int main (int argc, char **argv)
{
FILE *in_file, *out_file;
VImage image;
VAttrList list = VCreateAttrList ();
char prg[50];
sprintf(prg,"plaintov V%s", getVersion());
fprintf (stderr, "%s\n", prg);
VParseFilterCmd (VNumber (options), options, argc, argv,
& in_file, & out_file);
if (! (image = VReadPlain (in_file)))
exit (EXIT_FAILURE);
VHistory(VNumber(options),options,prg,&list,&list);
VAppendAttr (list, object_name, NULL, VImageRepn, image);
if (! VWriteFile (out_file, list))
exit (EXIT_FAILURE);
fprintf (stderr, "%s: Converted 1 file from Vista plain format"
" to Vista format.\n", argv[0]);
return EXIT_SUCCESS;
}
int
main (int argc,char *argv[])
{
static VFloat sigma = 1.5;
static VOptionDescRec options[] = {
{"sigma",VFloatRepn,1,(VPointer) &sigma,VOptionalOpt,NULL,"std dev"}
};
FILE *in_file,*out_file;
VAttrList list=NULL;
VAttrListPosn posn;
VImage src=NULL,dest=NULL;
char prg[50];
sprintf(prg,"vgauss2d V%s", getVersion());
fprintf (stderr, "%s\n", prg);
VParseFilterCmd (VNumber (options),options,argc,argv,&in_file,&out_file);
if (! (list = VReadFile (in_file, NULL))) exit (1);
fclose(in_file);
for (VFirstAttr (list, & posn); VAttrExists (& posn); VNextAttr (& posn)) {
if (VGetAttrRepn (& posn) != VImageRepn) continue;
VGetAttrValue (& posn, NULL,VImageRepn, & src);
dest = VFilterGauss2d (src,NULL,(double)sigma);
VSetAttrValue (& posn, NULL,VImageRepn,dest);
}
if (src == NULL) VError(" no input image found");
VHistory(VNumber(options),options,prg,&list,&list);
if (! VWriteFile (out_file, list)) exit (1);
fprintf (stderr, "%s: done.\n", argv[0]);
return 0;
}
int
main(int argc, char *argv[]) {
static VShort type = 0;
static VArgVector contrast;
static VOptionDescRec options[] = {
{"type", VShortRepn, 1, (VPointer) &type, VOptionalOpt, TYPDict, "type of output"},
{"contrast", VFloatRepn, 0, (VPointer) &contrast, VRequiredOpt, NULL, "contrast vector"}
};
FILE *in_file, *out_file;
VAttrList list = NULL, out_list = NULL;
gsl_vector_float *cont;
float u;
int i;
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "vgetcontrast V%s", ver);
fprintf(stderr, "%s\n", prg_name);
VParseFilterCmd(VNumber(options), options, argc, argv, &in_file, &out_file);
cont = gsl_vector_float_alloc(contrast.number);
for(i = 0; i < contrast.number; i++) {
u = ((VFloat *)contrast.vector)[i];
fvset(cont, i, u);
}
if(!(list = VReadFile(in_file, NULL)))
exit(1);
fclose(in_file);
out_list = VGetContrast(list, cont, type);
/* Output: */
VHistory(VNumber(options), options, prg_name, &list, &out_list);
if(! VWriteFile(out_file, out_list))
exit(1);
fprintf(stderr, "%s: done.\n", argv[0]);
return 0;
}
VBoolean VWriteObjects (FILE *file, VRepnKind repn, VAttrList attributes,
int nobjects, VPointer objects[])
{
VAttrList list;
VAttrListPosn posn;
int i;
VBoolean result;
/* Create an attribute list if none was supplied: */
list = attributes ? attributes : VCreateAttrList ();
/* Prepend to the attribute list an attribute for each object: */
for (i = nobjects - 1; i >= 0; i--)
VPrependAttr (list, VRepnName (repn), NULL, repn, objects[i]);
/* Write the attribute list: */
result = VWriteFile (file, list);
/* Remove the attributes just prepended: */
VFirstAttr (list, & posn);
for (i = 0; i < nobjects; i++)
VDeleteAttr (& posn);
if (list != attributes)
VDestroyAttrList (list);
return result;
}
int
main(int argc, char *argv[]) {
static VString cfile = "";
static VFloat tr = 2;
static VBoolean normalize = FALSE;
static VOptionDescRec options[] = {
{"in", VStringRepn, 1, (VPointer) &cfile, VRequiredOpt, NULL, "file"},
{"tr", VFloatRepn, 1, (VPointer) &tr, VRequiredOpt, NULL, "TR in seconds"},
{"normalize", VBooleanRepn, 1, (VPointer) &normalize, VOptionalOpt, NULL, "Whether to normalize"}
};
FILE *out_file = NULL;
VAttrList list = NULL;
VImage dest = NULL;
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "vcovariates V%s", ver);
fprintf(stderr, "%s\n", prg_name);
VParseFilterCmd(VNumber(options), options, argc, argv, NULL, &out_file);
if(tr > 500)
VError(" tr must be given in seconds, not milliseconds");
dest = VCovariates(cfile, tr, normalize);
list = VCreateAttrList();
VAppendAttr(list, "image", NULL, VImageRepn, dest);
/* Output: */
if(! VWriteFile(out_file, list))
exit(1);
fprintf(stderr, " %s: done.\n", argv[0]);
return 0;
}
int main(int argc, char **argv) {
static VString filename = "";
static VLong neighb = 2;
static VLong iter = 1;
static VOptionDescRec options[] = {
{
"n", VLongRepn, 1, &neighb, VOptionalOpt, TYPDict,
"type of neighbourhood used for smoothing"
},
{
"iter", VLongRepn, 1, &iter, VOptionalOpt, NULL,
"number of iterations"
},
{
"image", VStringRepn, 1, &filename, VOptionalOpt, NULL,
"grey value image"
},
};
FILE *in_file, *out_file, *fp;
VAttrList list, list1;
VImage src = NULL, dest, image = NULL;
VAttrListPosn posn;
/* Parse command line arguments: */
VParseFilterCmd(VNumber(options), options, argc, argv, &in_file, &out_file);
/* Read transformation image: */
fp = VOpenInputFile(filename, TRUE);
list1 = VReadFile(fp, NULL);
if(! list1)
VError("Error reading image");
fclose(fp);
for(VFirstAttr(list1, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & image);
if(VPixelRepn(image) != VUByteRepn)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & image);
break;
}
if(image == NULL)
VError(" image not found");
/* Read source image(s): */
if(!(list = VReadFile(in_file, NULL)))
exit(1);
for(VFirstAttr(list, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & src);
dest = VTopSmoothImage3d(src, image, NULL, neighb, iter);
if(dest == NULL)
exit(1);
VSetAttrValue(& posn, NULL, VImageRepn, dest);
VDestroyImage(src);
}
/* Write the results to the output file: */
if(VWriteFile(out_file, list))
fprintf(stderr, "%s: done.\n", argv[0]);
return 0;
}
int
main(int argc, char *argv[]) {
static VString filename = "";
static VBoolean fisher = FALSE;
static VShort minval = 0;
static VOptionDescRec options[] = {
{"mask", VStringRepn, 1, (VPointer) &filename, VRequiredOpt, NULL, "mask"},
{"fisher", VBooleanRepn, 1, (VPointer) &fisher, VOptionalOpt, NULL, "Whether to do fisher transform"},
{"minval", VShortRepn, 1, (VPointer) &minval, VOptionalOpt, NULL, "signal threshold"}
};
FILE *in_file, *out_file, *fp;
VAttrList list = NULL, list1 = NULL, list2 = NULL;
VAttrListPosn posn;
VImage dest = NULL, mask = NULL;
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "vsimmat V%s", ver);
fprintf(stderr, "%s\n", prg_name);
VParseFilterCmd(VNumber(options), options, argc, argv, &in_file, &out_file);
/*
** read mask
*/
fp = VOpenInputFile(filename, TRUE);
list1 = VReadFile(fp, NULL);
if(! list1)
VError("Error reading mask file");
fclose(fp);
for(VFirstAttr(list1, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & mask);
if(VPixelRepn(mask) != VBitRepn) {
mask = NULL;
continue;
}
}
if(mask == NULL)
VError(" no mask found");
/*
** read functional data
*/
if(!(list = VReadFile(in_file, NULL)))
exit(1);
fclose(in_file);
/*
** process
*/
dest = SimilarityMatrix(list, mask, minval, fisher);
list2 = VCreateAttrList();
VAppendAttr(list2, "matrix", NULL, VImageRepn, dest);
VHistory(VNumber(options), options, prg_name, &list, &list2);
if(! VWriteFile(out_file, list2))
exit(1);
fprintf(stderr, "%s: done.\n", argv[0]);
return 0;
}
int
main(int argc, char *argv[]) {
static VShort minval = 0;
static VFloat tdel = 5;
static VBoolean slicetime_correction = TRUE;
static VString slicetime = "";
static VString filename = "";
static VOptionDescRec options[] = {
{"minval", VShortRepn, 1, (VPointer) &minval, VOptionalOpt, NULL, "Signal threshold"},
{
"correction", VBooleanRepn, 1, (VPointer) &slicetime_correction, VOptionalOpt, NULL,
"Whether to perform slicetime correction"
},
{
"slicetime", VStringRepn, 1, (VPointer) &slicetime, VOptionalOpt, NULL,
"ASCII file containing slice times in milliseconds"
},
{
"scanfile", VStringRepn, 1, (VPointer) &filename, VOptionalOpt, NULL,
"ASCII file containing scan times in seconds"
},
{"del", VFloatRepn, 1, (VPointer) &tdel, VOptionalOpt, NULL, "First few seconds to be ignored"}
};
FILE *in_file = NULL, *out_file = NULL;
VAttrList list = NULL;
float *onset_array = NULL;
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "vslicetime V%s", ver);
fprintf(stderr, "%s\n", prg_name);
VParseFilterCmd(VNumber(options), options, argc, argv, &in_file, &out_file);
if(!(list = VReadFile(in_file, NULL)))
exit(1);
fclose(in_file);
if(strlen(slicetime) > 2)
onset_array = ReadSlicetimes(slicetime);
if(strlen(filename) < 2) {
VSlicetime(list, minval, tdel, slicetime_correction, onset_array);
} else {
VSlicetime_NC(list, minval, tdel, slicetime_correction, onset_array, filename);
}
VHistory(VNumber(options), options, prg_name, &list, &list);
if(! VWriteFile(out_file, list))
exit(1);
fprintf(stderr, "%s: done.\n", argv[0]);
exit(0);
}
int
main (int argc,char *argv[])
{
static VShort aneighb = 1;
static VShort arepn = 1;
static VOptionDescRec options[] = {
{"n",VShortRepn,1,(VPointer) &aneighb,
VOptionalOpt,ADJDict,"neighbourhood type"},
{"repn",VShortRepn,1,(VPointer) &arepn,
VOptionalOpt,TYPEDict,"output representation type (ubyte or short)"}
};
FILE *in_file,*out_file;
VAttrList list=NULL;
VAttrListPosn posn;
VImage src=NULL,dest=NULL;
int nl=0,neighb;
VRepnKind repn;
char prg[50];
sprintf(prg,"vlabel2d V%s", getVersion());
fprintf (stderr, "%s\n", prg);
VParseFilterCmd (VNumber (options),options,argc,argv,&in_file,&out_file);
if (arepn == 0) repn = VUByteRepn;
else repn = VShortRepn;
if (aneighb == 0) neighb = 4;
else neighb = 8;
if (! (list = VReadFile (in_file, NULL))) exit (1);
fclose(in_file);
for (VFirstAttr (list, & posn); VAttrExists (& posn); VNextAttr (& posn)) {
if (VGetAttrRepn (& posn) != VImageRepn) continue;
VGetAttrValue (& posn, NULL,VImageRepn, & src);
dest = VLabelImage2d(src,NULL, (int) neighb,repn,&nl);
fprintf(stderr," numlabels= %d\n",nl);
VSetAttrValue (& posn, NULL,VImageRepn,dest);
}
if (src == NULL) VError(" no input image found");
VHistory(VNumber(options),options,prg,&list,&list);
if (! VWriteFile (out_file, list)) exit (1);
fprintf (stderr, "%s: done.\n", argv[0]);
return 0;
}
int
main (int argc,char *argv[])
{
static VShort first = 0;
static VShort last = -1;
static VOptionDescRec options[] = {
{ "first", VShortRepn, 1, (VPointer) & first,
VOptionalOpt, NULL, "First slice" },
{ "last", VShortRepn, 1, (VPointer) & last,
VOptionalOpt, NULL, "Last slice " }
};
FILE *in_file, *out_file;
VAttrList list;
VAttrListPosn posn;
VImage src=NULL, result=NULL;
char prg[50];
sprintf(prg,"vselbands V%s", getVersion());
fprintf (stderr, "%s\n", prg);
/* Parse command line arguments and identify files: */
VParseFilterCmd (VNumber (options), options, argc, argv,& in_file, & out_file);
/* Read the input file: */
list = VReadFile (in_file, NULL);
if (! list) exit (1);
/* process */
for (VFirstAttr (list, & posn); VAttrExists (& posn); VNextAttr (& posn)) {
if (VGetAttrRepn (& posn) != VImageRepn) continue;
VGetAttrValue (& posn, NULL, VImageRepn, & src);
result = VSelSlices (src, NULL,first,last);
if (! result) exit (1);
VSetAttrValue (& posn, NULL, VImageRepn, result);
VDestroyImage (src);
}
/* Write out the results: */
VHistory(VNumber(options),options,prg,&list,&list);
if (! VWriteFile (out_file, list)) exit (1);
fprintf (stderr, "%s: done.\n", argv[0]);
return 0;
}
VBoolean WriteImages (VString Name, VAttrList Images, VAttrList& history_list)
{
FILE* file; /* output file */
VAttrList list; /* attribute list */
VAttrListPosn pos; /* position in list */
VImage image; /* image in list */
VBoolean success; /* success flag */
char history[]="history";
/* open file */
file = fopen (Name, "w");
if (!file)
{
VError ("Failed to open output file '%s'", Name);
return FALSE;
}
/* create list */
list = VCreateAttrList();
/* insert images */
for (VFirstAttr (Images, &pos); VAttrExists (&pos); VNextAttr (&pos))
{
VGetAttrValue (&pos, NULL, VImageRepn, &image);
VAppendAttr (list, VGetAttrName (&pos), NULL, VImageRepn, image);
}
/* Prepend history */
VPrependAttr(list, history ,NULL,VAttrListRepn,history_list);
/* write file */
success = VWriteFile (file, list);
if (!success) VError ("Failed to write output file '%s'", Name);
/* remove images */
for (VFirstAttr (list, &pos); VAttrExists (&pos); VNextAttr (&pos))
if (VGetAttrRepn (&pos) == VImageRepn)
VSetAttrValue (&pos, NULL, VImageRepn, NULL);
/* clean-up*/
VDestroyAttrList (list);
fclose (file);
return success;
} /* WriteImages */
int main (int argc,char *argv[])
{
static VLong hemi = 0;
static VOptionDescRec options[] = {
{ "hemi", VLongRepn, 1, & hemi, VOptionalOpt, HEMIDict,
"Hemisphere to retain" }
};
FILE *in_file, *out_file;
VAttrList list;
VAttrListPosn posn;
VImage isrc=NULL;
VGraph gsrc=NULL,dest=NULL;
char prg[50];
sprintf(prg,"vhemi V%s", getVersion());
fprintf (stderr, "%s\n", prg);
/* Parse command line arguments and identify files: */
VParseFilterCmd (VNumber (options), options, argc, argv,
& in_file, & out_file);
/* Read the grey input file: */
list = VReadFile (in_file, NULL);
if (! list) VError("Error reading input image");
fclose(in_file);
for (VFirstAttr (list, & posn); VAttrExists (& posn); VNextAttr (& posn)) {
if (VGetAttrRepn (& posn) == VImageRepn) {
VGetAttrValue (& posn, NULL, VImageRepn, & isrc);
VImageHemi(&isrc,hemi);
VSetAttrValue (& posn, NULL,VImageRepn,isrc);
}
else if (VGetAttrRepn (& posn) == VGraphRepn) {
VGetAttrValue (& posn, NULL, VGraphRepn, & gsrc);
dest = VGraphHemi(gsrc,hemi);
VSetAttrValue (& posn, NULL,VGraphRepn,dest);
}
}
/* Write out the results: */
VHistory(VNumber(options),options,prg,&list,&list);
if (! VWriteFile (out_file,list)) exit (1);
fprintf (stderr, "%s: done.\n", argv[0]);
return 0;
}
int main(int argc, char *argv[]) {
static VDouble d1 = 0;
static VDouble d2 = 3.0;
static VShort threshold = 155;
static VShort background = 30;
static VFloat edge = 20;
static VOptionDescRec options[] = {
{ "d1", VDoubleRepn, 1, &d1, VOptionalOpt, 0, "erosion" },
{ "d2", VDoubleRepn, 1, &d2, VOptionalOpt, 0, "dilation" },
{ "t", VShortRepn, 1, &threshold, VOptionalOpt, 0, "threshold" },
{ "background", VShortRepn, 1, &background, VOptionalOpt, 0, " image background" },
{ "edge", VFloatRepn, 1, &edge, VOptionalOpt, 0, "edge strength" }
};
VAttrList list;
VAttrListPosn posn;
VImage src = NULL, dst = NULL;
FILE *in_file, *out_file;
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "vbrainpeel V%s", ver);
fprintf(stderr, "%s\n", prg_name);
VParseFilterCmd(VNumber(options), options, argc, argv, &in_file, &out_file);
/* Read source image(s): */
if(!(list = VReadFile(in_file, NULL)))
return 1;
fclose(in_file);
/* Operate on each source image: */
for(VFirstAttr(list, &posn); VAttrExists(&posn); VNextAttr(&posn)) {
if(VGetAttrRepn(&posn) == VImageRepn) {
VGetAttrValue(&posn, NULL, VImageRepn, &src);
dst = VPeel(src, NULL, d1, d2, edge, threshold, background);
if(dst)
VSetAttrValue(&posn, NULL, VImageRepn, dst);
else
VError(" error in vbrainpeel");
}
}
/* Write the results to the output file: */
VHistory(VNumber(options), options, prg_name, &list, &list);
if(!VWriteFile(out_file, list))
return 1;
fprintf(stderr, " %s: done.\n", argv[0]);
return 0;
}
int main(int argc, char *argv[]) {
static VBoolean x_axis = FALSE;
static VBoolean y_axis = FALSE;
static VBoolean z_axis = FALSE;
static VOptionDescRec options[] = {
{ "x", VBooleanRepn, 1, (VPointer) &x_axis, VOptionalOpt, NULL, "Flip x-axis" },
{ "y", VBooleanRepn, 1, (VPointer) &y_axis, VOptionalOpt, NULL, "Flip y-axis" },
{ "z", VBooleanRepn, 1, (VPointer) &z_axis, VOptionalOpt, NULL, "Flip z-axis" },
};
FILE *in_file, *out_file;
VAttrList list;
VAttrListPosn posn;
VImage src = NULL, result = NULL;
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "vflip3d V%s", ver);
fprintf(stderr, "%s\n", prg_name);
VWarning("It is recommended to use the program vswapdim since vflip3d does not support extended header informations");
/* Parse command line arguments and identify files: */
VParseFilterCmd(VNumber(options), options, argc, argv, &in_file, &out_file);
/* Read the input file: */
list = VReadFile(in_file, NULL);
if(! list)
exit(1);
/* For each attribute read... */
for(VFirstAttr(list, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & src);
result = Flip3dImage(src, NULL, VAllBands, x_axis, y_axis, z_axis);
if(! result)
exit(1);
VSetAttrValue(& posn, NULL, VImageRepn, result);
VDestroyImage(src);
}
/* Write out the results: */
if(! VWriteFile(out_file, list))
exit(1);
fprintf(stderr, "%s: done.\n", argv[0]);
return 0;
}
int main (int argc,char *argv[])
{
FILE *in_file, *out_file;
VAttrList list;
VAttrListPosn posn;
VImage src=NULL, dest=NULL;
char prg[50];
sprintf(prg,"vthin3d V%s", getVersion());
fprintf (stderr, "%s\n", prg);
/* Parse command line arguments and identify files: */
VParseFilterCmd (0,NULL, argc, argv, & in_file, & out_file);
/* Read the input file: */
list = VReadFile (in_file, NULL);
if (! list) exit (1);
fclose(in_file);
/* For each attribute read... */
for (VFirstAttr (list, & posn); VAttrExists (& posn); VNextAttr (& posn)) {
if (VGetAttrRepn (& posn) != VImageRepn) continue;
VGetAttrValue (& posn, NULL, VImageRepn, & src);
if (VPixelRepn(src) != VBitRepn) continue;
dest = VThin3d(src, NULL,(int)26);
if (! dest) exit (1);
VSetAttrValue (& posn, NULL, VImageRepn, dest);
VDestroyImage (src);
}
/* output */
VHistory(0,NULL,prg,&list,&list);
if (! VWriteFile (out_file, list)) exit (1);
fprintf (stderr, "%s: done.\n", argv[0]);
return 0;
}
int
main (int argc,char *argv[])
{
static VDouble xmin = 0;
static VDouble xmax = 255;
static VOptionDescRec options[] = {
{"min",VDoubleRepn,1,(VPointer) &xmin,VOptionalOpt,NULL,"lower threshold"},
{"max",VDoubleRepn,1,(VPointer) &xmax,VOptionalOpt,NULL,"upper threshold"},
};
FILE *in_file,*out_file;
VAttrList list=NULL;
VAttrListPosn posn;
VImage src=NULL,dest=NULL;
char prg[50];
sprintf(prg,"vbinarize V%s", getVersion());
fprintf (stderr, "%s\n", prg);
VParseFilterCmd (VNumber (options),options,argc,argv,&in_file,&out_file);
if (! (list = VReadFile (in_file, NULL))) exit (1);
fclose(in_file);
for (VFirstAttr (list, & posn); VAttrExists (& posn); VNextAttr (& posn)) {
if (VGetAttrRepn (& posn) != VImageRepn) continue;
VGetAttrValue (& posn, NULL,VImageRepn, & src);
dest = VBinarizeImage (src,NULL,xmin,xmax);
VSetAttrValue (& posn, NULL,VImageRepn,dest);
}
if (src == NULL) VError(" no input image found");
VHistory(VNumber(options),options,prg,&list,&list);
if (! VWriteFile (out_file, list)) exit (1);
fprintf (stderr, "%s: done.\n", argv[0]);
return 0;
}
int
main(int argc, char *argv[]) {
static VString cfile = "";
static VOptionDescRec options[] = {
{"file", VStringRepn, 1, (VPointer) &cfile, VOptionalOpt, NULL, "file"}
};
FILE *in_file, *out_file;
VAttrList list = NULL;
VAttrListPosn posn;
VImage design = NULL, dest = NULL;
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "vaddcovariates V%s", ver);
fprintf(stderr, "%s\n", prg_name);
VParseFilterCmd(VNumber(options), options, argc, argv, &in_file, &out_file);
if(!(list = VReadFile(in_file, NULL)))
exit(1);
fclose(in_file);
for(VFirstAttr(list, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & design);
if(VPixelRepn(design) != VFloatRepn && VPixelRepn(design) != VDoubleRepn)
continue;
dest = VAddCovariates(design, cfile);
VSetAttrValue(& posn, NULL, VImageRepn, dest);
break;
}
if(design == NULL)
VError(" design matrix not found ");
/* Output: */
if(! VWriteFile(out_file, list))
exit(1);
fprintf(stderr, " %s: done.\n", argv[0]);
return 0;
}
int
main (int argc,char *argv[])
{
static VString filename = "";
static VString filename1 = "";
static VString filename2 = "";
static VShort first = 2;
static VShort length = 0;
static VShort type = 0;
static VShort minval = 0;
static VShort nproc = 4;
static VOptionDescRec options[] = {
{"in1",VStringRepn,1,(VPointer) &filename1,VRequiredOpt,NULL,"first input file"},
{"in2",VStringRepn,1,(VPointer) &filename2,VRequiredOpt,NULL,"second input file"},
{"mask",VStringRepn,1,(VPointer) &filename,VRequiredOpt,NULL,"mask"},
{"type",VShortRepn,1,(VPointer) &type,VOptionalOpt,TYPDict,"type of concordance measure"},
{"minval",VShortRepn,1,(VPointer) &minval,VOptionalOpt,NULL,"signal threshold"},
{"first",VShortRepn,1,(VPointer) &first,VOptionalOpt,NULL,"first timestep to use"},
{"length",VShortRepn,1,(VPointer) &length,VOptionalOpt,NULL,
"length of time series to use, '0' to use full length"},
{"j",VShortRepn,1,(VPointer) &nproc,VOptionalOpt,NULL,"number of processors to use, '0' to use all"}
};
FILE *out_file,*fp;
VAttrList list=NULL,list1=NULL,list2=NULL,out_list=NULL;
VAttrListPosn posn;
VImage mask=NULL,map=NULL,dest=NULL,disc=NULL;
float *A1=NULL,*A2=NULL,u=0,tiny=1.0e-6;
int b,r,c;
char *prg = "vccm2";
VParseFilterCmd (VNumber (options),options,argc,argv,NULL,&out_file);
if (type > 3) VError("illegal type");
/*
** read mask
*/
fp = VOpenInputFile (filename, TRUE);
list = VReadFile (fp, NULL);
if (! list) VError("Error reading mask file");
fclose(fp);
for (VFirstAttr (list, & posn); VAttrExists (& posn); VNextAttr (& posn)) {
if (VGetAttrRepn (& posn) != VImageRepn) continue;
VGetAttrValue (& posn, NULL,VImageRepn, & mask);
if (VPixelRepn(mask) == VFloatRepn || VPixelRepn(mask) == VDoubleRepn) {
mask = NULL;
continue;
}
}
if (mask == NULL) VError(" no mask found");
/* read files */
fp = VOpenInputFile (filename1, TRUE);
list1 = VReadFile (fp, NULL);
if (! list1) VError("Error reading 1st input file");
fclose(fp);
fp = VOpenInputFile (filename2, TRUE);
list2 = VReadFile (fp, NULL);
if (! list2) VError("Error reading 2nd input file");
fclose(fp);
/* get voxel map */
map = GetMap(list1,list2,mask,minval);
/* omp-stuff */
#ifdef _OPENMP
int num_procs=omp_get_num_procs();
if (nproc > 0 && nproc < num_procs) num_procs = nproc;
printf("using %d cores\n",(int)num_procs);
omp_set_num_threads(num_procs);
#endif /* _OPENMP */
/* compute corr matrices */
A1 = VCorrMatrix(list1,map,first,length);
A2 = VCorrMatrix(list2,map,first,length);
/* get concordance between two corr matrices */
dest = VCCM2(A1,A2,map,(int)type);
/* invert to get discordant map */
disc = VCreateImageLike(dest);
VFillImage(disc,VAllBands,0);
if (type < 2) {
for (b=0; b<VImageNBands(dest); b++) {
for (r=0; r<VImageNRows(dest); r++) {
for (c=0; c<VImageNColumns(dest); c++) {
if (VGetPixel(mask,b,r,c) < 1) continue;
u = VPixel(dest,b,r,c,VFloat);
if (u < tiny) continue;
VPixel(disc,b,r,c,VFloat) = 1-u;
}
}
}
}
/* output */
out_list = VCreateAttrList();
VHistory(VNumber(options),options,prg,&list,&out_list);
VAppendAttr(out_list,"concordant",NULL,VImageRepn,dest);
if (type < 2) VAppendAttr(out_list,"discordant",NULL,VImageRepn,disc);
if (! VWriteFile (out_file, out_list)) exit (1);
fprintf (stderr, "%s: done.\n", argv[0]);
return 0;
}
int
main(int argc, char *argv[]) {
static VArgVector in_files;
static VString out_filename;
static VBoolean in_found, out_found;
static VOptionDescRec options[] = {
{"in", VStringRepn, 0, & in_files, & in_found, NULL, "Input files" },
{"out", VStringRepn, 1, & out_filename, & out_found, NULL, "Output file" }
};
FILE *fp = NULL;
VStringConst in_filename;
VAttrList list = NULL, out_list = NULL;
VImage *design = NULL, tmp = NULL, dest = NULL;
VAttrListPosn posn;
int i, nimages;
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "vcatdesign V%s", ver);
fprintf(stderr, "%s\n", prg_name);
/* Parse command line arguments: */
if(! VParseCommand(VNumber(options), options, & argc, argv) ||
! VIdentifyFiles(VNumber(options), options, "in", & argc, argv, 0) ||
! VIdentifyFiles(VNumber(options), options, "out", & argc, argv, -1))
goto Usage;
if(argc > 1) {
VReportBadArgs(argc, argv);
Usage:
VReportUsage(argv[0], VNumber(options), options, NULL);
exit(EXIT_FAILURE);
}
/* Read each input file */
nimages = in_files.number;
design = (VImage *) VMalloc(sizeof(VImage) * nimages);
for(i = 0; i < nimages; i++) {
in_filename = ((VStringConst *) in_files.vector)[i];
fprintf(stderr, " reading: %s\n", in_filename);
fp = VOpenInputFile(in_filename, TRUE);
list = VReadFile(fp, NULL);
if(! list)
VError("Error reading file %s", in_filename);
fclose(fp);
for(VFirstAttr(list, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & tmp);
if(VPixelRepn(tmp) == VFloatRepn || VPixelRepn(tmp) == VDoubleRepn) {
design[i] = tmp;
break;
}
}
}
/* process */
dest = ConcatDesigns(design, nimages);
out_list = VCreateAttrList();
VAppendAttr(out_list, "image", NULL, VImageRepn, dest);
/* Output: */
VHistory(VNumber(options), options, prg_name, &list, &out_list);
fp = VOpenOutputFile(out_filename, TRUE);
if(!fp)
VError(" error opening outout file %s", out_filename);
if(! VWriteFile(fp, out_list))
exit(1);
fprintf(stderr, "%s: done.\n", argv[0]);
return 0;
}
int main(int argc, char *argv[]) {
/* command line arguments */
static VString out_filename;
static VArgVector in_files;
static VString trans_filename = "";
static VBoolean in_found, out_found;
static VShort minval = 0;
static VBoolean compress = TRUE;
static VFloat resolution = 3;
static VOptionDescRec options[] = {
{ "in", VStringRepn, 0, & in_files, & in_found, NULL, "Input file" },
{ "out", VStringRepn, 1, & out_filename, & out_found, NULL, "Output file" },
{
"trans", VStringRepn, 1, &trans_filename, VRequiredOpt, NULL,
"File containing transformation matrix"
},
{
"resolution", VFloatRepn, 1, &resolution, VOptionalOpt, NULL,
"Output voxel resolution in mm"
},
{
"minval", VShortRepn, 1, &minval, VOptionalOpt, NULL,
"Signal threshold"
},
{
"compress", VBooleanRepn, 1, &compress, VOptionalOpt, NULL,
"Whether to compress empty slices"
}
};
VStringConst in_filename;
FILE *in_file, *out_file, *fp;
VAttrList list, list1, out_list;
VAttrListPosn posn;
VImage trans = NULL;
VImage *dst_image;
VImageInfo *imageInfo;
int nobject = 0, ntimesteps = 0, nbands = 0, nrows = 0, ncols = 0;
VString ca, cp, extent, str;
int found = 0;
int j, dest_nbands;
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "vfunctrans V%s", ver);
fprintf(stderr, "%s\n", prg_name);
/* Parse command line arguments: */
if(! VParseCommand(VNumber(options), options, & argc, argv) ||
! VIdentifyFiles(VNumber(options), options, "in", & argc, argv, 0) ||
! VIdentifyFiles(VNumber(options), options, "out", & argc, argv, -1))
goto Usage;
if(argc > 1) {
VReportBadArgs(argc, argv);
Usage:
VReportUsage(argv[0], VNumber(options), options, NULL);
exit(EXIT_FAILURE);
}
if(resolution <= 0)
VError(" 'resolution' must be an integer > 0");
/*
** Read the transformation matrix:
*/
fp = VOpenInputFile(trans_filename, TRUE);
list1 = VReadFile(fp, NULL);
if(! list1)
VError("Error reading image");
fclose(fp);
for(VFirstAttr(list1, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
if(strncmp(VGetAttrName(&posn), "transform", 9) != 0)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & trans);
break;
}
if(trans == NULL)
VError("transformation matrix not found");
/*
** check attributes
*/
if(VGetAttr(VImageAttrList(trans), "ca", NULL,
VStringRepn, (VPointer) & ca) != VAttrFound)
VError(" attribute 'ca' missing in transformation matrix ");
if(VGetAttr(VImageAttrList(trans), "cp", NULL,
VStringRepn, (VPointer) & cp) != VAttrFound)
VError(" attribute 'cp' missing in transformation matrix ");
if(VGetAttr(VImageAttrList(trans), "extent", NULL,
VStringRepn, (VPointer) & extent) != VAttrFound)
VError(" attribute 'extent' missing in transformation matrix ");
/*
** open in-file
*/
if(in_files.number < 1 || in_files.number > 1)
VError(" incorrect number of input files: %d", in_files.number);
in_filename = ((VStringConst *) in_files.vector)[0];
if(strcmp(in_filename, "-") == 0)
in_file = stdin;
else {
in_file = fopen((char *)in_filename, "r");
if(! in_file)
VError("Failed to open input file %s", in_filename);
}
/*
** read file info
*/
if(! ReadHeader(in_file))
VError("error reading header");
if(!(list = ReadAttrList(in_file)))
VError("error reading attr list");
j = 0;
for(VFirstAttr(list, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
j++;
}
imageInfo = (VImageInfo *) VMalloc(sizeof(VImageInfo) * (j + 1));
nobject = nbands = found = 0;
for(VFirstAttr(list, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
str = VGetAttrName(&posn);
if(strncmp(str, "history", 7) == 0) {
nobject++;
continue;
}
VImageInfoIni(&imageInfo[nbands]);
if(! VGetImageInfo(in_file, list, nobject, &imageInfo[nbands]))
VError(" error reading image info");
if(imageInfo[nbands].repn == VShortRepn) {
found = 1;
nrows = imageInfo[nbands].nrows;
ncols = imageInfo[nbands].ncolumns;
ntimesteps = imageInfo[nbands].nbands;
nbands++;
}
nobject++;
}
fclose(in_file);
if(!found)
VError(" couldn't find functional data");
/*
** process each time step
*/
dst_image = VFunctrans(in_filename, imageInfo, nbands, trans, resolution,
ntimesteps, minval, compress, &dest_nbands);
/*
** output
*/
out_list = VCreateAttrList();
VHistory(VNumber(options), options, prg_name, &list, &out_list);
for(j = 0; j < dest_nbands; j++) {
VAppendAttr(out_list, "image", NULL, VImageRepn, dst_image[j]);
}
/* Open and write the output file: */
if(strcmp(out_filename, "-") == 0)
out_file = stdout;
else {
out_file = fopen(out_filename, "w");
if(! out_file)
VError("Failed to open output file %s", out_filename);
}
if(!VWriteFile(out_file, out_list) || fclose(out_file))
VSystemError("error writing output file");
fprintf(stderr, "\n%s: done.\n", argv[0]);
return (EXIT_SUCCESS);
}
int
main (int argc,char *argv[])
{
static VString filename = "";
static VShort first = 2;
static VShort length = 0;
static VFloat threshold = 0.5;
static VShort minval = 0;
static VShort nproc = 4;
static VOptionDescRec options[] = {
{"mask",VStringRepn,1,(VPointer) &filename,VOptionalOpt,NULL,"mask"},
{"minval",VShortRepn,1,(VPointer) &minval,VOptionalOpt,NULL,"signal threshold"},
{"first",VShortRepn,1,(VPointer) &first,VOptionalOpt,NULL,"first timestep to use"},
{"length",VShortRepn,1,(VPointer) &length,VOptionalOpt,NULL,"length of time series to use, '0' to use full length"},
{"threshold",VFloatRepn,1,(VPointer) &threshold,VOptionalOpt,NULL,"threshold"},
{"j",VShortRepn,1,(VPointer) &nproc,VOptionalOpt,NULL,"number of processors to use, '0' to use all"}
};
FILE *in_file,*out_file,*fp;
VAttrList list=NULL,list1=NULL,out_list=NULL;
VAttrListPosn posn;
VImage mask=NULL;
char *prg = "vncm";
VParseFilterCmd (VNumber (options),options,argc,argv,&in_file,&out_file);
/*
** read mask
*/
fp = VOpenInputFile (filename, TRUE);
list1 = VReadFile (fp, NULL);
if (! list1) VError("Error reading mask file");
fclose(fp);
for (VFirstAttr (list1, & posn); VAttrExists (& posn); VNextAttr (& posn)) {
if (VGetAttrRepn (& posn) != VImageRepn) continue;
VGetAttrValue (& posn, NULL,VImageRepn, & mask);
if (VPixelRepn(mask) != VBitRepn && VPixelRepn(mask) != VUByteRepn && VPixelRepn(mask) != VShortRepn) {
mask = NULL;
continue;
}
}
if (mask == NULL) VError(" no mask found");
/*
** read functional data
*/
if (! (list = VReadFile (in_file, NULL))) exit (1);
fclose(in_file);
/* omp-stuff */
#ifdef _OPENMP
int num_procs=omp_get_num_procs();
if (nproc > 0 && nproc < num_procs) num_procs = nproc;
printf("using %d cores\n",(int)num_procs);
omp_set_num_threads(num_procs);
#endif /* _OPENMP */
/*
** process
*/
out_list = VNCM(list,mask,minval,first,length,threshold);
VHistory(VNumber(options),options,prg,&list,&out_list);
if (! VWriteFile (out_file, out_list)) exit (1);
fprintf (stderr, "%s: done.\n", argv[0]);
return 0;
}
int main(int argc, char *argv[]) {
static VArgVector in_files;
static VString out_filename;
static VBoolean level = FALSE;
static VBoolean zscore = FALSE;
static VBoolean in_found, out_found;
static VOptionDescRec options[] = {
{
"in", VStringRepn, 0, & in_files, & in_found, NULL,
"Contrast images"
},
{
"out", VStringRepn, 1, & out_filename, & out_found, NULL,
"Output file"
},
{
"level", VBooleanRepn, 1, & level, VOptionalOpt, NULL,
"Whether to produce output to be used for 3rd level analysis"
}
/* { "zscore", VBooleanRepn, 1, & zscore, VOptionalOpt, NULL,
"Whether to produce z-scores as output"} */
};
FILE *f;
VStringConst in_filename;
VAttrList list, out_list;
VAttrListPosn posn;
VImage src = NULL;
VImage cbeta_images[N], sd_images[N];
int i, nimages = 0;
VString str = NULL;
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "vbayes V%s", ver);
fprintf(stderr, "%s\n", prg_name);
/* Parse command line arguments: */
if(! VParseCommand(VNumber(options), options, & argc, argv) ||
! VIdentifyFiles(VNumber(options), options, "in", & argc, argv, 0) ||
! VIdentifyFiles(VNumber(options), options, "out", & argc, argv, -1))
goto Usage;
if(argc > 1) {
VReportBadArgs(argc, argv);
Usage:
VReportUsage(argv[0], VNumber(options), options, NULL);
exit(EXIT_FAILURE);
}
nimages = in_files.number;
fprintf(stderr, "Processing %d input files\n\n", nimages);
if(nimages >= N)
VError("Too many input images, max: %d", N);
if(nimages == 0)
VError("Input images missing");
/* loop through all input files */
for(i = 0; i < nimages; i++) {
in_filename = ((VStringConst *) in_files.vector)[i];
fprintf(stderr, "%s\n", in_filename);
f = fopen((char *)in_filename, "r");
if(! f)
VError("Failed to open input file %s", in_filename);
if(!(list = VReadFile(f, NULL)))
exit(EXIT_FAILURE);
fclose(f);
for(VFirstAttr(list, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & src);
if(VPixelRepn(src) != VFloatRepn)
continue;
VGetAttr(VImageAttrList(src), "modality", NULL, VStringRepn, &str);
if(strcmp(str, "conimg") == 0) {
cbeta_images[i] = VCopyImage(src, NULL, VAllBands);
} else if(strcmp(str, "std_dev") == 0 || strcmp(str, "sd") == 0) {
sd_images[i] = VCopyImage(src, NULL, VAllBands);
} else
VError(" Illegal input file! Make sure to use con-images as input");
}
}
/* calculate probabilities */
out_list = VBayes(cbeta_images, sd_images, nimages, level, zscore);
if(out_list == NULL)
VError(" no result");
/*
** output
*/
VHistory(VNumber(options), options, prg_name, &list, &out_list);
if(strcmp(out_filename, "-") == 0)
VError("Output file required");
f = fopen(out_filename, "w");
if(! f)
VError("Failed to open output file %s", out_filename);
if(! VWriteFile(f, out_list))
exit(EXIT_FAILURE);
fprintf(stderr, "\n%s: done \n", argv[0]);
return EXIT_SUCCESS;
}
int
main(int argc, char *argv[]) {
static VLong i0 = 5;
static VLong maxiter = 200;
static VLong step = 3;
static VShort nproc = 4;
static VString filename = "";
static VOptionDescRec options[] = {
{"tref", VLongRepn, 1, (VPointer) &i0, VOptionalOpt, NULL, "reference time step"},
{"report", VStringRepn, 1, (VPointer) &filename, VOptionalOpt, NULL, "report file"},
{"step", VLongRepn, 1, (VPointer) &step, VOptionalOpt, NULL, "Step size (e.g. 2 or 3)"},
{"iterations", VLongRepn, 1, (VPointer) &maxiter, VOptionalOpt, NULL, "Max number of iterations"}/*,
{"j", VShortRepn, 1,(VPointer) &nproc, VOptionalOpt, NULL, "number of processors to use, '0' to use al l"} */
};
FILE *in_file = NULL, *out_file = NULL;
VImage motion = NULL;
VAttrList list = NULL;
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "vmovcorrection V%s", ver);
fprintf(stderr, "%s\n", prg_name);
/* parse command line */
VParseFilterCmd(VNumber(options), options, argc, argv, &in_file, &out_file);
if(step < 1)
VError(" illegal step size %d", step);
if(i0 < 0)
VError(" illegal reference time step %d", i0);
/*openmp stuff */
/*#ifdef _OPENMP
int num_procs=omp_get_num_procs();
if (nproc > 0 && nproc < num_procs) num_procs = nproc;
printf("using %d cores\n",(int)num_procs);
omp_set_num_threads(num_procs);
#endif /*OPENMP */
/* read data */
if(!(list = VReadFile(in_file, NULL)))
VError(" error reading data, perhaps insufficient memory ?");
/* spatial smoothing */
VSpatialFilter1(list);
/* estimate motion parameters using smoothed data */
motion = VMotionCorrection3d(list, i0, step, maxiter);
/* re-read original data from file */
VReleaseStorage(list);
list = NULL;
rewind(in_file);
if(!(list = VReadFile(in_file, NULL)))
VError(" error reading data, perhaps insufficient memory ?");
fclose(in_file);
/* apply motion correction */
VApplyMotionCorrection3d(list, motion, filename);
/* write output */
VHistory(VNumber(options), options, prg_name, &list, &list);
if(! VWriteFile(out_file, list))
exit(1);
fprintf(stderr, "%s: done.\n", argv[0]);
exit(0);
}
int main(int argc, char *argv[])
{
static VLong op = 0;
static VLong dim = 1;
static VShort radius = 2;
static VString mask_filename=" ";
static VOptionDescRec options[] = {
{ "op", VLongRepn, 1, &op, VOptionalOpt, OPDict,
"type of operation" },
{ "dim", VLongRepn, 1, &dim, VOptionalOpt, DIMDict,
"dim of structuring element (2D or 3D)" },
{ "radius", VShortRepn, 1,(VPointer) & radius,
VOptionalOpt, NULL,"radius of structuring element" },
{ "file", VStringRepn, 1, & mask_filename, VOptionalOpt, NULL,
"File containing structuring element" }
};
FILE *in_file, *out_file, *mask_file;
VAttrList list, list2;
VAttrListPosn posn;
VImage src=NULL, se=NULL, result, tmp;
char prg[50];
sprintf(prg,"vgreymorph3d V%s", getVersion());
fprintf (stderr, "%s\n", prg);
/* Parse command line arguments and identify files: */
VParseFilterCmd(VNumber(options),options,argc,argv,&in_file,&out_file);
if (strlen(mask_filename) < 2) {
if (dim == 0)
se = VGenSphere2d(radius);
else if (dim == 1)
se = VGenSphere3d(radius);
else
VError("illegal choice of parameter 'dim' (%d), must be 2 or 3",dim);
}
else {
mask_file = VOpenInputFile (mask_filename, TRUE);
list2 = VReadFile (mask_file, NULL);
if (! list2)
VError("Error reading structuring element");
fclose(mask_file);
for (VFirstAttr (list2,&posn); VAttrExists (& posn); VNextAttr (& posn)) {
if (VGetAttrRepn (& posn) != VImageRepn) continue;
VGetAttrValue (& posn, NULL, VImageRepn, & se);
if (VPixelRepn(se) != VBitRepn)
VError("Structuring element must be of type VBit");
}
}
/* Read the input file: */
list = VReadFile (in_file, 0); if (! list) exit(1);
fclose(in_file);
/* For each attribute read... */
for (VFirstAttr (list, & posn); VAttrExists (& posn); VNextAttr(& posn)) {
if (VGetAttrRepn (& posn) != VImageRepn) continue;
VGetAttrValue (& posn, NULL, VImageRepn, & src);
switch (op) {
case 0:
result = VGreyDilation3d(src,se,NULL);
break;
case 1:
result = VGreyErosion3d(src,se,NULL);
break;
case 2:
tmp = VGreyErosion3d(src,se,NULL);
result = VGreyDilation3d(tmp,se,NULL);
VDestroyImage(tmp);
break;
case 3:
tmp = VGreyDilation3d(src,se,NULL);
result = VGreyErosion3d(tmp,se,NULL);
VDestroyImage(tmp);
break;
}
if (! result) exit(1);
VSetAttrValue(&posn, 0, VImageRepn, result);
VDestroyImage (src);
}
/* Write out the results: */
VHistory(VNumber(options),options,prg,&list,&list);
if (! VWriteFile (out_file, list)) exit(1);
fprintf(stderr, "%s: done.\n", argv[0]);
return 0;
}
int main(int argc, char *argv[]) {
static VFloat reso = -1.0;
static VLong itype = 0;
static VBoolean flip = TRUE;
static VBoolean reorder = TRUE;
static VOptionDescRec options[] = {
{
"reso", VFloatRepn, 1, (VPointer) &reso,
VOptionalOpt, NULL, "New voxel resolution in mm, def: -1 means min(1.0,\"best source resolution\")"
},
{
"flip", VBooleanRepn, 1, (VPointer) &flip,
VOptionalOpt, NULL, "Whether to flip to natural convention"
},
{
"reorder", VBooleanRepn, 1, (VPointer) &reorder,
VOptionalOpt, NULL, "Whether to reorder axial slices from axial source image"
},
{
"interpolation", VLongRepn, 1, & itype, VOptionalOpt, ITYPDict,
"Type of interpolation (0: linear, 1: nearest neighbour, 2: cubic spline)"
}
};
FILE *in_file, *out_file;
VAttrList list;
VAttrListPosn posn;
int nobjects = 0;
VImage src = NULL, dest = NULL, result = NULL;
int i, b, r, c, nbands, nrows, ncols;
VString str, newstr, fixpointString, caString, cpString;
float fix_c, fix_r, fix_b;
float ca_c, ca_r, ca_b;
float cp_c, cp_r, cp_b;
float x, y, z, min;
VDouble v, scale_band, scale_row, scale_col;
float scale[3], shift[3];
/* print information */
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "visotrop V%s", ver);
fprintf(stderr, "%s\n", prg_name);
fflush(stderr);
/* Parse command line arguments: */
VParseFilterCmd(VNumber(options), options, argc, argv,
& in_file, & out_file);
/* Read source image(s): */
if(!(list = VReadFile(in_file, NULL)))
exit(EXIT_FAILURE);
/* Scale each object: */
for(VFirstAttr(list, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
switch(VGetAttrRepn(& posn)) {
case VImageRepn:
VGetAttrValue(& posn, NULL, VImageRepn, & src);
if(VGetAttr(VImageAttrList(src), "voxel", NULL,
VStringRepn, (VPointer) & str) == VAttrFound) {
sscanf(str, "%f %f %f", &x, &y, &z);
fprintf(stderr, " voxel: %f %f %f\n", x, y, z);
min = x < y ? x : y;
min = z < min ? z : min;
/* if resolution is not set, use default value 1 or
smaler value if the image resolution is better */
if(reso < 0.0)
reso = min < 1.0 ? min : 1.0;
if(reso <= 0.0)
exit(EXIT_FAILURE);
fprintf(stderr, " new resolution: %f \n", reso);
scale_col = x / reso;
scale_row = y / reso;
scale_band = z / reso;
nbands = VImageNBands(src) * scale_band;
nrows = VImageNRows(src) * scale_row;
ncols = VImageNColumns(src) * scale_col;
if(VImageNBands(src) == nbands
&& VImageNRows(src) == nrows
&& VImageNColumns(src) == ncols) {
itype = 0;
}
fprintf(stderr, " interpolation type: %s\n", ITYPDict[itype].keyword);
fprintf(stderr, " old dim: %3d %3d %3d\n",
VImageNBands(src), VImageNRows(src), VImageNColumns(src));
for(i = 0; i < 3; i++)
shift[i] = scale[i] = 0;
scale[0] = scale_band;
scale[1] = scale_row;
scale[2] = scale_col;
switch(itype) {
/* trilinear interpolation resampling */
case 0:
dest = VTriLinearScale3d(src, NULL, (int)nbands, (int)nrows, (int)ncols,
shift, scale);
break;
/* nearest neightbour resampling */
case 1:
dest = VNNScale3d(src, NULL, (int)nbands, (int)nrows, (int)ncols,
shift, scale);
break;
/* cubic spline */
case 2:
dest = VCubicSplineScale3d(src, NULL, (int)nbands, (int)nrows, (int)ncols,
shift, scale);
break;
case 3: /* no interpolation, just reshuffle */
dest = VCopyImage(src, NULL, VAllBands);
break;
default:
VError(" unknown resampling type %d", itype);
}
if(! dest)
exit(EXIT_FAILURE);
/*aa 2003/09/11 added function not to rotate siemens data*/
if(! VGetAttr(VImageAttrList(src), "orientation", NULL,
VStringRepn, (VPointer) & str) == VAttrFound)
VError(" attribute 'orientation' missing");
if(strcmp(str, "axial") == 0) {
fprintf(stderr, " new dim: %3d %3d %3d\n", nbands, nrows, ncols);
result = VCreateImage(nbands, nrows, ncols, VPixelRepn(src));
VFillImage(result, VAllBands, 0);
for(b = 0; b < nbands; b++)
for(r = 0; r < nrows; r++)
for(c = 0; c < ncols; c++) {
v = VGetPixel(dest, b, r, c);
if((flip == FALSE) && (reorder == FALSE))
VSetPixel(result, b, r, ncols - c - 1, v);
else if((flip == TRUE) && (reorder == FALSE))
VSetPixel(result, b, r, c, v);
else if((flip == FALSE) && (reorder == TRUE))
VSetPixel(result, nbands - b - 1, r, ncols - c - 1, v);
else if((flip == TRUE) && (reorder == TRUE))
VSetPixel(result, nbands - b - 1, r, c, v);
}
} else if(strcmp(str, "sagittal") == 0) {
/* re-arrange from sagittal to axial orientation */
fprintf(stderr, " new dim: %3d %3d %3d\n", nrows, ncols, nbands);
result = VCreateImage(nrows, ncols, nbands, VPixelRepn(src));
VFillImage(result, VAllBands, 0);
for(b = 0; b < nbands; b++)
for(r = 0; r < nrows; r++)
for(c = 0; c < ncols; c++) {
v = VGetPixel(dest, b, r, c);
if(flip == FALSE)
VSetPixel(result, r, c, nbands - b - 1, v);
else
VSetPixel(result, r, c, b, v);
}
} else if(strcmp(str, "coronal") == 0) {
/* re-arrange from coronal to axial orientation */
fprintf(stderr, " new dim: %3d %3d %3d\n", nrows, nbands, ncols);
result = VCreateImage(nrows, nbands, ncols, VPixelRepn(src));
VFillImage(result, VAllBands, 0);
for(b = 0; b < nbands; b++)
for(r = 0; r < nrows; r++)
for(c = 0; c < ncols; c++) {
v = VGetPixel(dest, b, r, c);
if(flip == FALSE)
VSetPixel(result, r, b, ncols - c - 1, v);
else
VSetPixel(result, r, b, c, v);
}
} else {
VError(" unknown resampling type %d", itype);
exit(EXIT_FAILURE);
}
/* copy attributes from source image */
VCopyImageAttrs(src, result);
// [TS] 08/03/27
// correct 'fixpoint', 'ca' and 'cp' if they exist in the source image
//
// NOTE:
// this is only done when no flipping or reordering is requested :-(
// (WARNING!!!!) '-flip true' actually means that no flipping is done (WHAAAAT ????)
// and therefore we test for reorder = false and flip = true
fixpointString = VMalloc(80);
caString = VMalloc(80);
cpString = VMalloc(80);
VBoolean _issueWarning = FALSE;
if(VGetAttr(VImageAttrList(src), "fixpoint", NULL, VStringRepn, (VPointer)&fixpointString) == VAttrFound) {
if(reorder == FALSE && flip == TRUE) {
sscanf(fixpointString, "%f %f %f", &fix_c, &fix_r, &fix_b);
fix_c *= scale_col;
fix_r *= scale_row;
fix_b *= scale_band;
sprintf((char *)fixpointString, "%f %f %f", fix_c, fix_r, fix_b);
VSetAttr(VImageAttrList(result), "fixpoint", NULL, VStringRepn, fixpointString);
} else {
_issueWarning = TRUE;
}
}
if(VGetAttr(VImageAttrList(src), "ca", NULL, VStringRepn, (VPointer)&caString) == VAttrFound) {
if(reorder == FALSE && flip == TRUE) {
sscanf(caString, "%f %f %f", &ca_c, &ca_r, &ca_b);
ca_c *= scale_col;
ca_r *= scale_row;
ca_b *= scale_band;
sprintf((char *)caString, "%f %f %f", ca_c, ca_r, ca_b);
VSetAttr(VImageAttrList(result), "ca", NULL, VStringRepn, caString);
} else {
_issueWarning = TRUE;
}
}
if(VGetAttr(VImageAttrList(src), "cp", NULL, VStringRepn, (VPointer)&cpString) == VAttrFound) {
if(reorder == FALSE && flip == TRUE) {
sscanf(cpString, "%f %f %f", &cp_c, &cp_r, &cp_b);
cp_c *= scale_col;
cp_r *= scale_row;
cp_b *= scale_band;
sprintf((char *)cpString, "%f %f %f", cp_c, cp_r, cp_b);
VSetAttr(VImageAttrList(result), "cp", NULL, VStringRepn, cpString);
} else {
_issueWarning = TRUE;
}
}
if(_issueWarning) {
VWarning("Attributes 'fixpoint', 'ca' and 'cp' exist but were not corrected and are therefore likely to be wrong");
VWarning("This was caused by setting -flip to false or -reorder to true");
VWarning("Please correct the values manually using vattredit");
}
/* set the attributes to the changed values */
newstr = VMalloc(80);
sprintf((char *)newstr, "%f %f %f", reso, reso, reso);
VSetAttr(VImageAttrList(result), "voxel", NULL, VStringRepn, newstr);
VSetAttr(VImageAttrList(result), "orientation", NULL, VStringRepn, "axial");
if(flip)
VSetAttr(VImageAttrList(result), "convention", NULL, VStringRepn, "natural");
else
VSetAttr(VImageAttrList(result), "convention", NULL, VStringRepn, "radiologic");
}
VSetAttrValue(& posn, NULL, VImageRepn, result);
VDestroyImage(src);
break;
default:
continue;
}
nobjects++;
}
/* Make History */
VHistory(VNumber(options), options, prg_name, &list, &list);
/* Write the results to the output file: */
if(! VWriteFile(out_file, list))
exit(EXIT_FAILURE);
fprintf(stderr, "%s: done.\n", argv[0]);
return EXIT_SUCCESS;
}
int main(int argc, char *argv[]) {
static VArgVector in_files1;
static VArgVector in_files2;
static VString out_filename;
static VShort type = 1;
static VBoolean gauss = FALSE;
static VOptionDescRec options[] = {
{"in1", VStringRepn, 0, & in_files1, VRequiredOpt, NULL, "Input files 1" },
{"in2", VStringRepn, 0, & in_files2, VRequiredOpt, NULL, "Input files 2" },
{"type", VShortRepn, 1, (VPointer) &type, VOptionalOpt, TypeDict, "output type"},
{"gaussianize", VBooleanRepn, 1, (VPointer) &gauss, VOptionalOpt, NULL, "Whether to Gaussianize"},
{"out", VStringRepn, 1, & out_filename, VRequiredOpt, NULL, "Output file" }
};
FILE *fp = NULL;
VStringConst in_filename, buf1, buf2;
VAttrList list1, list2, out_list;
VAttrListPosn posn;
VString str;
VImage src, *src1, *src2, dest = NULL;
int i, nimages, npix = 0;
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "vpaired_ttest V%s", ver);
fprintf(stderr, "%s\n", prg_name);
/*
** parse command line
*/
if(! VParseCommand(VNumber(options), options, & argc, argv)) {
VReportUsage(argv[0], VNumber(options), options, NULL);
exit(EXIT_FAILURE);
}
if(argc > 1) {
VReportBadArgs(argc, argv);
exit(EXIT_FAILURE);
}
if(type < 0 || type > 1)
VError(" illegal type");
/* ini */
nimages = in_files1.number;
if(in_files2.number != nimages)
VError(" inconsistent number of files %d %d", nimages, in_files2.number);
for(i = 0; i < nimages; i++) {
buf1 = ((VStringConst *) in_files1.vector)[i];
buf2 = ((VStringConst *) in_files2.vector)[i];
fprintf(stderr, "%3d: %s %s\n", i, buf1, buf2);
}
fprintf(stderr, "\n");
/* images 1 */
src1 = (VImage *) VCalloc(nimages, sizeof(VImage));
for(i = 0; i < nimages; i++) {
src1[i] = NULL;
in_filename = ((VStringConst *) in_files1.vector)[i];
fp = VOpenInputFile(in_filename, TRUE);
list1 = VReadFile(fp, NULL);
if(! list1)
VError("Error reading image");
fclose(fp);
for(VFirstAttr(list1, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & src);
if(VPixelRepn(src) != VFloatRepn)
continue;
if(VGetAttr(VImageAttrList(src), "modality", NULL, VStringRepn, &str) == VAttrFound) {
if(strcmp(str, "conimg") != 0)
continue;
}
if(i == 0)
npix = VImageNPixels(src);
else if(npix != VImageNPixels(src))
VError(" inconsistent image dimensions");
src1[i] = src;
break;
}
if(src1[i] == NULL)
VError(" no contrast image found in %s", in_filename);
}
/* images 2 */
src2 = (VImage *) VCalloc(nimages, sizeof(VImage));
for(i = 0; i < nimages; i++) {
src2[i] = NULL;
in_filename = ((VStringConst *) in_files2.vector)[i];
fp = VOpenInputFile(in_filename, TRUE);
list2 = VReadFile(fp, NULL);
if(! list2)
VError("Error reading image");
fclose(fp);
for(VFirstAttr(list2, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & src);
if(VPixelRepn(src) != VFloatRepn)
continue;
if(VGetAttr(VImageAttrList(src), "modality", NULL, VStringRepn, &str) == VAttrFound) {
if(strcmp(str, "conimg") != 0)
continue;
}
if(npix != VImageNPixels(src))
VError(" inconsistent image dimensions");
src2[i] = src;
break;
}
if(src2[i] == NULL)
VError(" no contrast image found in %s", in_filename);
}
/* make normally distributed */
if(gauss) {
VGaussianize(src1, nimages);
VGaussianize(src2, nimages);
}
/* paired t-test */
dest = PairedTest(src1, src2, dest, nimages, type);
/*
** output
*/
out_list = VCreateAttrList();
VHistory(VNumber(options), options, prg_name, &list1, &out_list);
VAppendAttr(out_list, "image", NULL, VImageRepn, dest);
fp = VOpenOutputFile(out_filename, TRUE);
if(! VWriteFile(fp, out_list))
exit(1);
fclose(fp);
fprintf(stderr, "%s: done.\n", argv[0]);
exit(0);
}
int main(int argc, char *argv[]) {
static VArgVector in_files1;
static VArgVector in_files2;
static VString out_filename;
static VOptionDescRec options[] = {
{ "in1", VStringRepn, 0, & in_files1, VRequiredOpt, NULL, "Input files 1" },
{ "in2", VStringRepn, 0, & in_files2, VRequiredOpt, NULL, "Input files 2" },
{ "out", VStringRepn, 1, & out_filename, VRequiredOpt, NULL, "Output file" }
};
FILE *fp = NULL;
VStringConst in_filename, buf1, buf2;
VAttrList list1, list2, out_list;
VAttrListPosn posn;
VImage src, *src1, *src2, dest = NULL;
int i, nimages, npix = 0;
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "vpaired_wilcoxtest V%s", ver);
fprintf(stderr, "%s\n", prg_name);
/*
** parse command line
*/
if(! VParseCommand(VNumber(options), options, & argc, argv)) {
VReportUsage(argv[0], VNumber(options), options, NULL);
exit(EXIT_FAILURE);
}
if(argc > 1) {
VReportBadArgs(argc, argv);
exit(EXIT_FAILURE);
}
/* number of images */
nimages = in_files1.number;
if(in_files2.number != nimages)
VError(" inconsistent number of files ");
for(i = 0; i < nimages; i++) {
buf1 = ((VStringConst *) in_files1.vector)[i];
buf2 = ((VStringConst *) in_files2.vector)[i];
fprintf(stderr, "%3d: %s %s\n", i, buf1, buf2);
}
fprintf(stderr, "\n");
/*
** read images 1
*/
src1 = (VImage *) VCalloc(nimages, sizeof(VImage));
for(i = 0; i < nimages; i++) {
src1[i] = NULL;
in_filename = ((VStringConst *) in_files1.vector)[i];
fp = VOpenInputFile(in_filename, TRUE);
list1 = VReadFile(fp, NULL);
if(! list1)
VError("Error reading image");
fclose(fp);
for(VFirstAttr(list1, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & src);
if(VPixelRepn(src) != VFloatRepn)
continue;
src1[i] = src;
break;
}
if(i == 0)
npix = VImageNPixels(src1[i]);
else if(npix != VImageNPixels(src1[i]))
VError(" inconsistent image dimensions");
if(src1[i] == NULL)
VError(" no image found in %s", in_filename);
}
/*
** read images 2
*/
src2 = (VImage *) VCalloc(nimages, sizeof(VImage));
for(i = 0; i < nimages; i++) {
src2[i] = NULL;
in_filename = ((VStringConst *) in_files2.vector)[i];
fp = VOpenInputFile(in_filename, TRUE);
list2 = VReadFile(fp, NULL);
if(! list2)
VError("Error reading image");
fclose(fp);
for(VFirstAttr(list2, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & src);
if(VPixelRepn(src) != VFloatRepn)
continue;
src2[i] = src;
break;
}
if(npix != VImageNPixels(src2[i]))
VError(" inconsistent image dimensions");
if(src2[i] == NULL)
VError(" no image found in %s", in_filename);
}
/*
** paired wilcoxon test
*/
dest = PairedWilcoxTest(src1, src2, dest, nimages);
/*
** output
*/
out_list = VCreateAttrList();
VHistory(VNumber(options), options, prg_name, &list1, &out_list);
VAppendAttr(out_list, "image", NULL, VImageRepn, dest);
fp = VOpenOutputFile(out_filename, TRUE);
if(! VWriteFile(fp, out_list))
exit(1);
fclose(fp);
fprintf(stderr, "%s: done.\n", argv[0]);
exit(0);
}
int main(int argc, char *argv[]) {
static VLong objnr = -1;
static VString name = "";
static VString value = "";
static VOptionDescRec options[] = {
{
"obj", VLongRepn, 1, (VPointer) &objnr,
VOptionalOpt, NULL, "object number, all objects (-1)"
},
{
"name", VStringRepn, 1, (VPointer) &name,
VRequiredOpt, NULL, "attribute name"
},
{
"value", VStringRepn, 1, (VPointer) &value,
VRequiredOpt, NULL, "attribute value"
}
};
FILE *in_file, *out_file;
VAttrList list, olist;
VAttrListPosn posn;
VImage isrc;
VGraph gsrc;
Volumes vsrc;
VString buf;
int nobj;
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "vattredit V%s", ver);
fprintf(stderr, "%s\n", prg_name);
/* Parse command line arguments and identify files: */
VParseFilterCmd(VNumber(options), options, argc, argv,
&in_file, & out_file);
/* Read source image(s): */
if(!(list = VReadFile(in_file, NULL)))
exit(1);
/* Process each image: */
nobj = 0;
for(VFirstAttr(list, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
olist = NULL;
if(nobj == objnr || objnr < 0) {
if(VGetAttrRepn(& posn) == VImageRepn) {
VGetAttrValue(& posn, NULL, VImageRepn, & isrc);
olist = VImageAttrList(isrc);
} else if(VGetAttrRepn(& posn) == VGraphRepn) {
VGetAttrValue(& posn, NULL, VGraphRepn, & gsrc);
olist = VGraphAttrList(gsrc);
} else if(VGetAttrRepn(& posn) == VolumesRepn) {
VGetAttrValue(& posn, NULL, VolumesRepn, & vsrc);
olist = VolumesAttrList(vsrc);
}
if(olist != NULL) {
if(VGetAttr(olist, name, NULL, VStringRepn, &buf) == VAttrFound)
fprintf(stderr, " object %3d, old value: %s\n", nobj, buf);
VSetAttr(olist, name, NULL, VStringRepn, value);
fprintf(stderr, " object %3d, new value: %s\n", nobj, value);
}
}
nobj++;
}
/* Make History */
VHistory(VNumber(options), options, prg_name, &list, &list);
/* Write out the results: */
if(! VWriteFile(out_file, list))
exit(1);
fprintf(stderr, "%s: done.\n", argv[0]);
return 0;
}
int
main(int argc, char *argv[]) {
static VArgVector in_files;
static VString out_filename;
static VString filename;
static VShort minval = 0;
static VFloat fwhm = 4.0;
static VOptionDescRec options[] = {
{"in", VStringRepn, 0, & in_files, VRequiredOpt, NULL, "Input files" },
{"out", VStringRepn, 1, & out_filename, VRequiredOpt, NULL, "Output file" },
{"design", VStringRepn, 1, (VPointer) &filename, VRequiredOpt, NULL, "Design file"},
{
"fwhm", VFloatRepn, 1, (VPointer) &fwhm, VOptionalOpt, NULL,
"FWHM of temporal Gaussian filter in seconds"
},
{"minval", VShortRepn, 1, (VPointer) &minval, VOptionalOpt, NULL, "Signal threshold"}
};
FILE *fp = NULL, *f = NULL;
VStringConst in_filename;
VString ifilename;
VAttrList list = NULL, list1 = NULL;
VAttrList out_list = NULL, history_list = NULL;
VAttrListPosn posn;
VImage design = NULL;
ListInfo *linfo;
VLong itr = 0;
VFloat sigma = 0, tr = 0;
int i, n, nimages;
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "vcolorglm V%s", ver);
fprintf(stderr, "%s\n", prg_name);
/*
** parse command line
*/
if(! VParseCommand(VNumber(options), options, & argc, argv)) {
VReportUsage(argv[0], VNumber(options), options, NULL);
exit(EXIT_FAILURE);
}
if(argc > 1) {
VReportBadArgs(argc, argv);
exit(EXIT_FAILURE);
}
/*
** read design matrix
*/
fp = VOpenInputFile(filename, TRUE);
list1 = VReadFile(fp, NULL);
if(! list1)
VError("Error reading design file");
fclose(fp);
n = 0;
for(VFirstAttr(list1, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & design);
if(VPixelRepn(design) != VFloatRepn /* && VPixelRepn(design) != VDoubleRepn */)
continue;
n++;
break;
}
if(n == 0)
VError(" design matrix not found ");
/*
** get pre-coloring info
*/
if(VGetAttr(VImageAttrList(design), "repetition_time", NULL, VLongRepn, &itr) != VAttrFound)
VError(" TR info missing in header");
tr = (float) itr / 1000.0;
sigma = 0;
if(tr > 0.001 && fwhm > 0.001) {
fprintf(stderr, " TR: %.3f seconds\n", tr);
sigma = fwhm / 2.35482;
sigma /= tr;
if(sigma < 0.1) {
VWarning(" 'fwhm/sigma' too small (%.3f / %.3f), will be set to zero", fwhm, sigma);
sigma = 0;
}
}
/*
** Read each input file
*/
nimages = in_files.number;
linfo = (ListInfo *) VMalloc(sizeof(ListInfo) * nimages);
for(i = 0; i < nimages; i++) {
in_filename = ((VStringConst *) in_files.vector)[i];
ifilename = VNewString(in_filename);
fprintf(stderr, " file: %s\n", ifilename);
list = GetListInfo(ifilename, &linfo[i]);
/* Create history */
if(i == 0) {
history_list = VReadHistory(&list);
if(history_list == NULL)
history_list = VCreateAttrList();
VPrependHistory(VNumber(options), options, prg_name, &history_list);
}
}
/*
** GLM
*/
out_list = VRegression(linfo, nimages, minval, design, sigma, itr);
/*
** Output:
*/
VPrependAttr(out_list, "history", NULL, VAttrListRepn, history_list);
f = VOpenOutputFile(out_filename, TRUE);
if(!f)
VError(" error opening outout file %s", out_filename);
if(! VWriteFile(f, out_list))
exit(1);
fprintf(stderr, "%s: done.\n", argv[0]);
return 0;
}
int main(int argc, char *argv[]) {
VAttrList list, out_list;
VImage src;
VImage dest = NULL;
VAttrListPosn posn;
VString str;
int nimages;
char historystr[] = "history";
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "vdelcereb V%s", ver);
fprintf(stderr, "%s\n", prg_name);
/* Parse command line arguments: */
if(!VParseCommand(VNumber(options), options, &argc, argv) ||
! VIdentifyFiles(VNumber(options), options, "in", & argc, argv, 0) ||
! VIdentifyFiles(VNumber(options), options, "out", & argc, argv, -1))
goto Usage;
if(argc > 1) {
VReportBadArgs(argc, argv);
Usage:
VReportUsage(argv[0], VNumber(options), options, NULL);
exit(EXIT_FAILURE);
}
/* Read source image(s): */
if(strcmp(in_filename, "-") == 0)
in_file = stdin;
else {
in_file = fopen(in_filename, "r");
if(! in_file)
VError("Failed to open input file %s", in_filename);
}
if(!(list = VReadFile(in_file, NULL)))
exit(EXIT_FAILURE);
fclose(in_file);
/* Process image */
nimages = 0;
for(VFirstAttr(list, & posn); VAttrExists(& posn); VNextAttr(& posn)) {
if(VGetAttrRepn(& posn) != VImageRepn)
continue;
VGetAttrValue(& posn, NULL, VImageRepn, & src);
dest = VCerebellum(src);
VSetAttrValue(& posn, NULL, VImageRepn, dest);
VDestroyImage(src);
nimages++;
break;
}
/* Create outlist */
out_list = VCreateAttrList();
/* Make History */
VHistory(VNumber(options), options, prg_name, &list, &out_list);
/* Alle Attribute (ausser history:) in die neue Liste schreiben: */
for(VFirstAttr(list, &posn); VAttrExists(&posn); VNextAttr(&posn)) {
if(strncmp(VGetAttrName(&posn), historystr, strlen(historystr)) == 0)
continue;
switch(VGetAttrRepn(&posn)) {
case VImageRepn:
VGetAttrValue(&posn, NULL, VImageRepn, &src);
VAppendAttr(out_list, VGetAttrName(&posn), NULL, VImageRepn, src);
break;
case VStringRepn:
VGetAttrValue(&posn, NULL, VStringRepn, &str);
VAppendAttr(out_list, VGetAttrName(&posn), NULL, VImageRepn, str);
break;
default:
break;
}
}
/* Write the results to the output file: */
if(strcmp(out_filename, "-") == 0)
out_file = stdout;
else {
out_file = fopen(out_filename, "w");
if(! out_file)
VError("Failed to open output file %s", out_filename);
}
if(VWriteFile(out_file, out_list)) {
if(verbose >= 1)
fprintf(stderr, "%s: processed %d image%s.\n",
argv[0], nimages, nimages == 1 ? "" : "s");
fprintf(stderr, "%s: done.\n", argv[0]);
}
return 0;
}
