nf: sse using surface et al (freesurfer#708)

* More of the necessary code but not enabled * Add the .py * fall thru seen to happen * mrisurf_base.h was being too widely used, causing conflicts * Start connection MRIS_MP in to the Surface support * Builds * Clean up the dev merge * make nsize and dist_nsize be the same type in MRIS and MRIS_MP * Add the dump code * MAX_NEIGHBOURS has increased * Next small step towards being able to use templates for more of the distortion code * latest dev merged, next steps towards a faster surface distortion * Closer but not there yet for implementing MRIScomputeSSE for MRIS_MP * Builds * builds * Add specific includes for mrisurf_metricProperties.h
ayendiki · Sep 13, 2019 · edd6c68 · edd6c68
1 parent f0d94f0
commit edd6c68
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diff --git a/anatomicuts/CMakeLists.txt b/anatomicuts/CMakeLists.txt
@@ -69,5 +69,5 @@ install(PROGRAMS
 
 install_pyscript(
 	diffusionUtils
-	anatomiCutsUtils
+	anatomiCutsUtils.py
 )
diff --git a/hiam_make_surfaces/hiam_make_surfaces.cpp b/hiam_make_surfaces/hiam_make_surfaces.cpp
@@ -43,29 +43,31 @@
 #include <math.h>
 #include <ctype.h>
 
+#include "macros.h"
+
+#include "mri.h"
+#include "mrimorph.h"
+#include "mrinorm.h"
+
 #include "mrisurf.h"
+#include "mrisurf_project.h"
 #include "mrishash_internals.h"
 
-#include "macros.h"
 #include "error.h"
 #include "diag.h"
 #include "proto.h"
 #include "timer.h"
-#include "mri.h"
-#include "macros.h"
-#include "mrimorph.h"
-#include "mrinorm.h"
 #include "matrix.h"
 
-#define VERTEX_EDGE(vec, v0, v1)   VECTOR_LOAD(vec,v1->x-v0->x,v1->y-v0->y,v1->z-v0->z)
-
 #define MAX_4_NEIGHBORS     100
 #define MAX_3_NEIGHBORS     70
 #define MAX_2_NEIGHBORS     20
 #define MAX_1_NEIGHBORS     8
-
 #define REPULSE_K           1.0
+
+#undef  REPULSE_E           // differs from mrisurf_base.h 0.25
 #define REPULSE_E           0.5
+
 #define MAX_MOMENTUM_MM     1
 
 static int    get_option(int argc, char *argv[]) ;
@@ -94,8 +96,8 @@ static double mrisComputeGaussianCurvatureSpringEnergy(MRI_SURFACE *mris, double
 
 static double mrismomentumTimeStep(MRI_SURFACE *mris, float momentum, float dt, float tol,
                                    float n_averages);
-static int    mrisProjectSurface(MRI_SURFACE *mris);
-static int    mrisComputeTangentPlanes(MRI_SURFACE *mris);
+static int    my_mrisProjectSurface(MRI_SURFACE *mris);
+static int    my_mrisComputeTangentPlanes(MRI_SURFACE *mris);
 static int    FindSpikes(MRI_SURFACE *mris, int iter);
 static int    SmoothSpikes(MRI_SURFACE *mris, int niter);
 
@@ -1122,7 +1124,7 @@ mrisComputeQuadraticCurvatureTerm(MRI_SURFACE *mris, double l_curv) {
   if (FZERO(l_curv))
     return(NO_ERROR) ;
 
-  mrisComputeTangentPlanes(mris) ;
+  my_mrisComputeTangentPlanes(mris) ;
   v_n = VectorAlloc(3, MATRIX_REAL) ;
   v_A = VectorAlloc(2, MATRIX_REAL) ;
   v_e1 = VectorAlloc(3, MATRIX_REAL) ;
@@ -1197,7 +1199,7 @@ mrisComputeQuadraticCurvatureEnergy(MRI_SURFACE *mris) {
   double   sse = 0.0 ;
 
 
-  mrisComputeTangentPlanes(mris) ;
+  my_mrisComputeTangentPlanes(mris) ;
   v_n = VectorAlloc(3, MATRIX_REAL) ;
   v_A = VectorAlloc(2, MATRIX_REAL) ;
   v_e1 = VectorAlloc(3, MATRIX_REAL) ;
@@ -1782,12 +1784,12 @@ mrismomentumTimeStep(MRI_SURFACE *mris, float momentum, float dt, float tol,
     }
   }
 
-  mrisProjectSurface(mris) ;
+  my_mrisProjectSurface(mris) ;
   return(delta_t) ;
 }
 
 static int
-mrisProjectSurface(MRI_SURFACE *mris) {
+my_mrisProjectSurface(MRI_SURFACE *mris) {
 
   /*  MRISupdateSurface(mris) ;*/
   switch (mris->status) {
@@ -1815,7 +1817,7 @@ mrisProjectSurface(MRI_SURFACE *mris) {
 
 
 static int
-mrisComputeTangentPlanes(MRI_SURFACE *mris) {
+my_mrisComputeTangentPlanes(MRI_SURFACE *mris) {
   VECTOR  *v_n, *v_e1, *v_e2, *v ;
   int     vno ;
   VERTEX  *vertex ;

diff --git a/hiam_register/hiam_register.cpp b/hiam_register/hiam_register.cpp
@@ -31,12 +31,14 @@
 #include <ctype.h>
 
 #include "macros.h"
+
+#include "mri.h"
+#include "mrisurf.h"
+#include "mrisurf_project.h"
+
 #include "error.h"
 #include "diag.h"
 #include "proto.h"
-#include "mrisurf.h"
-#include "mri.h"
-#include "macros.h"
 #include "timer.h"
 
 static char vcid[] = "$Id: hiam_register.c,v 1.6 2011/12/12 03:28:32 greve Exp $";
@@ -92,7 +94,6 @@ static int use_defaults = 1 ;
 
 #define IMAGES_PER_SURFACE   3   /* mean, variance, and dof */
 #define SURFACES         sizeof(curvature_names) / sizeof(curvature_names[0])
-#define PARAM_IMAGES         (IMAGES_PER_SURFACE*SURFACES)
 #define NSIGMAS  (sizeof(sigmas)  / sizeof(sigmas[0]))
 #define MAX_NBHD_SIZE  200
 

diff --git a/include/mrishash_SurfaceFromMRIS.h b/include/mrishash_SurfaceFromMRIS.h
@@ -19,8 +19,10 @@
 #include "mrishash.h"
 #include "mrisurf_SurfaceFromMRIS_generated.h"
 
-MRIS_HASH_TABLE* MHTcreateFaceTable             (SurfaceFromMRIS::Analysis::Surface surface);
-MRIS_HASH_TABLE* MHTcreateFaceTable_Resolution  (SurfaceFromMRIS::Analysis::Surface surface, int which, float res);
-MRIS_HASH_TABLE* MHTcreateVertexTable           (SurfaceFromMRIS::Analysis::Surface surface, int which);
-MRIS_HASH_TABLE* MHTcreateVertexTable_Resolution(SurfaceFromMRIS::Analysis::Surface surface, int which, float res);
+namespace Minimal_Surface_MRIS = SurfaceFromMRIS::XYZPosition;
+
+MRIS_HASH_TABLE* MHTcreateFaceTable             (Minimal_Surface_MRIS::Surface surface);
+MRIS_HASH_TABLE* MHTcreateFaceTable_Resolution  (Minimal_Surface_MRIS::Surface surface, int which, float res);
+MRIS_HASH_TABLE* MHTcreateVertexTable           (Minimal_Surface_MRIS::Surface surface, int which);
+MRIS_HASH_TABLE* MHTcreateVertexTable_Resolution(Minimal_Surface_MRIS::Surface surface, int which, float res);
 
diff --git a/include/mrisurf.h b/include/mrisurf.h
@@ -122,10 +122,6 @@ void MRIS_checkAcquiredTemp(MRIS* mris, MRIS_TempAssigned temp, int MRIS_acquire
 void MRIS_releaseTemp      (MRIS* mris, MRIS_TempAssigned temp, int MRIS_acquireTemp_result);  // ... be allowed to release it
 
 
-FaceNormCacheEntry const * getFaceNorm(MRIS const * const mris, int fno);
-void setFaceNorm(MRIS const * const mris, int fno, float nx, float ny, float nz);
-
-
 // Support for writing traces that can be compared across test runs to help find where differences got introduced  
 //
 void mrisVertexHash(MRIS_HASH* hash, MRIS const * mris, int vno);
@@ -668,9 +664,6 @@ int   MRISintegrate(MRI_SURFACE *mris, INTEGRATION_PARMS *parms, int n_avgs);
 int   mrisLogIntegrationParms(FILE *fp, MRI_SURFACE *mris,
 			      INTEGRATION_PARMS *parms) ;
 
-MRIS* MRISprojectOntoSphere   (MRIS* mris_src, MRIS* mris_dst, double r) ;
-MRIS* MRISprojectOntoEllipsoid(MRIS* mris_src, MRIS* mris_dst, float a, float b, float c) ;
-
 int          MRISsampleDistances(MRI_SURFACE *mris, int *nbr_count,int n_nbrs);
 int          MRISsampleAtEachDistance(MRI_SURFACE *mris, int nbhd_size,
                                       int nbrs_per_distance) ;
@@ -777,11 +770,6 @@ MRI_SURFACE  *MRISremoveNegativeVertices(MRI_SURFACE *mris,
 int          MRIScomputeFaceAreas(MRI_SURFACE *mris) ;
 int          MRISupdateEllipsoidSurface(MRI_SURFACE *mris) ;
 
-MRIS* MRIStranslate_along_vertex_dxdydz(MRIS* mris_src, MRIS* mris_dst, double dt);
-
-MRIS* MRISrotate(MRIS* mris_src, MRIS* mris_dst,
-                         float alpha, float beta, float gamma) ;
-
 MRI          *MRISwriteIntoVolume(MRI_SURFACE *mris, MRI *mri, int which) ;
 MRI_SURFACE  *MRISreadFromVolume(MRI *mri, MRI_SURFACE *mris, int which) ;
 
@@ -2123,15 +2111,13 @@ void mrisRemoveEdge(MRIS *mris, int vno1, int vno2);
 
 // Neighbourhoods
 //
-#define MAX_NEIGHBORS (1024)
 void mrisVertexReplacingNeighbors(MRIS * mris, int vno, int vnum);
 void mrisForgetNeighborhoods     (MRIS * mris);
 
 int  MRISresetNeighborhoodSize      (MRIS *mris, int nsize) ;
 void MRISsetNeighborhoodSize        (MRIS *mris, int nsize) ;   // Doesn't compute distances if not already present
 void MRISsetNeighborhoodSizeAndDist (MRIS *mris, int nsize) ;   // Always computes distances
 
-#define MRIS_MAX_NEIGHBORHOOD_LINKS 50  // bound on nlinks
 int  MRISfindNeighborsAtVertex      (MRIS *mris, int vno, int nlinks, size_t listCapacity, int* vlist, int* hops);
     // sets vlist[*] to the neighboring vno
     // sets hops [*] to -1 for [vno] and the number of hops for all entries returned in the vlist
@@ -2185,8 +2171,14 @@ int  MRIStranslate (MRIS *mris, float dx, float dy, float dz);
 void MRISmoveOrigin(MRIS *mris, float x0, float y0, float z0);
 int  MRISscale     (MRIS *mris, double scale);
 
-void MRISblendXYZandTXYZ(MRIS* mris, float xyzScale, float txyzScale);  // x = x*xyzScale + tx*txyzScale  etc.
-void MRISblendXYZandNXYZ(MRIS* mris,                 float nxyzScale);  // x = x          + nx*nxyzScale  etc.
+void MRISblendXYZandTXYZ(MRIS* mris, float xyzScale, float txyzScale);          // x = x*xyzScale + tx*txyzScale  etc.
+void MRISblendXYZandNXYZ(MRIS* mris,                 float nxyzScale);          // x = x          + nx*nxyzScale  etc.
+
+
+void MRIStranslate_along_vertex_dxdydz(MRIS*    dst, MRIS*    src, double dt);  // dst.x = src.x + src.dx*dt, etc.
+void MRIStranslate_along_vertex_dxdydz(MRIS_MP* dst, MRIS_MP* src, double dt);
+
+MRIS* MRISrotate(MRIS* mris_src, MRIS* mris_dst, float alpha, float beta, float gamma) ;
 
 void mrisDisturbVertices(MRIS *mris, double amount);
 
@@ -2209,7 +2201,9 @@ int mrisComputeSurfaceDimensions(MRIS *mris);
 // dist is created by calls to MRISsetNeighborhoodSizeAndDist
 // dist_orig must be explicitly created
 //
-void MRISfreeDistsButNotOrig(MRIS *mris);
+void MRISfreeDistsButNotOrig(MRIS*    mris);
+void MRISfreeDistsButNotOrig(MRISPV*  mris);
+void MRISfreeDistsButNotOrig(MRIS_MP* mris);
 
 void MRISmakeDistOrig (MRIS *mris, int vno);                        // makes it the same size as the current VERTEX.dist
 void MRISgrowDistOrig (MRIS *mris, int vno, int minimumCapacity);   // same size as current or bigger

diff --git a/include/mrisurf_FACE_VERTEX_MRIS_generated.h b/include/mrisurf_FACE_VERTEX_MRIS_generated.h
@@ -1,7 +1,9 @@
 
+#pragma once
 // GENERATED SOURCE - DO NOT DIRECTLY EDIT
 // 
 // =======================================
+#include "mrisurf_aaa.h"
 #define SEPARATE_VERTEX_TOPOLOGY
 struct face_type_ {
       vertices_per_face_t v          ;
@@ -20,17 +22,16 @@ struct VERTEX_TOPOLOGY {
     //  the whole fits in much less than one cache line, so further ordering is no use
     pSeveralInt   f             ;  // size() is num.    array[v->num] the fno's of the neighboring faces         
     pSeveralUchar n             ;  // size() is num.    array[v->num] the face.v[*] index for this vertex        
-    pSeveralInt   e             ;  //  edge state for neighboring vertices (used by MRI_EDGE,MRI_CORNER)              
+    pSeveralInt   e             ;  //  edge state for neighboring vertices                      
     pSeveralInt   v             ;  // size() is vtotal.    array[v->vtotal or more] of vno, head sorted by hops     
-    short const   vnum          ;  //  number of 1-hop neighbors    should use [p]VERTEXvnum(i, 
+    short         vnum          ;  //  number of 1-hop neighbors    should use [p]VERTEXvnum(i) 
     short         v2num         ;  //  number of 1, or 2-hop neighbors                          
     short         v3num         ;  //  number of 1,2,or 3-hop neighbors                         
     short         vtotal        ;  //  total # of neighbors. copy of vnum.nsizeCur              
     short         nsizeMaxClock ;  //  copy of mris->nsizeMaxClock when v#num                   
     uchar         nsizeMax      ;  //  the max nsize that was used to fill in vnum etc          
     uchar         nsizeCur      ;  //  index of the current v#num in vtotal                     
-    uchar         num           ;  //  number of neighboring faces 
-    VERTEX_TOPOLOGY() : vnum(0) {}                             
+    uchar         num           ;  //  number of neighboring faces                              
 };		// VERTEX_TOPOLOGY
 
 struct vertex_type_ {
@@ -185,6 +186,7 @@ struct MRIS {
     float                         x0                       ;  //  center of spherical expansion
     float                         y0                       ;
     float                         z0                       ;
+    //  v_temporal_pole, v_frontal_pole, and v_occipital_pole don't appear to be used, and are unusual being pointers to vertices
     PVERTEX                       v_temporal_pole          ;
     PVERTEX                       v_frontal_pole           ;
     PVERTEX                       v_occipital_pole         ;
@@ -282,7 +284,7 @@ struct MRIS {
     ELTX(short,nsizeMaxClock)  SEP \
     ELTT(uchar,nsizeMax)  SEP \
     ELTT(uchar,nsizeCur)  SEP \
-    ELTT(uchar,num)  SEP \
+    ELTT(uchar,num)  \
 // end of macro
 
 #define LIST_OF_VERTEX_ELTS_1 \
@@ -435,6 +437,7 @@ struct MRIS {
     ELTT(int,tempsAssigned)  SEP \
     ELTP(FACE,faces)  SEP \
     ELTP(MRI_EDGE,edges)  SEP \
+    ELTP(MRI_CORNER,corners)  SEP \
     ELTP(FaceNormCacheEntry,faceNormCacheEntries)  SEP \
     ELTP(FaceNormDeferredEntry,faceNormDeferredEntries)  SEP \
     ELTP(STRIP,strips)  SEP \

diff --git a/include/mrisurf_MRIS.h b/include/mrisurf_MRIS.h
@@ -0,0 +1 @@
+#include "mrisurf_FACE_VERTEX_MRIS_generated.h"
diff --git a/include/mrisurf_MRISPV.h b/include/mrisurf_MRISPV.h
@@ -0,0 +1 @@
+#include "mrisurf_MRIS_PropertiesInVectors.h"
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		#include "mrisurf_FACE_VERTEX_MRIS_generated.h"