdir)/$(NrrdIO_dir)/parseAir.c \ - $(srcdir)/$(NrrdIO_dir)/encodingBzip2.c \ - $(srcdir)/$(NrrdIO_dir)/parseNrrd.c \ - $(srcdir)/$(NrrdIO_dir)/encoding.c \ - $(srcdir)/$(NrrdIO_dir)/encodingGzip.c \ - $(srcdir)/$(NrrdIO_dir)/encodingHex.c \ - $(srcdir)/$(NrrdIO_dir)/read.c \ - $(srcdir)/$(NrrdIO_dir)/encodingRaw.c \ - $(srcdir)/$(NrrdIO_dir)/reorder.c \ - $(srcdir)/$(NrrdIO_dir)/endianAir.c \ - $(srcdir)/$(NrrdIO_dir)/endianNrrd.c \ - $(srcdir)/$(NrrdIO_dir)/sane.c \ - $(srcdir)/$(NrrdIO_dir)/enum.c \ - $(srcdir)/$(NrrdIO_dir)/simple.c \ - $(srcdir)/$(NrrdIO_dir)/enumsNrrd.c \ - $(srcdir)/$(NrrdIO_dir)/string.c \ - $(srcdir)/$(NrrdIO_dir)/format.c \ - $(srcdir)/$(NrrdIO_dir)/subset.c \ - $(srcdir)/$(NrrdIO_dir)/formatEPS.c \ - $(srcdir)/$(NrrdIO_dir)/write.c \ - $(srcdir)/$(NrrdIO_dir)/formatNRRD.c - -libutils_a_SOURCES=\ - $(libutils_main_SOURCES) \ - $(libutils_cephes_SOURCES) \ - $(libutils_nrrdio_SOURCES) - -## ---- -## CUDA -## ---- - -# BUILDCUDA is defined if configure.in finds CUDA -if BUILDCUDA -# rules for building cuda files -NVCCINCLUDES = $(CUDA_CFLAGS) -I$(top_srcdir)/include $(MNI_CFLAGS) - -if HAVE_FERMI_GPU -# Fermi flags: -NVCC_ARCH = -DGCAMORPH_ON_GPU -CUDA_GCA_CFLAGS = -DGCAMORPH_ON_GPU -AM_CXXFLAGS = -DGCAMORPH_ON_GPU -DFS_CUDA -DCUDA_FORCE_SYNC -DCUDA_SHOW_TIMINGS -else -# Tesla flags (default): -NVCC_ARCH = -CUDA_GCA_CFLAGS = -endif - -G++FLAGS = -Wall -Wextra -Weffc++ - -CUDA_DEPS = $(top_srcdir)/include/volumegpu.hpp\ - $(top_srcdir)/include/volumegpu_impl.hpp\ - $(top_srcdir)/include/mriframegpu.hpp\ - $(top_srcdir)/include/gcamorphgpu.hpp\ - $(top_srcdir)/include/mriconvolve_cuda.hpp\ - $(top_srcdir)/include/mrimean_cuda.hpp\ - $(top_srcdir)/include/gcamorphenergy.hpp\ - $(top_srcdir)/include/gcamorphtermgpu.hpp\ - $(top_srcdir)/include/fixedmap.hpp\ - $(top_srcdir)/include/vecvolgpu.hpp\ - $(top_srcdir)/include/ctfactory.hpp - -.cu.o: - $(NVCC) -o $@ -c $< $(NVCCFLAGS) $(NVCCINCLUDES) $(NVCC_ARCH) \ - -DFS_CUDA -DCUDA_FORCE_SYNC -DCUDA_SHOW_TIMINGS \ - --compiler-options -O3 - -noinst_LIBRARIES += libutils_cuda.a - -libutils_cuda_a_SOURCES=\ - $(libutils_main_SOURCES) \ - $(libutils_cephes_SOURCES) \ - $(libutils_nrrdio_SOURCES) \ - mriframegpu.cu \ - devicemanagement.cu \ - mriconvolve_cuda.cu \ - mrivol2vol_cuda.cu \ - mrisurf_cuda.cu \ - affinegpu.cu\ - mrimean_cuda.cu\ - gcasgpu.cu\ - cudatypeutils.cu\ - gcamorphgpu.cu\ - gcamorphenergygpu.cu\ - gcamfots_cuda.cu\ - gcamorphtermgpu.cu\ - gcamorphcpu.cpp\ - gcamcomputegradient_cuda.cu\ - gcamregisterlevel_cuda.cu\ - gcamregisterpipeline_cuda.cu\ - mrilabels_cuda.cu\ - gcanodegpu.cu\ - gcapriorgpu.cu\ - vecvolgpu.cu - -libutils_cuda_a_CFLAGS=-DFS_CUDA $(CUDA_CFLAGS) $(CUDA_GCA_CFLAGS) - -# We have some templating dependencies -mriframegpu_cuda.o: $(CUDA_DEPS) -mriconvolve_cuda.o: $(CUDA_DEPS) -mrimean_cuda.o: $(CUDA_DEPS) -mrivol2vol_cuda.o: $(CUDA_DEPS) -affinegpu.o: $(CUDA_DEPS) -gcasgpu.o: $(CUDA_DEPS) -gcamorphgpu.o: $(CUDA_DEPS) $(top_srcdir)/include/volumegpucompare.hpp -cudatypeutils.o: $(top_srcdir)/include/cudatypeutils.hpp -gcamorphenergygpu.o: $(CUDA_DEPS) -gcamorphtermgpu.o: $(CUDA_DEPS) $(top_srcdir)/include/volumecpu.hpp -gcamorphcpu.o: $(top_srcdir)/include/gcamorphcpu.hpp $(CUDA_DEPS) -mrilabels_cuda.o: $(CUDA_DEPS) $(top_srcdir)/include/mrilabels_cuda.hpp -gcanodegpu.o: $(CUDA_DEPS) $(top_srcdir)/include/gcanodegpu.hpp $(top_srcdir)/include/gcalinearnode.hpp -gcapriorgpu.o: $(CUDA_DEPS) $(top_srcdir)/include/gcapriorgpu.hpp $(top_srcdir)/include/gcalinearprior.hpp -gcamregisterlevel_cuda.o : $(CUDA_DEPS) $(top_srcdir)/include/gcamremovenegativenodes_cuda.hpp - -CALLDEPTH ?= -1 - -%.calltree : %.dot - dot -Grankdir=LR -Tpdf < $< > $*.pdf - -%.dot : %.cflow - cflow2dot < $< > $@ - -%.cflow : - cflow -d ${CALLDEPTH} \ - --format=posix --omit-arguments \ - --level-indent='0=\t' --level-indent='1=\t' \ - --level-indent=start='\t' --main=$* \ - *.c > $@ - - -endif - - - -bin_PROGRAMS=gifti_tool gifti_test fsPrintHelp xmlToHtml - -gifti_tool_SOURCES=gifti_tool.c gifti_tool.h \ - gifti_io.c gifti_xml.c nifti1_io.c znzlib.c -gifti_tool_LDADD=$(top_builddir)/expat/libexpat.a -lz -lm \ - $(OPENMP_FLAG) $(LIBS_NIFTI) - -gifti_test_SOURCES=gifti_test.c gifti_test.h gifti_io.c gifti_xml.c \ - nifti1_io.c znzlib.c -gifti_test_LDADD=$(top_builddir)/expat/libexpat.a -lz $(LIBS_NIFTI) - -fsPrintHelp_SOURCES=fsPrintHelp.c -fsPrintHelp_CFLAGS=-DBUILD_MAIN -fsPrintHelp_LDADD=$(top_builddir)/xml2/libxml2.a -lz -fsPrintHelp_LDFLAGS=$(OS_LDFLAGS) - -xmlToHtml_SOURCES=xmlToHtml.c -xmlToHtml_LDADD=$(top_builddir)/xml2/libxml2.a -lz - -install-exec-hook: - cp $(DESTDIR)$(bindir)/fsPrintHelp $(DESTDIR)$(bindir)/fshelp - cp $(DESTDIR)$(bindir)/fsPrintHelp $(DESTDIR)$(bindir)/fsman - -uninstall-hook: - rm -f $(DESTDIR)$(bindir)/fs* - -EXTRA_DIST=$(srcdir)/$(NrrdIO_dir)/copyright.NrrdIO $(CUDA_DEPS) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/utils/NrrdIO/Makefile.am b/utils/NrrdIO/Makefile.am deleted file mode 100644 index 65ebdc83d6e..00000000000 --- a/utils/NrrdIO/Makefile.am +++ /dev/null @@ -1,56 +0,0 @@ -# -# Makefile.am for NrrdIO directory -# - -# (source files included in libutils build) - -EXTRA_DIST=\ - 754.c \ - formatPNG.c \ - accessors.c \ - formatPNM.c \ - array.c \ - formatText.c \ - arraysNrrd.c \ - formatVTK.c \ - axis.c \ - gzio.c \ - biffbiff.c \ - keyvalue.c \ - comment.c \ - methodsNrrd.c \ - defaultsNrrd.c \ - miscAir.c \ - dio.c \ - mop.c \ - encodingAscii.c \ - parseAir.c \ - encodingBzip2.c \ - parseNrrd.c \ - encoding.c \ - encodingGzip.c \ - qnanhibit.c \ - encodingHex.c \ - read.c \ - encodingRaw.c \ - reorder.c \ - endianAir.c \ - sampleIO.c \ - endianNrrd.c \ - sane.c \ - enum.c \ - simple.c \ - enumsNrrd.c \ - string.c \ - format.c \ - subset.c \ - formatEPS.c \ - write.c \ - formatNRRD.c - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - diff --git a/utils/cephes/Makefile.am b/utils/cephes/Makefile.am deleted file mode 100644 index b0a48a22531..00000000000 --- a/utils/cephes/Makefile.am +++ /dev/null @@ -1,15 +0,0 @@ -# -# Makefile.am for cephes directory -# - -# (source files included in libutils build) - -EXTRA_DIST=bdtr.c const.c gamma.c igami.c incbi.c ndtr.c polevl.c \ -chdtr.c fdtr.c igam.c incbet.c mtherr.c ndtri.c stdtr.c - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - diff --git a/utils/test/MRIScomputeBorderValues/Makefile.am b/utils/test/MRIScomputeBorderValues/Makefile.am deleted file mode 100644 index 788b453a47c..00000000000 --- a/utils/test/MRIScomputeBorderValues/Makefile.am +++ /dev/null @@ -1,22 +0,0 @@ -## -## Makefile.am -## - -AM_CPPFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -check_PROGRAMS = test_MRIScomputeBorderValues - -TESTS=run_test_MRIScomputeBorderValues - -test_MRIScomputeBorderValues_SOURCES=test_MRIScomputeBorderValues.cpp -test_MRIScomputeBorderValues_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -test_MRIScomputeBorderValues_LDFLAGS= $(OS_LDFLAGS) - -EXTRA_DIST=run_test_MRIScomputeBorderValues testdata.tar.gz - -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -clean-local: - rm -f *.o diff --git a/utils/test/MRISpositionSurface/Makefile.am b/utils/test/MRISpositionSurface/Makefile.am deleted file mode 100644 index 2a9ed98ce16..00000000000 --- a/utils/test/MRISpositionSurface/Makefile.am +++ /dev/null @@ -1,22 +0,0 @@ -## -## Makefile.am -## - -AM_CPPFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -check_PROGRAMS = test_MRISpositionSurface - -TESTS=run_test_MRISpositionSurface - -test_MRISpositionSurface_SOURCES=test_MRISpositionSurface.cpp -test_MRISpositionSurface_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -test_MRISpositionSurface_LDFLAGS= $(OS_LDFLAGS) - -EXTRA_DIST=run_test_MRISpositionSurface testdata.tar.gz - -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -clean-local: - rm -f *.o diff --git a/utils/test/Makefile.am b/utils/test/Makefile.am deleted file mode 100644 index ac152e5df89..00000000000 --- a/utils/test/Makefile.am +++ /dev/null @@ -1,142 +0,0 @@ -# -# Makefile.am -# -SUBDIRS=\ - mriBuildVoronoiDiagramFloat \ - MRIScomputeBorderValues \ - mrishash \ - mriSoapBubbleFloat - - # MRISpositionSurface \ # currently unstable - - -AM_CPPFLAGS=-I$(top_srcdir)/include \ - -I$(top_srcdir)/include/dicom \ - -I$(top_srcdir)/include/NrrdIO -LDADD=$(addprefix $(top_builddir)/, $(LIBS_MGH)) - -#bin_PROGRAMS = MRISresampleOntoSphere -#MRISresampleOntoSphere_SOURCES=MRISresampleOntoSphere.cpp -#MRISresampleOntoSphere_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ -# $(ANN_LIBS) -lANN -#MRISresampleOntoSphere_LDFLAGS=$(OS_LDFLAGS) - -CHECKS=\ - testcolortab \ - test_c_nr_wrapper \ - extest \ - inftest \ - tiff_write_image \ - sc_test - -BROKEN_CHECKS=\ - checkanalyze \ - test_mri_identify \ - mghxform \ - i2rtest \ - icotest \ - mnitest \ - difftool \ - test_mriio \ - mris_compute_thickness \ - mri_compute_stats \ - surftest \ - mri_ms_LDA \ - mri_fslmat_to_lta \ - mri_concatenate_lta \ - mri_transform_to_COR \ - mri_compute_all_CNR \ - mri_ms_compute_CNR \ - mri_apply_INU \ - mri_edit_wm \ - mri_apply_EM_mask \ - mri_extract \ - mri_ms_gca_EM - -# trick to get test data into the build directory -foo_SOURCES= -foo: - if ! test -f "$(top_builddir)/utils/test/test_data.tar.gz"; then \ - cp -v $(top_srcdir)/utils/test/test_data.tar.gz \ - $(top_builddir)/utils/test/; fi; -# if ! test -f "$(top_builddir)/distribution/lib/bem/ic0.tri"; then \ -# cp -v $(top_srcdir)/distribution/lib/bem/*.tri \ -# $(top_builddir)/distribution/lib/bem/; fi; - if ! test -f "$(top_builddir)/distribution/FreeSurferColorLUT.txt"; then \ - cp -v $(top_srcdir)/distribution/FreeSurferColorLUT.txt \ - $(top_builddir)/distribution/FreeSurferColorLUT.txt; fi; - -if HAVE_CPPUNIT -CPPUNIT_CHECKS= -# these break on travis build: test_nr_wrapper test_matrix -else -CPPUNIT_CHECKS= -endif -check_PROGRAMS=foo $(CHECKS) $(CPPUNIT_CHECKS) - -TESTS=setup_test_data $(CHECKS) $(CPPUNIT_CHECKS) cleanup_test_data - -testcolortab_SOURCES=testcolortab.c -mnitest_SOURCES=mnitest.cpp -i2rtest_SOURCES=i2rtest.cpp -#icotest_SOURCES=icotest.cpp -extest_SOURCES=extest.cpp -mghxform_SOURCES=mghxform.cpp -inftest_SOURCES=inftest.cpp -checkanalyze_SOURCES=checkanalyze.cpp -test_mri_identify_SOURCES=test_mri_identify.cpp -test_c_nr_wrapper_SOURCES=test_c_nr_wrapper.c -sc_test_SOURCES=sc_test.c -tiff_write_image_SOURCES=tiff_write_image.c -#test_mriio_SOURCES=test_mriio.cpp -#surftest_SOURCES=surftest.cpp -#difftool_SOURCES=difftool.cpp -#mris_compute_thickness_SOURCES=mris_compute_thickness.cpp -#mri_edit_wm_SOURCE=mri_edit_wm.c -#mri_apply_EM_mask_SOURCE=mri_apply_EM_mask.c -#mri_ms_gca_EM_SOURCE=mri_ms_EM.c -#mri_ms_LDA_SOURCE=mri_ms_LDA.c -#mri_apply_INU_SOURCE=mri_apply_INU.c -#mri_compute_stats_SOURCE=mri_compute_stats.c -#mri_compute_all_CNR_SOURCE=mri_compute_all_CNR.c -#mri_fslmat_to_lta_SOURCE=mri_fslmat_to_lta.c -#mri_transform_to_COR_SOURCE=mri_transform_to_COR.c -#mri_concatenate_lta_SOURCE=mri_concatenate_lta.c -#mri_ms_compute_CNR_SOURCES=mri_ms_compute_CNR.c -#mri_extract_SOURCE=mri_extract.c - -if HAVE_CPPUNIT - -# -Wno-non-virtual-dtor suppresses valid scuba and cppunit warnings: -# "has virtual functions but non-virtual destructor" -# these warnings appear with gcc 4.# - -test_nr_wrapper_SOURCES=test_nr_wrapper.cpp -test_nr_wrapper_CXXFLAGS=$(CPPUNIT_CFLAGS) -Wno-non-virtual-dtor -test_nr_wrapper_LDADD=$(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(CPPUNIT_LIBS) -lcppunit -ldl - -test_matrix_SOURCES=test_matrix.cpp -test_matrix_CXXFLAGS=$(CPPUNIT_CFLAGS) -Wno-non-virtual-dtor -test_matrix_LDADD=$(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(CPPUNIT_LIBS) -lcppunit -ldl -endif - -EXTRA_DIST=setup_test_data test_data.tar.gz cleanup_test_data \ - mri_ms_LDA.c mri_apply_EM_mask.c mri_ms_compute_CNR.c mri_remove.cpp \ - mri_uchar.cpp mri_flip2analyze.cpp mri_extract.c mri_fslmat_to_lta.c \ - mri_ms_gca_EM.c mri_transform_to_COR.c mri_compute_all_CNR.c \ - mri_compute_stats.c mri_edit_wm.c mri_apply_INU.c mri_concatenate_lta.c \ - mri_copy_params.cpp \ - mris_compute_thickness.cpp mris_indirect_morph.cpp mris_diff_on_surface.c \ - mris_diff.cpp mris_gethires.cpp ANN.h ANNperf.h ANNx.h difftool.cpp \ - fmarching3dnband.c fmarching3dnband.h gcaread.cpp heap_mesh.c heap_mesh.h \ - MRISresampleOntoSphere.cpp MRISwaveletsTransform.cpp rastest.cpp \ - surf2surf.cpp surftest.cpp testcras.cpp testm3d.cpp test_mriio.cpp \ - tixtest.c vltest.cpp xtqli.c - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES="" -include $(top_srcdir)/Makefile.extra diff --git a/utils/test/mriBuildVoronoiDiagramFloat/Makefile.am b/utils/test/mriBuildVoronoiDiagramFloat/Makefile.am deleted file mode 100644 index 0d5985372fb..00000000000 --- a/utils/test/mriBuildVoronoiDiagramFloat/Makefile.am +++ /dev/null @@ -1,22 +0,0 @@ -## -## Makefile.am -## - -AM_CPPFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -check_PROGRAMS = test_mriBuildVoronoiDiagramFloat - -TESTS=test_mriBuildVoronoiDiagramFloat_withData - -test_mriBuildVoronoiDiagramFloat_SOURCES=test_mriBuildVoronoiDiagramFloat.cpp -test_mriBuildVoronoiDiagramFloat_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -test_mriBuildVoronoiDiagramFloat_LDFLAGS= $(OS_LDFLAGS) - -EXTRA_DIST=testdata.tar.gz - -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -clean-local: - rm -f *.o diff --git a/utils/test/mriSoapBubbleFloat/Makefile.am b/utils/test/mriSoapBubbleFloat/Makefile.am deleted file mode 100644 index 78a364130c2..00000000000 --- a/utils/test/mriSoapBubbleFloat/Makefile.am +++ /dev/null @@ -1,22 +0,0 @@ -## -## Makefile.am -## - -AM_CPPFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -check_PROGRAMS = test_mriSoapBubbleFloat - -TESTS=test_mriSoapBubbleFloat_withData - -test_mriSoapBubbleFloat_SOURCES=test_mriSoapBubbleFloat.cpp -test_mriSoapBubbleFloat_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -test_mriSoapBubbleFloat_LDFLAGS= $(OS_LDFLAGS) - -EXTRA_DIST=test_mriSoapBubbleFloat_withData testdata.tar.gz - -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -clean-local: - rm -f *.o diff --git a/utils/test/mrishash/Makefile.am b/utils/test/mrishash/Makefile.am deleted file mode 100644 index fe3663d4695..00000000000 --- a/utils/test/mrishash/Makefile.am +++ /dev/null @@ -1,44 +0,0 @@ -## -## Makefile.am -## - -AM_CFLAGS=-I$(top_srcdir)/include -AM_LDFLAGS= - -check_PROGRAMS = mrishash_demo_100_find_coverage \ - mrishash_demo_200_mht_hatch \ - mrishash_test_100_find_tests \ - mrishash_test_200_intersect - -TESTS=mrishash_test_100_find_tests mrishash_test_200_intersect - -#------------- exercise ---------------- - -mrishash_demo_100_find_coverage_SOURCES=mrishash_demo_100_find_coverage.c -mrishash_demo_100_find_coverage_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mrishash_demo_100_find_coverage_LDFLAGS= $(OS_LDFLAGS) - -mrishash_demo_200_mht_hatch_SOURCES=mrishash_demo_200_mht_hatch.c -mrishash_demo_200_mht_hatch_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mrishash_demo_200_mht_hatch_LDFLAGS= $(OS_LDFLAGS) - -##------------- test ---------------- - -mrishash_test_100_find_tests_SOURCES=mrishash_test_100_find_tests.c -mrishash_test_100_find_tests_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mrishash_test_100_find_tests_LDFLAGS= $(OS_LDFLAGS) - -mrishash_test_200_intersect_SOURCES=mrishash_test_200_intersect.c -mrishash_test_200_intersect_LDADD= $(addprefix $(top_builddir)/, $(LIBS_MGH)) -mrishash_test_200_intersect_LDFLAGS= $(OS_LDFLAGS) - -EXTRA_DIST= - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -clean-local: - rm -f *_mri.mgz *_log.txt *.tri *.o diff --git a/utilscpp/Makefile.am b/utilscpp/Makefile.am deleted file mode 100644 index 3c742cc0052..00000000000 --- a/utilscpp/Makefile.am +++ /dev/null @@ -1,21 +0,0 @@ -# -# Makefile.am for libutilscpp.a -# - -AM_CPPFLAGS=-std=c++0x $(X_CFLAGS) \ - -I$(top_srcdir)/include \ - -I$(top_srcdir)/include/dicom - -SUBDIRS=test - -noinst_LIBRARIES= libutilscpp.a - -libutilscpp_a_SOURCES = argparse.cpp log.cpp mris_fastmarching.cpp globals.cpp face.cpp \ - vertex.cpp loop.cpp fastloop.cpp surface.cpp patchdisk.cpp \ - mris_topology.cpp segment.cpp patchdisk.cpp - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/utilscpp/test/Makefile.am b/utilscpp/test/Makefile.am deleted file mode 100644 index e45412dcca1..00000000000 --- a/utilscpp/test/Makefile.am +++ /dev/null @@ -1,26 +0,0 @@ -# -# Makefile.am -# - -# we pick linker to be g++, since it knows where to find -# the right libstdc++ and other -# files needed to resolve symbols in the library of C++ code -CCLD=g++ - -AM_CFLAGS=-I$(top_srcdir)/include \ - -I$(top_srcdir)/include/dicom - -check_PROGRAMS=ctest - -ctest_SOURCES=ctest.c -ctest_LDFLAGS=$(OS_LDFLAGS) - -#segfaults: TESTS=ctest - -LDADD=$(addprefix $(top_builddir)/, $(LIBS_MGH) utilscpp/libutilscpp.a) - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra diff --git a/vtkfsio/Makefile.am b/vtkfsio/Makefile.am deleted file mode 100644 index 8d3cf219716..00000000000 --- a/vtkfsio/Makefile.am +++ /dev/null @@ -1,68 +0,0 @@ -# -# Makefile.am for libvtkfsio.a -# - -if HAVE_VTK_LIBS - -AM_CPPFLAGS= -Wno-deprecated \ - $(X_CFLAGS) \ - $(VXL_CFLAGS) \ - -I$(top_srcdir)/include \ - $(VTK_CXXFLAGS) \ - $(KWWIDGETS_CXXFLAGS) - -AM_LDFLAGS= - -noinst_LIBRARIES= libvtkfsio.a - -libvtkfsio_a_SOURCES=\ - vtkFSSurfaceLabelSource.cxx \ - vtkFSSurfaceLabelSource.h \ - vtkFSSurfaceWriter.cxx \ - vtkFSSurfaceWriter.h \ - vtkFSSurfaceScalarsReader.cxx \ - vtkFSSurfaceScalarsReader.h \ - vtkFSSurfaceSource.cxx \ - vtkFSSurfaceSource.h \ - vtkFSVolumeSource.cxx \ - vtkFSVolumeSource.h - -EXTRA_DIST=$(libvtkfsio_a_SOURCES) lh.vtkFSSurfaceWriterTestFile - -if ENABLE_KWWIDGETS_APPS -check_PROGRAMS = vtkFSSurfaceWriterTester -#TESTS = vtkFSSurfaceWriterTester -else -check_PROGRAMS = -#TESTS = -endif - -vtkFSSurfaceWriterTester_SOURCES=vtkFSSurfaceWriterTester.cxx - -vtkFSSurfaceWriterTester_LDADD=\ - $(top_builddir)/fsgdf/libfsgdf.a \ - $(top_builddir)/vtkfsio/libvtkfsio.a \ - $(top_builddir)/vtkutils/libvtkutils.a \ - $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(LDFLAGS_TCL) $(LIBS_TCL_OPENGL) \ - $(VTK_LIBS) $(VTK_VERDICT_LIB) -lvtkWidgets -lvtkGraphics \ - -lvtkImaging -lvtkFiltering $(VTK_SQLITE_LIB) \ - -lvtkCommon -lvtksys \ - -lvtkHybrid -lvtkexoIIc -lvtkNetCDF \ - -lvtkVolumeRendering -lvtkRendering -lvtkftgl \ - $(VTK_EXPAT_LIB) $(VTK_FREETYPE_LIB) \ - $(VTK_TIFF_LIB) $(VTK_JPEG_LIB) \ - $(VTK_PNG_LIB) $(VTK_Z_LIB) $(VTK_METAIO_LIB) \ - -lvtkIO -lvtkDICOMParser $(VTK_MPEG2ENCODE_LIB) \ - -lvtkImagingTCL -lvtkVolumeRenderingTCL -lvtkRenderingTCL \ - -lvtkFilteringTCL -lvtkWidgetsTCL \ - -lvtkHybridTCL -lvtkGraphicsTCL -lvtkImagingTCL -lvtkIOTCL \ - -lvtkCommonTCL - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -endif diff --git a/vtkutils/Makefile.am b/vtkutils/Makefile.am deleted file mode 100644 index f3aee8bf13d..00000000000 --- a/vtkutils/Makefile.am +++ /dev/null @@ -1,194 +0,0 @@ -# -# Makefile.am for libvtkutils.a -# - -if USE_LOCAL_TIFF -TIFF_THINGS=-I$(top_srcdir)/tiff -L$(top_srcdir)/tiff -else -TIFF_THINGS=$(TIFF_CFLAGS) -endif - -if USE_LOCAL_JPEG -JPEG_THINGS=-I$(top_srcdir)/jpeg -L$(top_srcdir)/jpeg -else -JPEG_THINGS=$(JPEG_CFLAGS) -endif - -if USE_LOCAL_EXPAT -EXPAT_THINGS=-I$(top_srcdir)/expat -L$(top_srcdir)/expat -else -EXPAT_THINGS=$(EXPAT_CFLAGS) -endif - - -AM_CPPFLAGS= -Wno-deprecated \ - $(TIFF_THINGS) $(JPEG_THINGS) $(EXPAT_THINGS) \ - $(GL_CFLAGS) \ - $(TCL_CFLAGS) \ - $(VXL_CFLAGS) \ - -I$(top_srcdir)/include \ - $(VTK_CXXFLAGS) \ - $(KWWIDGETS_CXXFLAGS) - -AM_CXXFLAGS=$(AM_CPPFLAGS) - -AM_LDFLAGS= - -if ENABLE_KWWIDGETS_APPS -noinst_LIBRARIES= libvtkutils.a -else -noinst_LIBRARIES= -endif - -libvtkutils_a_SOURCES= \ - vtkKWProgressDialog.cxx \ - vtkKWRGBATransferFunctionEditor.cxx \ - vtkKWRGBATransferFunctionEditorTcl.cxx \ - vtkKWBltGraph.cxx vtkKWBltGraphTcl.cxx \ - vtkFreesurferLookupTable.cxx \ - vtkArrowPipeline.cxx \ - vtkRGBATransferFunction.cxx \ - vtkRGBAColorTransferFunction.cxx \ - vtkFDTensorGlyph.cxx \ - vtkODFGlyph.cxx \ - vtkInflatePolyData.cxx \ - IconLoader.cxx - -# We use vtkWrapTcl to create the Tcl wrapped code for this object. -vtkKWRGBATransferFunctionEditorTcl.cxx: vtkKWRGBATransferFunctionEditor.h - ${VTK_DIR}/bin/vtkWrapTcl vtkKWRGBATransferFunctionEditor.h \ - ${VTK_LIB_VTK}/hints 1 vtkKWRGBATransferFunctionEditorTcl.cxx - -vtkKWBltGraphTcl.cxx: vtkKWBltGraph.h - ${VTK_DIR}/bin/vtkWrapTcl vtkKWBltGraph.h \ - ${VTK_LIB_VTK}/hints 1 vtkKWBltGraphTcl.cxx - -if ENABLE_KWWIDGETS_APPS -foo_SOURCES= -foo: - if ! test -f "$(top_builddir)/vtkutils/vtkKWRGBATransferFunctionEditorTester-scalars.mgh"; then \ - cp -v $(top_srcdir)/vtkutils/vtkKWRGBATransferFunctionEditorTester-scalars.mgh \ - $(top_builddir)/vtkutils/; fi; - if ! test -f "$(top_builddir)/vtkutils/IconLoaderTestIcons.txt"; then \ - cp -v $(top_srcdir)/vtkutils/IconLoaderTestIcons.txt \ - $(top_builddir)/vtkutils/; fi; - -if HAVE_MAC_OSX -check_PROGRAMS=foo vtkArrowPipelineTester -else -check_PROGRAMS=foo IconLoaderTest \ -vtkKWRGBATransferFunctionEditorTester vtkArrowPipelineTester -endif -#these commented-out because the tests are interactive (can't run automatically) -#TESTS=vtkKWRGBATransferFunctionEditorTester vtkArrowPipelineTester -#TESTS=testIconLoader -else -check_PROGRAMS= -TESTS= -endif - -IconLoaderTest_SOURCES=IconLoaderTest.cxx IconLoaderTest.h IconLoader.cxx - -IconLoaderTest_LDADD=\ - $(top_builddir)/vtkfsio/libvtkfsio.a \ - $(top_builddir)/vtkutils/libvtkutils.a \ - $(LDFLAGS_TCL) $(LIBS_TCL_OPENGL) \ - $(VTK_LIBS) $(VTK_VERDICT_LIB) $(VTK_SQLITE_LIB) \ - -lvtkIO -lvtkWidgets -lvtkGraphics \ - -lvtkImaging -lvtkFiltering \ - -lvtkCommon -lvtksys \ - -lvtkHybrid -lvtkexoIIc -lvtkNetCDF \ - -lvtkVolumeRendering -lvtkRendering -lvtkftgl \ - -lexpat $(VTK_EXPAT_LIB) $(VTK_FREETYPE_LIB) \ - -ltiff $(VTK_TIFF_LIB) -ljpeg $(VTK_JPEG_LIB) \ - $(VTK_PNG_LIB) $(VTK_Z_LIB) $(VTK_METAIO_LIB) \ - -lvtkIO -lvtkDICOMParser $(VTK_MPEG2ENCODE_LIB) \ - -lvtkImagingTCL -lvtkVolumeRenderingTCL -lvtkRenderingTCL \ - -lvtkFilteringTCL -lvtkWidgetsTCL \ - -lvtkHybridTCL -lvtkGraphicsTCL -lvtkImagingTCL -lvtkIOTCL \ - -lvtkCommonTCL \ - $(KWWIDGETS_LIBS) -lKWWidgets - - -# vtkKWRGBATransferFunctionEditorTester test program -vtkKWRGBATransferFunctionEditorTester_SOURCES=vtkKWRGBATransferFunctionEditorTester.cxx \ - vtkKWRGBATransferFunctionEditorTesterTcl.cxx \ - RgbatransferfunctioneditortesterLibInit.cxx - -vtkKWRGBATransferFunctionEditorTesterTcl.cxx: vtkKWRGBATransferFunctionEditorTester.h - ${VTK_DIR}/bin/vtkWrapTcl vtkKWRGBATransferFunctionEditorTester.h \ - ${VTK_LIB_VTK}/hints 1 vtkKWRGBATransferFunctionEditorTesterTcl.cxx - -RgbatransferfunctioneditortesterLibInit.cxx: RgbatransferfunctioneditortesterLibInit.data - ${VTK_DIR}/bin/vtkWrapTclInit RgbatransferfunctioneditortesterLibInit.data \ - RgbatransferfunctioneditortesterLibInit.cxx - -vtkKWRGBATransferFunctionEditorTester_LDADD=\ - $(top_builddir)/fsgdf/libfsgdf.a \ - $(top_builddir)/vtkfsio/libvtkfsio.a \ - $(top_builddir)/vtkutils/libvtkutils.a \ - $(addprefix $(top_builddir)/, $(LIBS_MGH)) \ - $(LDFLAGS_TCL) $(LIBS_TCL_OPENGL) \ - $(VTK_LIBS) $(VTK_VERDICT_LIB) $(VTK_SQLITE_LIB) \ - -lvtkWidgets -lvtkGraphics \ - -lvtkImaging -lvtkFiltering \ - -lvtkCommon -lvtksys \ - -lvtkHybrid -lvtkexoIIc -lvtkNetCDF \ - -lvtkVolumeRendering -lvtkRendering -lvtkftgl \ - -lexpat $(VTK_EXPAT_LIB) $(VTK_FREETYPE_LIB) \ - -ltiff $(VTK_TIFF_LIB) -ljpeg $(VTK_JPEG_LIB) \ - $(VTK_PNG_LIB) $(VTK_Z_LIB) $(VTK_METAIO_LIB) \ - -lvtkIO -lvtkDICOMParser $(VTK_MPEG2ENCODE_LIB) \ - -lvtkImagingTCL -lvtkVolumeRenderingTCL -lvtkRenderingTCL \ - -lvtkFilteringTCL -lvtkWidgetsTCL \ - -lvtkHybridTCL -lvtkGraphicsTCL -lvtkImagingTCL -lvtkIOTCL \ - -lvtkCommonTCL \ - $(KWWIDGETS_LIBS) -lKWWidgets - -# vtkArrowPipelineTester test program -vtkArrowPipelineTester_SOURCES=vtkArrowPipelineTester.cxx - -vtkArrowPipelineTester_LDADD=\ - $(top_builddir)/vtkutils/libvtkutils.a \ - $(LDFLAGS_TCL) $(LIBS_TCL_OPENGL) \ - $(VTK_LIBS) $(VTK_VERDICT_LIB) -lvtkWidgets -lvtkGraphics \ - -lvtkImaging -lvtkFiltering \ - -lvtkCommon -lvtksys \ - -lvtkHybrid -lvtkexoIIc -lvtkNetCDF \ - -lvtkVolumeRendering -lvtkRendering -lvtkftgl \ - -lexpat $(VTK_EXPAT_LIB) $(VTK_FREETYPE_LIB) \ - -ltiff $(VTK_TIFF_LIB) -ljpeg $(VTK_JPEG_LIB) $(VTK_SQLITE_LIB) \ - $(VTK_PNG_LIB) $(VTK_Z_LIB) $(VTK_METAIO_LIB) \ - -lvtkIO -lvtkDICOMParser $(VTK_MPEG2ENCODE_LIB) \ - -lvtkImagingTCL -lvtkVolumeRenderingTCL -lvtkRenderingTCL \ - -lvtkFilteringTCL -lvtkWidgetsTCL \ - -lvtkHybridTCL -lvtkGraphicsTCL -lvtkImagingTCL -lvtkIOTCL \ - -lvtkCommonTCL - -clean-local: - rm -f vtkKWBltGraphTcl.cxx vtkKWRGBATransferFunctionEditorTcl.cxx - -EXTRA_DIST=IconLoader.h \ -vtkArrowPipeline.h \ -vtkFDTensorGlyph.h \ -vtkFreesurferLookupTable.h \ -vtkInflatePolyData.h \ -vtkKWBltGraph.h \ -vtkKWProgressDialog.h \ -vtkKWRGBATransferFunctionEditor.h \ -vtkKWRGBATransferFunctionEditorTester.h \ -vtkODFGlyph.h \ -vtkRGBATransferFunction.h \ -vtkRGBAColorTransferFunction.h \ -RgbatransferfunctioneditortesterLibInit.data \ -vtkKWRGBATransferFunctionEditorTester-scalars.mgh \ -IconLoaderTest.cxx IconLoaderTestIcons.txt testIconLoader - -# Our release target. Include files to be excluded here. They will be -# found and removed after 'make install' is run during the 'make -# release' target. -EXCLUDE_FILES= -include $(top_srcdir)/Makefile.extra - -clean-local: - -rm *Tcl.cxx diff --git a/x86cpucaps/cpucaps b/x86cpucaps/cpucaps deleted file mode 100755 index d566fc84af6..00000000000 Binary files a/x86cpucaps/cpucaps and /dev/null differ