/* set the correct set of vectorial parameters */
static void setParms(INTEGRATION_PARMS *parms)
{
/* default template fields*/
parms->nfields=3;
SetFieldLabel(&parms->fields[0],
INFLATED_CURV_CORR_FRAME,
0,
0.0,
0.0,
0,
which_norm);
/* only use sulc for rigid registration */
SetFieldLabel(&parms->fields[1],SULC_CORR_FRAME,1,1.0,0.0,0,which_norm);
SetFieldLabel(&parms->fields[2],CURVATURE_CORR_FRAME,2,0.0,0.0,0,which_norm);
}
void wxControl::SetLabel(const wxString& label)
{
if(IsPalmField())
SetFieldLabel(label);
// unlike other native controls, slider has no label
if(IsPalmControl() && !wxDynamicCast(this,wxSlider))
SetControlLabel(label);
}
/*----------------------------------------------------------------------
Parameters:
Description:
----------------------------------------------------------------------*/
static int
get_option(int argc, char *argv[],INTEGRATION_PARMS *parms)
{
int n,nargs = 0 ;
char *option ;
option = argv[1] + 1 ; /* past '-' */
if (!stricmp(option, "help") || !stricmp(option, "-help"))
print_help() ;
else if (!stricmp(option, "version") || !stricmp(option, "-version"))
print_version() ;
else if (!stricmp(option, "nbrs"))
{
nbrs = atoi(argv[2]) ;
nargs = 1 ;
fprintf(stderr, "using neighborhood size = %d\n", nbrs) ;
}
else if (!stricmp(option, "sdir"))
{
strcpy(subjects_dir, argv[2]) ;
nargs = 1 ;
fprintf(stderr, "using SUBJECTS_DIR=%s\n", subjects_dir) ;
}
else if (!stricmp(option, "median"))
{
which_norm = NORM_MEDIAN ;
printf("using median normalization\n") ;
}
else if (!stricmp(option, "nonorm"))
{
which_norm = NORM_NONE ;
printf("not normalizing input data\n") ;
}
else if (!stricmp(option, "infname"))
{
char fname[STRLEN] ;
surface_names[0] = argv[2] ;
nargs = 1 ;
printf("using %s instead of inflated\n", argv[2]) ;
sprintf(fname, "%s.H", argv[2]) ;
curvature_names[0] = (char *)calloc(strlen(fname)+1, sizeof(char)) ;
strcpy(curvature_names[0], fname) ;
}
else if (!stricmp(option, "sulc"))
{
nargs = 1 ;
printf("using %s instead of sulc\n", argv[2]) ;
curvature_names[1] = (char *)calloc(strlen(argv[2])+1, sizeof(char)) ;
strcpy(curvature_names[1], argv[2]) ;
}
else if (!stricmp(option, "norot"))
{
no_rot = 1 ;
fprintf(stderr, "not aligning hemispheres before averaging.\n") ;
}
else if (!stricmp(option, "rot"))
{
no_rot = 0 ;
fprintf(stderr, "rigidly aligning hemispheres before averaging.\n") ;
}
else if (!stricmp(option, "nodefault"))
{
base_default=0;
atlas_size = 0;
parms->nfields=0;
for (n=0;n<3;n++)
InitFieldLabel(&parms->fields[n]);
}
else if (!stricmp(option, "size"))
{
int size=atoi(argv[2]);
if (size<=0)
{
fprintf(stderr,"ERROR: size should at least 1!\n");
exit(1);
}
atlas_size = size;
fprintf(stderr,"Setting up atlas size to %d\n",size);
nargs=1;
}
else if (!stricmp(option, "annot"))
{
annot_name = argv[2] ;
fprintf(stderr,"zeroing medial wall in %s\n", annot_name) ;
nargs=1;
}
else if (!strcmp(option, "overlay"))
{
int navgs ;
overlays[noverlays++] = argv[2] ;
navgs = atoi(argv[3]) ;
printf("reading overlay from %s...\n", argv[2]) ;
multiframes = 1 ;
n=parms->nfields++;
SetFieldLabel(&parms->fields[n],
OVERLAY_FRAME,
atlas_size,
0.0,
0.0,
navgs,
which_norm);
SetFieldName(&parms->fields[n], argv[2]) ;
atlas_size++ ;
nargs = 2 ;
}
else if (!strcmp(option, "distance"))
{
int navgs ;
overlays[noverlays++] = argv[2] ;
navgs = atoi(argv[3]) ;
printf("reading overlay from %s...\n", argv[2]) ;
multiframes = 1 ;
n=parms->nfields++;
SetFieldLabel(&parms->fields[n],
DISTANCE_TRANSFORM_FRAME,
atlas_size,
0.0,
0.0,
navgs,
NORM_MAX);
SetFieldName(&parms->fields[n], argv[2]) ;
atlas_size++ ;
nargs = 2 ;
}
else if (!strcmp(option, "overlay-dir"))
{
overlay_dir = argv[2] ;
printf("Setting overlay_dir to %s\n",overlay_dir);
nargs = 1 ;
}
else if (!stricmp(option, "vector"))
{
fprintf(stderr,"\nMultiframe Mode:\n");
fprintf(stderr,
"Use <addframe> option to add extra-fields into average atlas\n");
fprintf(stderr,"Use <size> option to set up the # of frames\n");
fprintf(stderr,"field code:\n");
for (n=0 ; n < NUMBER_OF_VECTORIAL_FIELDS ; n++)
fprintf(stderr," field %d is '%s' (type = %d)\n",n,
ReturnFieldName(n),IsDistanceField(n));
}
else if (!stricmp(option, "addframe"))
{
int which_field,where_in_atlas;
if (multiframes==0) /* activate multiframes mode */
multiframes = 1;
which_field=atoi(argv[2]);
where_in_atlas=atoi(argv[3]);
fprintf(stderr,
"adding field %d into average atlas at location %d\n",
which_field,where_in_atlas) ;
if ( base_default && (where_in_atlas<3) )
{
fprintf(stderr,"ERROR: Cannot add field %d into atlas\n",which_field);
fprintf(stderr," By default, the first 3 fields are:\n");
fprintf(stderr," -curvature of inflated surface \n");
fprintf(stderr," -sulc of smoothwm surface \n");
fprintf(stderr," -curvature of smoothwm surface \n");
fprintf(stderr,"To cancel this option, use <nodefault> first\n");
exit(1);
}
/* check if this field exist or not */
for (n = 0 ; n < parms->nfields ; n++)
{
if (parms->fields[n].field==which_field)
{
fprintf(stderr,"ERROR: field already exists\n");
exit(1);
}
}
/* adding field into parms */
n=parms->nfields++;
SetFieldLabel(&parms->fields[n],
which_field,
where_in_atlas,
0.0,
0.0,
0,
which_norm);
if (where_in_atlas >= atlas_size)
{
atlas_size = where_in_atlas+1;
fprintf(stderr,
"Atlas size increased to contain at least %d frames\n",
atlas_size);
}
nargs = 2 ;
}
else switch (toupper(*option))
{
case 'W':
Gdiag |= DIAG_WRITE ;
if (isdigit((int)*argv[2]))
nargs = 1 ;
break ;
case 'S':
scale = atof(argv[2]) ;
fprintf(stderr, "scaling parameterization by %2.1f\n", scale) ;
nargs = 1 ;
break ;
case 'O':
surface_names[1] = surface_names[2] = argv[2] ;
nargs = 1 ;
printf("using %s instead of smoothwm\n", argv[2]) ;
break ;
case 'A':
navgs = atoi(argv[2]) ;
fprintf(stderr, "averaging curvature patterns %d times.\n", navgs) ;
nargs = 1 ;
break ;
case '?':
case 'U':
print_usage() ;
exit(1) ;
break ;
default:
fprintf(stderr, "unknown option %s\n", argv[1]) ;
exit(1) ;
break ;
}
return(nargs) ;
}
/*----------------------------------------------------------------------
Parameters:
Description:
----------------------------------------------------------------------*/
static int
get_option(int argc, char *argv[])
{
int n,nargs = 0 ;
char *option ;
float f ;
option = argv[1] + 1 ; /* past '-' */
if (!stricmp(option, "-help")||!stricmp(option, "-usage"))
{
print_help() ;
}
else if (!stricmp(option, "-version"))
{
print_version() ;
}
else if (!stricmp(option, "median"))
{
which_norm = NORM_MEDIAN ;
printf("using median normalization\n") ;
}
else if (!stricmp(option, "vnum") || !stricmp(option, "distances"))
{
parms.nbhd_size = atof(argv[2]) ;
parms.max_nbrs = atof(argv[3]) ;
nargs = 2 ;
fprintf(stderr, "nbr size = %d, max neighbors = %d\n",
parms.nbhd_size, parms.max_nbrs) ;
}
else if (!stricmp(option, "nonorm"))
{
which_norm = NORM_NONE ;
printf("disabling normalization\n") ;
}
else if (!stricmp(option, "vsmooth"))
{
parms.var_smoothness = 1 ;
printf("using space/time varying smoothness weighting\n") ;
}
else if (!stricmp(option, "sigma"))
{
if (nsigmas >= MAX_SIGMAS)
{
ErrorExit(ERROR_NOMEMORY, "%s: too many sigmas specified (%d)\n",
Progname, nsigmas) ;
}
sigmas[nsigmas] = atof(argv[2]) ;
nargs = 1 ;
nsigmas++ ;
}
else if (!stricmp(option, "vector"))
{
fprintf(stderr,
"\nMultiframe Mode:\n");
fprintf(stderr,
"Use -addframe option to add extra-fields into average atlas\n");
fprintf(stderr,
"\t-addframe which_field where_in_atlas l_corr l_pcorr\n");
fprintf(stderr,
"\tfield code:\n");
for (n=0 ; n < NUMBER_OF_VECTORIAL_FIELDS ; n++)
fprintf(stderr,
"\t field %d is '%s' (type = %d)\n",
n,ReturnFieldName(n),IsDistanceField(n));
exit(1);
}
else if (!stricmp(option, "annot"))
{
annot_name = argv[2] ;
fprintf(stderr,"zeroing medial wall in %s\n", annot_name) ;
nargs=1;
}
else if (!stricmp(option, "init"))
{
use_initial_registration=1;
fprintf(stderr,"use initial registration\n");
}
else if (!stricmp(option, "addframe"))
{
int which_field,where_in_atlas;
float l_corr,l_pcorr;
if (multiframes==0)
{
/* activate multiframes mode */
initParms();
multiframes = 1;
}
which_field=atoi(argv[2]);
where_in_atlas=atoi(argv[3]);
l_corr=atof(argv[4]);
l_pcorr=atof(argv[5]);
fprintf(stderr,
"adding field %d (%s) with location %d in the atlas\n",
which_field,ReturnFieldName(which_field),where_in_atlas) ;
/* check if this field exist or not */
for (n = 0 ; n < parms.nfields ; n++)
{
if (parms.fields[n].field==which_field)
{
fprintf(stderr,"ERROR: field already exists\n");
exit(1);
}
}
/* adding field into parms */
n=parms.nfields++;
SetFieldLabel(&parms.fields[n],
which_field,
where_in_atlas,
l_corr,
l_pcorr,
0,
which_norm);
nargs = 4 ;
}
/* else if (!stricmp(option, "hippocampus")) */
/* { */
/* if(multiframes==0){ */
/* multiframes = 1 ; */
/* initParms(); */
/* } */
/* where=atoi(argv[2]); */
/* parms.l_corrs[]=atof(argv[3]); */
/* parms.l_pcorrs[]=atof(argv[4]); */
/* parms.frames[]=; */
/* parms. */
/* fprintf(stderr, "using hippocampus distance map\n") ; */
/* nargs=3; */
/* } */
else if (!stricmp(option, "topology"))
{
parms.flags |= IPFLAG_PRESERVE_SPHERICAL_POSITIVE_AREA;
fprintf(stderr, "preserving the topology of positive area triangles\n");
}
else if (!stricmp(option, "vnum") || !stricmp(option, "distances"))
{
parms.nbhd_size = atof(argv[2]) ;
parms.max_nbrs = atof(argv[3]) ;
nargs = 2 ;
fprintf(stderr, "nbr size = %d, max neighbors = %d\n",
parms.nbhd_size, parms.max_nbrs) ;
}
else if (!stricmp(option, "rotate"))
{
dalpha = atof(argv[2]) ;
dbeta = atof(argv[3]) ;
dgamma = atof(argv[4]) ;
fprintf(stderr, "rotating brain by (%2.2f, %2.2f, %2.2f)\n",
dalpha, dbeta, dgamma) ;
nargs = 3 ;
}
else if (!stricmp(option, "reverse"))
{
reverse_flag = 1 ;
fprintf(stderr, "mirror image reversing brain before morphing...\n") ;
}
else if (!stricmp(option, "min_degrees"))
{
min_degrees = atof(argv[2]) ;
fprintf(stderr,
"setting min angle for search to %2.2f degrees\n",
min_degrees) ;
nargs = 1 ;
}
else if (!stricmp(option, "max_degrees"))
{
max_degrees = atof(argv[2]) ;
fprintf(stderr,
"setting max angle for search to %2.2f degrees\n",
max_degrees) ;
nargs = 1 ;
}
else if (!stricmp(option, "nangles"))
{
nangles = atoi(argv[2]) ;
fprintf(stderr, "setting # of angles/search per scale to %d\n", nangles) ;
nargs = 1 ;
}
else if (!stricmp(option, "jacobian"))
{
jacobian_fname = argv[2] ;
nargs = 1 ;
printf("writing out jacobian of mapping to %s\n", jacobian_fname) ;
}
else if (!stricmp(option, "dist"))
{
sscanf(argv[2], "%f", &parms.l_dist) ;
nargs = 1 ;
use_defaults = 0 ;
fprintf(stderr, "l_dist = %2.3f\n", parms.l_dist) ;
}
else if (!stricmp(option, "norot"))
{
fprintf(stderr, "disabling initial rigid alignment...\n") ;
parms.flags |= IP_NO_RIGID_ALIGN ;
}
else if (!stricmp(option, "inflated"))
{
fprintf(stderr, "using inflated surface for initial alignment\n") ;
parms.flags |= IP_USE_INFLATED ;
}
else if (!stricmp(option, "multi_scale"))
{
multi_scale = atoi(argv[2]) ;
fprintf(stderr, "using %d scales for morphing\n", multi_scale) ;
nargs = 1 ;
}
else if (!stricmp(option, "nsurfaces"))
{
parms.nsurfaces = atoi(argv[2]) ;
nargs = 1 ;
fprintf(stderr,
"using %d surfaces/curvatures for alignment\n",
parms.nsurfaces) ;
}
else if (!stricmp(option, "infname"))
{
char fname[STRLEN] ;
inflated_name = argv[2] ;
surface_names[0] = argv[2] ;
nargs = 1 ;
printf("using %s as inflated surface name, "
"and using it for initial alignment\n", inflated_name) ;
sprintf(fname, "%s.H", argv[2]) ;
curvature_names[0] = (char *)calloc(strlen(fname)+1, sizeof(char)) ;
strcpy(curvature_names[0], fname) ;
parms.flags |= IP_USE_INFLATED ;
}
else if (!stricmp(option, "nosulc"))
{
fprintf(stderr, "disabling initial sulc alignment...\n") ;
parms.flags |= IP_NO_SULC ;
}
else if (!stricmp(option, "sulc"))
{
curvature_names[1] = argv[2] ;
fprintf(stderr, "using %s to replace 'sulc' alignment\n",
curvature_names[1]) ;
nargs = 1 ;
MRISsetSulcFileName(argv[2]);
}
else if (!stricmp(option, "surf0"))
{
surface_names[0] = argv[2];
fprintf(stderr, "using %s as input surface 0.\n",
surface_names[0]) ;
nargs = 1 ;
}
else if (!stricmp(option, "surf1"))
{
surface_names[1] = argv[2];
fprintf(stderr, "using %s as input surface 1.\n",
surface_names[1]) ;
nargs = 1 ;
}
else if (!stricmp(option, "surf2"))
{
surface_names[2] = argv[2];
fprintf(stderr, "using %s as input surface 2.\n",
surface_names[2]) ;
nargs = 1 ;
}
else if (!stricmp(option, "curv0"))
{
curvature_names[0] = argv[2];
fprintf(stderr, "using %s as curvature function for surface 0.\n",
curvature_names[0]) ;
nargs = 1 ;
}
else if (!stricmp(option, "curv1"))
{
curvature_names[1] = argv[2];
fprintf(stderr, "using %s as curvature function for surface 1.\n",
curvature_names[1]) ;
nargs = 1 ;
}
else if (!stricmp(option, "curv2"))
{
curvature_names[2] = argv[2];
fprintf(stderr, "using %s as curvature function for surface 2.\n",
curvature_names[2]) ;
nargs = 1 ;
}
else if (!stricmp(option, "lm"))
{
parms.integration_type = INTEGRATE_LINE_MINIMIZE ;
fprintf(stderr, "integrating with line minimization\n") ;
}
else if (!stricmp(option, "search"))
{
parms.integration_type = INTEGRATE_LM_SEARCH ;
fprintf(stderr, "integrating with binary search line minimization\n") ;
}
else if (!stricmp(option, "dt"))
{
parms.dt = atof(argv[2]) ;
parms.base_dt = .2*parms.dt ;
nargs = 1 ;
fprintf(stderr, "momentum with dt = %2.2f\n", parms.dt) ;
}
else if (!stricmp(option, "area"))
{
use_defaults = 0 ;
sscanf(argv[2], "%f", &parms.l_area) ;
nargs = 1 ;
fprintf(stderr, "using l_area = %2.3f\n", parms.l_area) ;
}
else if (!stricmp(option, "parea"))
{
use_defaults = 0 ;
sscanf(argv[2], "%f", &parms.l_parea) ;
nargs = 1 ;
fprintf(stderr, "using l_parea = %2.3f\n", parms.l_parea) ;
}
else if (!stricmp(option, "nlarea"))
{
use_defaults = 0 ;
sscanf(argv[2], "%f", &parms.l_nlarea) ;
nargs = 1 ;
fprintf(stderr, "using l_nlarea = %2.3f\n", parms.l_nlarea) ;
}
else if (!stricmp(option, "spring"))
{
use_defaults = 0 ;
sscanf(argv[2], "%f", &parms.l_spring) ;
nargs = 1 ;
fprintf(stderr, "using l_spring = %2.3f\n", parms.l_spring) ;
}
else if (!stricmp(option, "corr"))
{
use_defaults = 0 ;
sscanf(argv[2], "%f", &parms.l_corr) ;
nargs = 1 ;
fprintf(stderr, "using l_corr = %2.3f\n", parms.l_corr) ;
}
else if (!stricmp(option, "remove_negative"))
{
remove_negative = atoi(argv[2]) ;
nargs = 1 ;
fprintf(stderr, "%sremoving negative triangles with iterative smoothing\n",
remove_negative ? "" : "not ") ;
}
else if (!stricmp(option, "curv"))
{
parms.flags |= IP_USE_CURVATURE ;
fprintf(stderr, "using smoothwm curvature for final alignment\n") ;
}
else if (!stricmp(option, "nocurv"))
{
parms.flags &= ~IP_USE_CURVATURE ;
fprintf(stderr, "NOT using smoothwm curvature for final alignment\n") ;
}
else if (!stricmp(option, "sreg"))
{
starting_reg_fname = argv[2] ;
nargs = 1 ;
fprintf(stderr, "starting registration with coordinates in %s\n",
starting_reg_fname) ;
}
else if (!stricmp(option, "adaptive"))
{
parms.integration_type = INTEGRATE_ADAPTIVE ;
fprintf(stderr, "using adaptive time step integration\n") ;
}
else if (!stricmp(option, "nbrs"))
{
nbrs = atoi(argv[2]) ;
nargs = 1 ;
fprintf(stderr, "using neighborhood size=%d\n", nbrs) ;
}
else if (!stricmp(option, "tol"))
{
if (sscanf(argv[2], "%e", &f) < 1)
ErrorExit(ERROR_BADPARM, "%s: could not scan tol from %s",
Progname, argv[2]) ;
parms.tol = (double)f ;
nargs = 1 ;
fprintf(stderr, "using tol = %2.2e\n", (float)parms.tol) ;
}
else if (!stricmp(option, "error_ratio"))
{
parms.error_ratio = atof(argv[2]) ;
nargs = 1 ;
fprintf(stderr, "error_ratio=%2.3f\n", parms.error_ratio) ;
}
else if (!stricmp(option, "dt_inc"))
{
parms.dt_increase = atof(argv[2]) ;
nargs = 1 ;
fprintf(stderr, "dt_increase=%2.3f\n", parms.dt_increase) ;
}
else if (!stricmp(option, "lap") || !stricmp(option, "lap"))
{
parms.l_lap = atof(argv[2]) ;
nargs = 1 ;
fprintf(stderr, "l_laplacian = %2.3f\n", parms.l_lap) ;
}
else if (!stricmp(option, "vnum"))
{
parms.nbhd_size = atof(argv[2]) ;
parms.max_nbrs = atof(argv[3]) ;
nargs = 2 ;
fprintf(stderr, "nbr size = %d, max neighbors = %d\n",
parms.nbhd_size, parms.max_nbrs) ;
}
else if (!stricmp(option, "dt_dec"))
{
parms.dt_decrease = atof(argv[2]) ;
nargs = 1 ;
fprintf(stderr, "dt_decrease=%2.3f\n", parms.dt_decrease) ;
}
else if (!stricmp(option, "ocorr"))
{
l_ocorr = atof(argv[2]) ;
printf("setting overlay correlation coefficient to %2.1f\n", l_ocorr) ;
nargs = 1 ;
fprintf(stderr, "dt_decrease=%2.3f\n", parms.dt_decrease) ;
}
else if (!stricmp(option, "overlay"))
{
int navgs ;
if (noverlays == 0)
{
atlas_size = 0 ;
}
if (multiframes == 0)
{
initParms() ;
multiframes = 1 ;
}
overlays[noverlays++] = argv[2] ;
navgs = atof(argv[3]) ;
printf("reading overlay from %s and smoothing it %d times\n",
argv[2], navgs) ;
n=parms.nfields++;
SetFieldLabel(&parms.fields[n],
OVERLAY_FRAME,
atlas_size,
l_ocorr,
0.0,
navgs,
which_norm);
SetFieldName(&parms.fields[n], argv[2]) ;
atlas_size++ ;
nargs = 2 ;
}
else if (!stricmp(option, "distance"))
{
int navgs ;
if (noverlays == 0)
{
atlas_size = 0 ;
}
if (multiframes == 0)
{
initParms() ;
multiframes = 1 ;
}
overlays[noverlays++] = argv[2] ;
navgs = atof(argv[3]) ;
printf("reading overlay from %s and smoothing it %d times\n",
argv[2], navgs) ;
n=parms.nfields++;
SetFieldLabel(&parms.fields[n],
DISTANCE_TRANSFORM_FRAME,
atlas_size,
l_ocorr,
0.0,
navgs,
NORM_MAX) ;
SetFieldName(&parms.fields[n], argv[2]) ;
atlas_size++ ;
nargs = 2 ;
}
else if (!stricmp(option, "canon"))
{
canon_name = argv[2] ;
nargs = 1 ;
fprintf(stderr, "using %s for canonical properties...\n", canon_name) ;
}
else if (!stricmp(option, "overlay-dir"))
{
parms.overlay_dir = strcpyalloc(argv[2]) ;
nargs = 1 ;
}
else switch (toupper(*option))
{
case 'M':
parms.integration_type = INTEGRATE_MOMENTUM ;
parms.momentum = atof(argv[2]) ;
nargs = 1 ;
fprintf(stderr, "momentum = %2.2f\n", (float)parms.momentum) ;
break ;
case 'L':
if (nlabels >= MAX_LABELS-1)
ErrorExit(ERROR_NO_MEMORY,
"%s: too many labels specified (%d max)",
Progname, MAX_LABELS) ;
nargs = 3 ;
labels[nlabels] = LabelRead(NULL, argv[2]) ;
if (labels[nlabels] == NULL)
ErrorExit(ERROR_NOFILE,
"%s: could not read label file %s",
Progname, argv[2]) ;
label_gcsa[nlabels] = GCSAread(argv[3]) ;
if (label_gcsa[nlabels] == NULL)
ErrorExit(ERROR_NOFILE,
"%s: could not read GCSA file %s",
Progname, argv[3]) ;
label_names[nlabels] = argv[4] ;
CTABfindName(label_gcsa[nlabels]->ct, argv[4],&label_indices[nlabels]) ;
if (label_indices[nlabels] < 0)
ErrorExit(ERROR_NOFILE,
"%s: could not map name %s to index",
Progname, argv[3]) ;
CTABannotationAtIndex(label_gcsa[nlabels]->ct, label_indices[nlabels],
&label_annots[nlabels]);
nlabels++ ;
gMRISexternalSSE = gcsaSSE ;
break ;
case 'E':
parms.l_external = atof(argv[2]) ;
nargs = 1 ;
printf("setting l_external = %2.1f\n", parms.l_external) ;
break ;
case 'C':
strcpy(curvature_fname, argv[2]) ;
nargs = 1 ;
break ;
case 'A':
sscanf(argv[2], "%d", &parms.n_averages) ;
nargs = 1 ;
fprintf(stderr, "using n_averages = %d\n", parms.n_averages) ;
break ;
case '1':
single_surf = True ;
printf("treating target as a single subject's surface...\n") ;
break ;
case 'S':
scale = atof(argv[2]) ;
fprintf(stderr, "scaling distances by %2.2f\n", scale) ;
nargs = 1 ;
break ;
case 'N':
sscanf(argv[2], "%d", &parms.niterations) ;
nargs = 1 ;
fprintf(stderr, "using niterations = %d\n", parms.niterations) ;
break ;
case 'W':
Gdiag |= DIAG_WRITE ;
sscanf(argv[2], "%d", &parms.write_iterations) ;
nargs = 1 ;
fprintf(stderr,
"using write iterations = %d\n",
parms.write_iterations) ;
break ;
case 'V':
Gdiag_no = atoi(argv[2]) ;
nargs = 1 ;
break ;
case 'O':
orig_name = argv[2] ;
nargs = 1 ;
fprintf(stderr, "using %s for original properties...\n", orig_name) ;
break ;
case 'P':
max_passes = atoi(argv[2]) ;
fprintf(stderr, "limiting unfolding to %d passes\n", max_passes) ;
nargs = 1 ;
break ;
case '?':
case 'H':
case 'U':
print_help() ;
exit(1) ;
break ;
default:
fprintf(stderr, "unknown option %s\n", argv[1]) ;
exit(1) ;
break ;
}
return(nargs) ;
}
