third-party package rearranging and pysurfer bindings (freesurfer#616)

* renamed wrappers dir to bindings

* rename labelfusion algorithms

* added basic util bindings

* move all labelfusion stuff to infant dir

* configure infant labelfusion

* more labelfusion updates

* finalize surface bindings

* remove old packages dirs

* add packages locally so we can build all with -fPIC

* fix warnings

* fix glut includes

* fix osx pthread_getcpuclockid

* add jpeg config file

* bf: setup.py config

* really no need for users to build kwwidgets anymore

* added licenses in packages folders

* suppress warnings

CMakeLists.txt

@@ -116,21 +116,6 @@ if(NOT APPLE)
 
 endif()
 
-# -------- jpeg --------
-find_package(JPEG REQUIRED)
-
-# -------- tiff --------
-find_package(TIFF REQUIRED)
-
-# -------- expat --------
-find_package(Expat REQUIRED)
-
-# -------- xml2 --------
-find_package(XML2 REQUIRED)
-
-# -------- tetgen --------
-find_package(Tetgen REQUIRED)
-
 # -------- petsc --------
 find_package(PETSC)
 
@@ -182,9 +167,6 @@ if(BUILD_GUIS)
   find_package(OpenGL)
   if(OPENGL_FOUND)
     add_definitions(-DHAVE_OPENGL)
-    # since we have OpenGL, make sure we have glut too
-    find_package(GLUT REQUIRED)
-    add_definitions(-DHAVE_GLUT_LIBS)
   endif()
 
   # -------- qt --------
@@ -217,6 +199,11 @@ add_definitions(-D${CMAKE_SYSTEM_NAME})
 
 # general check for big endian
 test_big_endian(IS_BIG_ENDIAN)
+if(IS_BIG_ENDIAN)
+  set(BYTEORDER 4321)
+else()
+  set(BYTEORDER 1234)
+endif()
 
 # compiler warnings
 set(C_CXX_FLAGS "${C_CXX_FLAGS} -Wall")
@@ -233,7 +220,7 @@ add_definitions(-DANSI)
 # SSE matrix and math functions (affine.h and sse_mathfun.h)
 # todo: write some logic to set this correctly
 add_definitions(-DUSE_SSE_MATHFUN)
-set(C_CXX_FLAGS "${C_CXX_FLAGS} -msse2 -mfpmath=sse")
+set(C_CXX_FLAGS "${C_CXX_FLAGS} -msse2 -mfpmath=sse -fPIC")
 
 # large file support: support for files > 2GB
 if(APPLE)
@@ -336,17 +323,29 @@ endif()
 set(FS_INCLUDE_DIRS
   ${CMAKE_SOURCE_DIR}
   ${CMAKE_SOURCE_DIR}/include
-  ${CMAKE_SOURCE_DIR}/minc_1_5_1
-  ${CMAKE_SOURCE_DIR}/netcdf_3_6_0_p1
+  ${CMAKE_SOURCE_DIR}/packages/minc
+  ${CMAKE_SOURCE_DIR}/packages/netcdf
 )
 
+# build third-party libraries
 # make sure to use the local minc source
 add_definitions(-DUSE_LOCAL_MINC)
+add_subdirectories(
+  packages/jpeg
+  packages/expat
+  packages/tiff
+  packages/xml2
+  packages/minc
+  packages/netcdf
+  packages/tetgen
+)
+
+if(OPENGL_FOUND)
+  add_subdirectory(packages/glut)
+endif()
 
 # now build the freesurfer static libraries (order here matters!)
 add_subdirectories(
-  minc_1_5_1
-  netcdf_3_6_0_p1
   unix
   log
   rgb

netcdf_3_6_0_p1/COPYRIGHT → distribution/docs/license.netcdf.txt

@@ -29,7 +29,3 @@ INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING
 FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
 NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
 WITH THE ACCESS, USE OR PERFORMANCE OF THIS SOFTWARE.
-
-
-
-

distribution/docs/license.tetgen.txt

@@ -0,0 +1,66 @@
+TetGen License
+--------------
+
+The software (TetGen) is licensed under the terms of the  MIT  license
+with the following exceptions:
+
+Distribution of  modified  versions  of this code is permissible UNDER
+THE CONDITION THAT  THIS CODE AND ANY MODIFICATIONS  MADE TO IT IN THE
+SAME SOURCE FILES  tetgen.h AND tetgen.cxx  REMAIN UNDER  COPYRIGHT OF
+THE  ORIGINAL AUTHOR,  BOTH  SOURCE AND OBJECT  CODE  ARE MADE  FREELY
+AVAILABLE  WITHOUT   CHARGE,   AND  CLEAR   NOTICE  IS  GIVEN  OF  THE 
+MODIFICATIONS.
+
+Distribution of this code for  any  commercial purpose  is permissible
+ONLY BY DIRECT ARRANGEMENT WITH THE COPYRIGHT OWNER.
+
+The full  license text is reproduced below.
+
+This means that TetGen is no free software, but for private, research,
+and  educational purposes it  can be  used at  absolutely no  cost and
+without further arrangements.
+
+
+For details, see http://tetgen.berlios.de
+
+==============================================================================
+
+TetGen
+A Quality Tetrahedral Mesh Generator and 3D Delaunay Triangulator
+Version 1.4 (Released on January 14, 2006).
+
+Copyright 2002, 2004, 2005, 2006 
+Hang Si
+Rathausstr. 9, 10178 Berlin, Germany
+[email protected]
+
+Permission is hereby granted, free  of charge, to any person obtaining
+a  copy  of this  software  and  associated  documentation files  (the
+"Software"), to  deal in  the Software without  restriction, including
+without limitation  the rights to  use, copy, modify,  merge, publish,
+distribute,  sublicense and/or  sell copies  of the  Software,  and to
+permit persons to whom the Software  is furnished to do so, subject to
+the following conditions:
+
+Distribution of  modified  versions  of this code is permissible UNDER
+THE CONDITION THAT  THIS CODE AND ANY MODIFICATIONS  MADE TO IT IN THE
+SAME SOURCE FILES  tetgen.h AND tetgen.cxx  REMAIN UNDER  COPYRIGHT OF
+THE  ORIGINAL AUTHOR,  BOTH  SOURCE AND OBJECT  CODE  ARE MADE  FREELY
+AVAILABLE  WITHOUT   CHARGE,   AND  CLEAR   NOTICE  IS  GIVEN  OF  THE 
+MODIFICATIONS.
+
+Distribution of this code for  any  commercial purpose  is permissible
+ONLY BY DIRECT ARRANGEMENT WITH THE COPYRIGHT OWNER.
+
+The  above  copyright  notice  and  this permission  notice  shall  be
+included in all copies or substantial portions of the Software.
+
+THE  SOFTWARE IS  PROVIDED  "AS  IS", WITHOUT  WARRANTY  OF ANY  KIND,
+EXPRESS OR  IMPLIED, INCLUDING  BUT NOT LIMITED  TO THE  WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+IN NO EVENT  SHALL THE AUTHORS OR COPYRIGHT HOLDERS  BE LIABLE FOR ANY
+CLAIM, DAMAGES OR  OTHER LIABILITY, WHETHER IN AN  ACTION OF CONTRACT,
+TORT  OR OTHERWISE, ARISING  FROM, OUT  OF OR  IN CONNECTION  WITH THE
+SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+==============================================================================