void VParseFilterCmd (int noptions, VOptionDescRec opts[],
int argc, char **argv, FILE **inp, FILE **outp)
{
static VStringConst in_file, out_file;
static VBoolean in_found, out_found;
static VOptionDescRec io_opts[] = {
{ "in", VStringRepn, 1, & in_file, & in_found, NULL, "Input file" },
{ "out", VStringRepn, 1, & out_file, & out_found, NULL, "Output file" }
};
int i, n;
VOptionDescRec options[100];
/* Check that number of options will not overflow the options array. */
if (noptions >= 98) {
VWarning("VParseFilterCmd: Too many options allowed");
noptions = 98;
}
/* Copy options into a new list and add the "in" and "out" options. */
n = 0;
if (inp)
options[n++] = io_opts[0];
if (outp)
options[n++] = io_opts[1];
for (i = 0; i < noptions; i++, n++)
options[n] = opts[i];
/* Parse command line arguments and identify the input and output files: */
if (! VParseCommand (n, options, & argc, argv) ||
(inp && ! VIdentifyFiles (n, options, "in", & argc, argv, 0)) ||
(outp && ! VIdentifyFiles (n, options, "out", & argc, argv, 1)))
goto Usage;
/* Any remaining unparsed arguments are erroneous: */
if (argc > 1) {
VReportBadArgs (argc, argv);
Usage: VReportUsage (argv[0], n, options,
inp ? (outp ? "[infile] [outfile]" : "[infile]") :
(outp ? "[outfile]" : NULL));
exit (EXIT_FAILURE);
}
/* Open the input and output files: */
if (inp)
*inp = VOpenInputFile (in_file, TRUE);
if (outp)
*outp = VOpenOutputFile (out_file, TRUE);
}
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;
}
/* the main routine */
int main (int argc,char *argv[]) {
QApplication::setColorSpec( QApplication::ManyColor );
/* initialize preferences variables */
pr = prefsini();
/* write out the revision string */
char prg_name[100];
char ver[100];
getLipsiaVersion(ver, sizeof(ver));
sprintf(prg_name, "vlview V%s", ver);
fprintf (stderr, "%s\n", prg_name);
/* Parse command line arguments and identify files: */
if (! VParseCommand (VNumber (options), options, & argc, argv) ||
! VIdentifyFiles (VNumber (options), options, "in", & argc, argv, 0))
goto Usage;
if (argc > 1) {
VReportBadArgs (argc, argv);
Usage: VReportUsage (argv[0], VNumber (options), options, NULL);
exit (EXIT_FAILURE);
}
/* A. Hagert: exceptions */
if (mincol == 123456 && maxcol == 123456) { pr->col_min = 0; pr->col_max = 0; }
else if (mincol != 123456 && maxcol == 123456)
{ printf("ERROR: maximum not given -> ignoring given minimum.\n"); pr->col_min = 0; pr->col_max = 0; }
else if (mincol == 123456 && maxcol != 123456)
{ printf("ERROR: minimum not given -> ignoring given maximum.\n"); pr->col_min = 0; pr->col_max = 0; }
else if (mincol<=maxcol) { pr->col_min=mincol; pr->col_max=maxcol; }
else { printf("ERROR: given minimum is higher than maximum -> ignoring both.\n");
pr->col_min = 0; pr->col_max = 0;
}
/* set verbose option to prefs */
pr->prg_name=prg_name;
pr->verbose=verbose;
pr->raw=rawfile;
pr->des=desfile;
pr->beta=betafile;
pr->colortable=colortable_filename;
pr->graph[0]=graphfile;
pr->files=0;
pr->infilenum=in_files.number;
pr->zmapfilenum=zmap_files.number;
pr->thresh=th11;
pr->background0=background[0];
pr->background1=background[1];
if (pr->infilenum > pr->zmapfilenum)
pr->files=pr->infilenum;
else
pr->files=pr->zmapfilenum;
if (pr->infilenum==0)
VError("No infile specified");
if (pr->files>1)
VError("Use 'vlv' for visualization of data sets > 1");
/* get the number of graphs (pr->g_number) */
myload_.testFiles();
/* initialize open the main window */
QApplication a( argc, argv );
lView ww;
a.setMainWidget( &ww );
ww.show();
return a.exec();
/* end of the program */
}
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;
}
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[]) {
/* 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);
}
