int
main(int argc, char *argv[])
{
char **av, *in_fname,fname[STRLEN],hemi[10], path[STRLEN],
name[STRLEN],*cp ;
int ac, nargs, nhandles ;
MRI_SURFACE *mris ;
double ici, fi, var ;
/* rkt: check for and handle version tag */
nargs = handle_version_option
(argc, argv,
"$Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $",
"$Name: stable5 $");
if (nargs && argc - nargs == 1)
{
exit (0);
}
argc -= nargs;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++)
{
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (argc < 2)
{
usage_exit() ;
}
in_fname = argv[1] ;
FileNamePath(in_fname, path) ;
FileNameOnly(in_fname, name) ;
cp = strchr(name, '.') ;
if (!cp)
ErrorExit(ERROR_BADPARM, "%s: could not scan hemisphere from '%s'",
Progname, fname) ;
strncpy(hemi, cp-2, 2) ;
hemi[2] = 0 ;
if (patch_flag) /* read the orig surface, then the patch file */
{
sprintf(fname, "%s/%s.orig", path, hemi) ;
mris = MRISfastRead(fname) ;
if (!mris)
ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
Progname, in_fname) ;
if (Gdiag & DIAG_SHOW)
{
fprintf(stderr, "reading patch file %s...\n", in_fname) ;
}
if (MRISreadPatch(mris, in_fname) != NO_ERROR)
ErrorExit(ERROR_NOFILE, "%s: could not read patch file %s",
Progname, in_fname) ;
}
else /* just read the surface normally */
{
mris = MRISread(in_fname) ;
if (!mris)
ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
Progname, in_fname) ;
}
MRISsetNeighborhoodSize(mris, nbrs) ;
if (nbhd_size > 0)
{
MRISsampleAtEachDistance(mris, nbhd_size, nbrs_per_distance) ;
}
if (max_mm > 0)
{
float ratio ;
MRISstoreMetricProperties(mris) ;
if (MRISreadCanonicalCoordinates(mris, "sphere") != NO_ERROR)
{
ErrorExit(ERROR_NOFILE,
"%s: could not read canonical coordinates from ?h.sphere",
Progname);
}
MRISsaveVertexPositions(mris, ORIGINAL_VERTICES) ;
MRISrestoreVertexPositions(mris, CANONICAL_VERTICES) ;
MRIScomputeMetricProperties(mris) ;
ratio = mris->orig_area / M_PI * mris->radius * mris->radius * 4.0 ;
ratio = mris->orig_area / mris->total_area ;
MRISscaleBrain(mris, mris, sqrt(ratio)) ;
MRISsaveVertexPositions(mris, CANONICAL_VERTICES) ;
MRISrestoreVertexPositions(mris, ORIGINAL_VERTICES) ;
MRIScomputeMetricProperties(mris) ;
MRIScomputeNeighbors(mris, max_mm) ;
}
if (param_file)
{
MRI_SP *mrisp ;
mrisp = MRISPread(param_file) ;
if (normalize_param)
{
MRISnormalizeFromParameterization(mrisp, mris, param_no) ;
}
else
{
MRISfromParameterization(mrisp, mris, param_no) ;
}
MRISPfree(&mrisp) ;
if (normalize)
{
MRISnormalizeCurvature(mris,which_norm) ;
}
sprintf(fname, "%s/%s%s.param", path,name,suffix) ;
fprintf(stderr, "writing parameterized curvature to %s...", fname) ;
MRISwriteCurvature(mris, fname) ;
fprintf(stderr, "done.\n") ;
}
else
{
MRIScomputeSecondFundamentalFormThresholded(mris, cthresh) ;
nhandles = nint(1.0 - mris->Ktotal / (4.0*M_PI)) ;
fprintf(stderr, "total integrated curvature = %2.3f*4pi (%2.3f) --> "
"%d handles\n", (float)(mris->Ktotal/(4.0f*M_PI)),
(float)mris->Ktotal, nhandles) ;
#if 0
fprintf(stderr, "0: k1 = %2.3f, k2 = %2.3f, H = %2.3f, K = %2.3f\n",
mris->vertices[0].k1, mris->vertices[0].k2,
mris->vertices[0].H, mris->vertices[0].K) ;
fprintf(stderr, "0: vnum = %d, v2num = %d, total=%d, area=%2.3f\n",
mris->vertices[0].vnum, mris->vertices[0].v2num,
mris->vertices[0].vtotal,mris->vertices[0].area) ;
#endif
MRIScomputeCurvatureIndices(mris, &ici, &fi);
var = MRIStotalVariation(mris) ;
fprintf(stderr,"ICI = %2.1f, FI = %2.1f, variation=%2.3f\n", ici, fi, var);
if (diff_flag)
{
MRISuseCurvatureDifference(mris) ;
MRISaverageCurvatures(mris, navgs) ;
sprintf(fname, "%s/%s%s.diff", path,name,suffix) ;
fprintf(stderr, "writing curvature difference to %s...", fname) ;
MRISwriteCurvature(mris, fname) ;
fprintf(stderr, "done.\n") ;
}
if (ratio_flag)
{
MRISuseCurvatureRatio(mris) ;
MRISaverageCurvatures(mris, navgs) ;
if (normalize)
{
MRISnormalizeCurvature(mris,which_norm) ;
}
sprintf(fname, "%s/%s%s.ratio", path,name,suffix) ;
fprintf(stderr, "writing curvature ratio to %s...", fname) ;
MRISwriteCurvature(mris, fname) ;
fprintf(stderr, "done.\n") ;
}
if (contrast_flag)
{
MRISuseCurvatureContrast(mris) ;
MRISaverageCurvatures(mris, navgs) ;
if (normalize)
{
MRISnormalizeCurvature(mris,which_norm) ;
}
sprintf(fname, "%s/%s%s.contrast", path,name,suffix) ;
fprintf(stderr, "writing curvature contrast to %s...", fname) ;
MRISwriteCurvature(mris, fname) ;
fprintf(stderr, "done.\n") ;
}
if (neg_flag)
{
int neg ;
if (mris->patch)
{
mris->status = MRIS_PLANE ;
}
MRIScomputeMetricProperties(mris) ;
neg = MRIScountNegativeTriangles(mris) ;
MRISuseNegCurvature(mris) ;
MRISaverageCurvatures(mris, navgs) ;
sprintf(fname, "%s/%s%s.neg", path,name,suffix) ;
fprintf(stderr, "writing negative vertex curvature to %s...", fname) ;
MRISwriteCurvature(mris, fname) ;
fprintf(stderr, "%d negative triangles\n", neg) ;
fprintf(stderr, "done.\n") ;
{
int vno, fno ;
VERTEX *v ;
FACE *f ;
for (vno = 0 ; vno < mris->nvertices ; vno++)
{
v = &mris->vertices[vno] ;
if (v->ripflag)
{
continue ;
}
neg = 0 ;
for (fno = 0 ; fno < v->num ; fno++)
{
f = &mris->faces[v->f[fno]] ;
if (f->area < 0.0f)
{
neg = 1 ;
}
}
if (neg)
{
fprintf(stdout, "%d\n", vno) ;
}
}
}
}
if (max_flag)
{
MRISuseCurvatureMax(mris) ;
MRISaverageCurvatures(mris, navgs) ;
if (normalize)
{
MRISnormalizeCurvature(mris,which_norm) ;
}
sprintf(fname, "%s/%s%s.max", path,name,suffix) ;
fprintf(stderr, "writing curvature maxima to %s...", fname) ;
MRISwriteCurvature(mris, fname) ;
fprintf(stderr, "done.\n") ;
}
if (min_flag)
{
MRISuseCurvatureMin(mris) ;
MRISaverageCurvatures(mris, navgs) ;
if (normalize)
{
MRISnormalizeCurvature(mris,which_norm) ;
}
sprintf(fname, "%s/%s%s.min", path,name,suffix) ;
fprintf(stderr, "writing curvature minima to %s...", fname) ;
MRISwriteCurvature(mris, fname) ;
fprintf(stderr, "done.\n") ;
}
if (stretch_flag)
{
MRISreadOriginalProperties(mris, NULL) ;
MRISuseCurvatureStretch(mris) ;
MRISaverageCurvatures(mris, navgs) ;
if (normalize)
{
MRISnormalizeCurvature(mris,which_norm) ;
}
sprintf(fname, "%s/%s%s.stretch", path,name,suffix) ;
fprintf(stderr, "writing curvature stretch to %s...", fname) ;
MRISwriteCurvature(mris, fname) ;
fprintf(stderr, "done.\n") ;
}
if (write_flag)
{
MRISuseGaussianCurvature(mris) ;
if (cthresh > 0)
{
MRIShistoThresholdCurvature(mris, cthresh) ;
}
MRISaverageCurvatures(mris, navgs) ;
sprintf(fname, "%s/%s%s.K", path,name, suffix) ;
fprintf(stderr, "writing Gaussian curvature to %s...", fname) ;
if (normalize)
{
MRISnormalizeCurvature(mris,which_norm) ;
}
MRISwriteCurvature(mris, fname) ;
MRISuseMeanCurvature(mris) ;
if (cthresh > 0)
{
MRIShistoThresholdCurvature(mris, cthresh) ;
}
MRISaverageCurvatures(mris, navgs) ;
if (normalize)
{
MRISnormalizeCurvature(mris,which_norm) ;
}
sprintf(fname, "%s/%s%s.H", path,name, suffix) ;
fprintf(stderr, "done.\nwriting mean curvature to %s...", fname) ;
MRISwriteCurvature(mris, fname) ;
fprintf(stderr, "done.\n") ;
}
}
exit(0) ;
return(0) ; /* for ansi */
}
int
main(int argc, char *argv[]) {
char *cp, **av, *in_fname, fname[100], path[100],
name[100], hemi[100] ;
int ac, nargs ;
/* rkt: check for and handle version tag */
nargs = handle_version_option (argc, argv, "$Id: mris_errors.c,v 1.11 2011/03/02 00:04:31 nicks Exp $", "$Name: $");
if (nargs && argc - nargs == 1)
exit (0);
argc -= nargs;
Progname = argv[0] ;
ErrorInit(NULL, NULL, NULL) ;
DiagInit(NULL, NULL, NULL) ;
ac = argc ;
av = argv ;
for ( ; argc > 1 && ISOPTION(*argv[1]) ; argc--, argv++) {
nargs = get_option(argc, argv) ;
argc -= nargs ;
argv += nargs ;
}
if (argc < 2)
usage_exit() ;
in_fname = argv[1] ;
#if 0
out_fname = argv[2] ;
cp = strrchr(out_fname, '.') ;
#endif
if (patch_flag) /* read in orig surface before reading in patch */
{
FileNamePath(in_fname, path) ;
FileNameOnly(in_fname, name) ;
cp = strchr(name, '.') ;
if (cp) {
strncpy(hemi, cp-2, 2) ;
hemi[2] = 0 ;
} else
strcpy(hemi, "lh") ;
sprintf(fname, "%s/%s.smoothwm", path, hemi) ;
mris = MRISread(fname) ;
if (!mris)
ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
Progname, fname) ;
FileNameOnly(in_fname, name) ;
MRISstoreMetricProperties(mris) ;
MRISsaveVertexPositions(mris, ORIGINAL_VERTICES) ;
if (MRISreadPatch(mris, name) != NO_ERROR)
ErrorExit(ERROR_NOFILE, "%s: could not read patch file %s",
Progname, name) ;
} else {
mris = MRISread(in_fname) ;
if (!mris)
ErrorExit(ERROR_NOFILE, "%s: could not read surface file %s",
Progname, in_fname) ;
MRISreadOriginalProperties(mris, "smoothwm") ;
}
MRISsaveVertexPositions(mris, TMP_VERTICES) ;
MRISrestoreVertexPositions(mris, ORIGINAL_VERTICES) ;
MRISsampleAtEachDistance(mris, nbhd_size, max_nbrs) ;
MRIScomputeMetricProperties(mris) ;
MRISstoreMetricProperties(mris) ;
MRISrestoreVertexPositions(mris, TMP_VERTICES) ;
MRIScomputeMetricProperties(mris) ;
MRIScomputeDistanceErrors(mris, nbhd_size, max_nbrs) ;
#if 0
if (write_flag) {
MRISareaErrors(mris) ;
MRISangleErrors(mris) ;
}
if (area_flag) {
sprintf(fname, "%s.area_error", in_fname) ;
printf("writing area errors to %s\n", fname) ;
MRISwriteAreaError(mris, fname) ;
sprintf(fname, "%s.angle_error", in_fname) ;
printf("writing angle errors to %s\n", fname) ;
MRISwriteAngleError(mris, fname) ;
}
#else
sprintf(fname, "%s.distance_error", in_fname) ;
fprintf(stderr, "writing errors to %s\n", fname) ;
MRISwriteValues(mris, fname) ;
#endif
MRISfree(&mris) ;
exit(0) ;
return(0) ; /* for ansi */
}
