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[]) { 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_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 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[]) { 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); }
int main(int argc, char *argv[]) { static VArgVector in_files1; static VArgVector in_files2; static VArgVector mask_file; static VArgVector report_file; static VOptionDescRec options[] = { { "in1", VStringRepn, 0, & in_files1, VRequiredOpt, NULL, "Input files 1" }, { "in2", VStringRepn, 0, & in_files2, VRequiredOpt, NULL, "Input files 2" }, { "report", VStringRepn, 0, & report_file, VRequiredOpt, NULL, "Report file" }, { "mask", VStringRepn, 0, & mask_file, VRequiredOpt, NULL, "Mask file(s)" } }; FILE *fp = NULL; VStringConst in_filename; VAttrList list1, list2, list3; VAttrListPosn posn; VString str; VImage src, *src1, *src2, *mask; int i, nimages = 0, mimages = 0; char prg_name[100]; char ver[100]; getLipsiaVersion(ver, sizeof(ver)); sprintf(prg_name, "vROIpaired_ttest V%s", ver); fprintf(stderr, "%s\n", prg_name); if(!VParseCommand(VNumber(options), options, & argc, argv)) { VReportUsage(argv[0], VNumber(options), options, NULL); exit(0); } /* get number of input images */ nimages = in_files1.number; if(in_files2.number != nimages) VError(" inconsistent number of files: in1: %d, in2: %d ", nimages, in_files2.number); mimages = mask_file.number; if(nimages != mimages && mimages > 1) VError(" inconsistent number of files, images: %d, masks: %d", nimages, mimages); /* images 1 */ src1 = (VImage *) VMalloc(sizeof(VImage) * nimages); for(i = 0; i < nimages; i++) { src1[i] = NULL; in_filename = ((VStringConst *) in_files1.vector)[i]; fp = VOpenInputFile(in_filename, TRUE); if(!fp) VError("Error opening file %s", in_filename); list1 = VReadFile(fp, NULL); if(! list1) VError("Error reading file %s", in_filename); 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; } src1[i] = src; break; } if(src1[i] == NULL) VError(" no contrast image found in %s", in_filename); } /* images 2 */ src2 = (VImage *) VMalloc(sizeof(VImage) * nimages); for(i = 0; i < nimages; i++) { src2[i] = NULL; in_filename = ((VStringConst *) in_files2.vector)[i]; fp = VOpenInputFile(in_filename, TRUE); if(!fp) VError("Error opening file %s", in_filename); list2 = VReadFile(fp, NULL); if(! list2) VError("Error reading file %s", in_filename); 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; } src2[i] = src; break; } if(src2[i] == NULL) VError(" no contrast image found in %s", in_filename); } for(i = 0; i < nimages; i++) { fprintf(stderr, "%3d: %s %s\n", i, ((VStringConst *) in_files1.vector)[i], ((VStringConst *) in_files2.vector)[i]); } fprintf(stderr, "\n"); /* mask images */ mask = (VImage *) VMalloc(sizeof(VImage) * mimages); for(i = 0; i < mimages; i++) { mask[i] = NULL; in_filename = ((VStringConst *) mask_file.vector)[i]; fp = VOpenInputFile(in_filename, TRUE); if(!fp) VError("Error opening file %s", in_filename); list3 = VReadFile(fp, NULL); if(! list3) VError("Error reading file", in_filename); fclose(fp); for(VFirstAttr(list3, & posn); VAttrExists(& posn); VNextAttr(& posn)) { if(VGetAttrRepn(& posn) != VImageRepn) continue; VGetAttrValue(& posn, NULL, VImageRepn, & src); if(VPixelRepn(src) != VUByteRepn) mask[i] = VConvertImageCopy(src, NULL, VAllBands, VUByteRepn); else mask[i] = src; break; } if(mask[i] == NULL) VError(" mask %d not found", i); } /* open report_file */ fp = NULL; in_filename = ((VStringConst *) report_file.vector)[0]; fp = fopen(in_filename, "w"); if(!fp) VError(" error opening file %s", in_filename); /* paired t-test in ROIs */ VROIpaired_ttest(src1, src2, mask, nimages, mimages, fp); exit(0); }
int main(int argc, char *argv[]) { /* Command line options: */ static VString mat = NULL; static VBoolean funconly = FALSE; static VOptionDescRec options[] = { {"out", VStringRepn, 1, &mat, VRequiredOpt, 0, "Matfile"}, {"funconly", VBooleanRepn, 1, &funconly, VOptionalOpt, 0, "Functional data only (in one single 4D-object)"}, }; FILE *in_file; VAttrList in_list; VAttrListPosn posn; VImage src = NULL; VBit *bit_pp = NULL, *pbSRC = NULL; VShort *short_pp = NULL, *psSRC = NULL; VUByte *ubyte_pp = NULL, *puSRC = NULL; VFloat *float_pp = NULL, *pfSRC = NULL; VDouble *double_pp = NULL, *pdSRC = NULL; VString mode = NULL, name = NULL; mxArray *SRC = NULL; MATFile *fp; int n = 0, dims[4]; int bands = 0, rows = 0, cols = 0; char prg_name[100]; char ver[100]; getLipsiaVersion(ver, sizeof(ver)); sprintf(prg_name, "vtomat 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 */ NULL); /* Read the input file */ in_list = VReadFile(in_file, NULL); if(!in_list) exit(1); /* strings */ mode = (VString)malloc(sizeof(char)); name = (VString)malloc(sizeof(char) * 50); strcpy(mode, "w"); fp = matOpen(mat, mode); if(funconly == TRUE) { /******************************************************************* * * * L O O P over objects in vista file * * * *******************************************************************/ n = 0; for(VFirstAttr(in_list, & posn); VAttrExists(& posn); VNextAttr(& posn)) { if(VGetAttrRepn(& posn) != VImageRepn) continue; VGetAttrValue(& posn, NULL, VImageRepn, & src); if(VPixelRepn(src) == VShortRepn) { if(bands < 2) bands = VImageNBands(src); if(rows < 2) rows = VImageNRows(src); if(cols < 2) cols = VImageNColumns(src); if(bands != VImageNBands(src)) VError("Different bands in functional objects"); if(rows != VImageNRows(src)) VError("Different rows in functional objects"); if(cols != VImageNColumns(src)) VError("Different cols in functional objects"); n++; } } /*dimensions */ dims[3] = n; dims[2] = bands; dims[1] = rows; dims[0] = cols; SRC = mxCreateNumericArray(4, dims, mxINT16_CLASS, mxREAL); psSRC = (VShort *) mxGetPr(SRC); /* copy data to SRC */ for(VFirstAttr(in_list, & posn); VAttrExists(& posn); VNextAttr(& posn)) { if(VGetAttrRepn(& posn) != VImageRepn) continue; VGetAttrValue(& posn, NULL, VImageRepn, & src); if(VPixelRepn(src) == VShortRepn) { short_pp = (VShort *) VPixelPtr(src, 0, 0, 0); memcpy(psSRC, short_pp, sizeof(VShort) * dims[0] * dims[1] * dims[2]); psSRC += dims[0] * dims[1] * dims[2]; } } /* save data into file */ if(matPutVariable(fp, "fnc", SRC)) VError("Could not save data in MATLAB file"); /* destroy array */ mxDestroyArray(SRC); } else { /******************************************************************* * * * L O O P over objects in vista file * * * *******************************************************************/ n = 0; for(VFirstAttr(in_list, & posn); VAttrExists(& posn); VNextAttr(& posn)) { if(VGetAttrRepn(& posn) != VImageRepn) continue; VGetAttrValue(& posn, NULL, VImageRepn, & src); /*dimensions */ dims[3] = 1; dims[2] = VImageNBands(src); dims[1] = VImageNRows(src); dims[0] = VImageNColumns(src); sprintf(name, "obj%d\0", n); /* Bit ONLY */ if(VPixelRepn(src) == VBitRepn) { SRC = mxCreateNumericArray(3, dims, mxLOGICAL_CLASS, mxREAL); pbSRC = (VBit *) mxGetPr(SRC); bit_pp = (VBit *) VPixelPtr(src, 0, 0, 0); memcpy(pbSRC, bit_pp, sizeof(VBit) * dims[0] * dims[1] * dims[2]); } /* Short ONLY */ if(VPixelRepn(src) == VShortRepn) { SRC = mxCreateNumericArray(3, dims, mxINT16_CLASS, mxREAL); psSRC = (VShort *) mxGetPr(SRC); short_pp = (VShort *) VPixelPtr(src, 0, 0, 0); memcpy(psSRC, short_pp, sizeof(VShort) * dims[0] * dims[1] * dims[2]); } /* UByte ONLY */ if(VPixelRepn(src) == VUByteRepn) { SRC = mxCreateNumericArray(3, dims, mxUINT8_CLASS, mxREAL); puSRC = (VUByte *) mxGetPr(SRC); ubyte_pp = (VUByte *) VPixelPtr(src, 0, 0, 0); memcpy(puSRC, ubyte_pp, sizeof(VUByte) * dims[0] * dims[1] * dims[2]); } /* Float ONLY */ if(VPixelRepn(src) == VFloatRepn) { SRC = mxCreateNumericArray(3, dims, mxSINGLE_CLASS, mxREAL); pfSRC = (VFloat *) mxGetPr(SRC); float_pp = (VFloat *) VPixelPtr(src, 0, 0, 0); memcpy(pfSRC, float_pp, sizeof(VFloat) * dims[0] * dims[1] * dims[2]); } /* Double ONLY */ if(VPixelRepn(src) == VDoubleRepn) { SRC = mxCreateNumericArray(3, dims, mxDOUBLE_CLASS, mxREAL); pdSRC = (VDouble *) mxGetPr(SRC); double_pp = (VDouble *) VPixelPtr(src, 0, 0, 0); memcpy(pdSRC, double_pp, sizeof(VDouble) * dims[0] * dims[1] * dims[2]); } /* save data into file */ if(matPutVariable(fp, name, SRC)) VError("Could not save data in MATLAB file"); /* destroy array */ mxDestroyArray(SRC); n++; } } /* Terminate */ matClose(fp); return 0; }