int main (int argc, char *argv[]) { /*************/ /* image I/O */ /*************/ FILE *fp_img, *fp_out; IFH ifh; char imgfile[MAXL], outfile[MAXL], imgroot[MAXL], outroot[MAXL]; char *str, command[MAXL], program[MAXL]; /**************/ /* processing */ /**************/ char control = '\0'; int dimension, c, i, j, k; int imgdim[4], orient, isbig; float voxdim[3], voxdimn[3]; float *imgz, *imgp; double q; /*********/ /* flags */ /*********/ int status = 0; int p_flag = 0; int two_sided = 0; int defined; int debug = 0; printf ("%s\n", rcsid); setprog (program, argv); /************************/ /* process command line */ /************************/ for (k = 0, i = 1; i < argc; i++) { if (*argv[i] == '-') { strcpy (command, argv[i]); str = command; while (c = *str++) switch (c) { case 'd': debug++; break; case 'p': p_flag++; break; case '2': two_sided++; break; case '@': control = *str++; *str = '\0'; break; } } else switch (k) { case 0: getroot (argv[i], imgroot); k++; break; } } if (k < 1) usage (program); /**************************/ /* get input 4dfp z-image */ /**************************/ sprintf (imgfile, "%s.4dfp.img", imgroot); if (get_4dfp_dimoe (imgfile, imgdim, voxdim, &orient, &isbig) < 0) errr (program, imgfile); if (Getifh (imgfile, &ifh)) errr (program, imgfile); if (!control) control = (isbig) ? 'b' : 'l'; dimension = imgdim[0] * imgdim[1] * imgdim[2]; if (!(imgz = (float *) malloc (dimension * sizeof (float)))) errm (program); if (!(imgp = (float *) malloc (dimension * sizeof (float)))) errm (program); /***************************/ /* prepare 4dfp read/write */ /***************************/ fprintf (stdout, "Reading: %s\n", imgfile); if (!(fp_img = fopen (imgfile, "rb"))) errr (program, imgfile); sprintf (outroot, "%s_%s", imgroot, (p_flag) ? "p" : "log10p"); sprintf (outfile, "%s.4dfp.img", outroot); fprintf (stdout, "Writing: %s\n", outfile); if (!(fp_out = fopen (outfile, "wb"))) errw (program, outfile); /***********/ /* process */ /***********/ for (j = 0; j < imgdim[3]; j++) { if (eread (imgz, dimension, isbig, fp_img)) errr (program, imgfile); for (i = 0; i < dimension; i++) { q = (double) imgz[i]; defined = !isnan (q) && imgz[i] != (float) 1.e-37 && finite (q); if (defined) { if (two_sided) { q = fabs (q); imgp[i] = (p_flag) ? 2.*p_z (q) : (-1./M_LN10)*(lnp_z (q) + M_LN2); } else { if (q > 0) { imgp[i] = (p_flag) ? p_z (q) : (-1./M_LN10)*lnp_z (q); } else { imgp[i] = (p_flag) ? 1.0 : 0.0; } } } else { imgp[i] = 1.e-37; } } if (ewrite (imgp, dimension, control, fp_out)) errw (program, outfile); } if (fclose (fp_img)) errr (program, imgfile); if (fclose (fp_out)) errw (program, outfile); /*******/ /* ifh */ /*******/ if (Writeifh (program, outfile, &ifh, control)) errw (program, outroot); /*******/ /* hdr */ /*******/ sprintf (command, "ifh2hdr %s", outroot); status |= system (command); /*******/ /* rec */ /*******/ startrece (outfile, argc, argv, rcsid, control); catrec (imgfile); endrec (); free (imgz); free (imgp); exit (status); }
int main (int argc, char *argv[]) { FILE *fp; IFH ifh; char imgroot[2][MAXR][MAXL], Nmgroot[2][MAXL], lstfile[2][MAXL]; int nimg[2], isbig[2][MAXR], isbigN[2]; int orient, orient1, imgdim[4], imgdim1[4], dimension, vdim; char outroot[MAXL] = "", imgfile[MAXL], outfile[MAXL]; float voxdim[3], voxdim1[3]; float amin = FLT_MAX, amax = -FLT_MAX; float *img1, **imgN; double **imgs, **imgv; int **imgm, ngroup; char control = '\0'; /***********/ /* utility */ /***********/ double u; int c, i, j, k, m; char *ptr, *str, command[MAXL]; char *srgv[MAXL]; /* string field pointers */ /*********/ /* flags */ /*********/ int defined; int debug = 0; int NaN_flag = 'E'; /* 'E' 1.e-37; 'Z' 0.0; 'N' NaN; */ int status = 0; int saverec = 1; printf ("%s\n", rcsid); setprog (program, argv); /************************/ /* process command line */ /************************/ k = 0; for (i = 1; i < argc; i++) { if (*argv[i] == '-') { strcpy (command, argv[i]); ptr = command; while (c = *ptr++) switch (c) { case 'R': saverec = 0; break; case 'd': debug++; break; case 'o': getroot (ptr, outroot); *ptr = '\0'; break; case '@': control = *ptr++; *ptr = '\0'; break; } } else switch (k) { case 0: strcpy (lstfile[0], argv[i]); k++; break; case 1: getroot (argv[i], Nmgroot[0]); k++; break; case 2: strcpy (lstfile[1], argv[i]); k++; break; case 3: getroot (argv[i], Nmgroot[1]); k++; break; } } if (k != 2 && k != 4) usage (); ngroup = k/2; /********************/ /* parse list files */ /********************/ for (k = 0; k < ngroup; k++) { nimg[k] = 0; if (!(fp = fopen (lstfile[k], "r"))) errr (program, lstfile[k]); printf ("Reading: %s\n", lstfile[k]); while (fgets (command, MAXL, fp)) { if (nimg[k] >= MAXR) { fprintf (stderr, "%s: maximum number of input images (%d) exceeded\n", program, MAXR); exit (-1); } if (ptr = strchr (command, '#')) *ptr = '\0'; if (!strlen (command)) continue; /* skip blank lines */ if (ptr = strchr (command, '\n')) *ptr = '\0'; /* strip terminal nl */ i = m = 0; while (m < MAXL && i < MAXL) { while (!isgraph ((int) command[i]) && command[i]) i++; if (!command[i]) break; srgv[m++] = command + i; while (isgraph ((int) command[i])) i++; if (!command[i]) break; command[i++] = '\0'; } getroot (srgv[0], imgroot[k][nimg[k]++]); } fclose (fp); if (!nimg[k]) usage (); /*********************************/ /* check dimensional consistency */ /*********************************/ for (i = 0; i < nimg[k]; i++) { printf ("image %3d: %s\n", i + 1, imgroot[k][i]); if (!i && !k) { if (get_4dfp_dimoe (imgroot[k][i], imgdim, voxdim, &orient, isbig[k] + i)) exit (-1); if (Getifh (imgroot[k][i], &ifh)) errr (program, imgroot[k][i]); } else { if (get_4dfp_dimoe (imgroot[k][i], imgdim1, voxdim1, &orient1, isbig[k] + i)) exit (-1); status = (orient1 != orient); for (j = 0; j < 4; j++) status |= (imgdim1[j] != imgdim[j]); for (j = 0; j < 3; j++) status |= (fabs (voxdim1[j] - voxdim[j]) > 1.e-4); } if (status) { fprintf (stderr, "%s: %s %s dimension mismatch\n", program, imgroot[0][0], imgroot[k][i]); exit (-1); } } if (get_4dfp_dimoe (Nmgroot[k], imgdim1, voxdim1, &orient1, isbigN + k)) exit (-1); status = (orient1 != orient); for (j = 0; j < 3; j++) status |= (imgdim1[j] != imgdim[j]); for (j = 0; j < 3; j++) status |= (fabs (voxdim1[j] - voxdim[j]) > 1.e-4); if (status) { fprintf (stderr, "%s: %s %s dimension mismatch\n", program, imgroot[0][0], Nmgroot[k]); exit (-1); } } if (!control) control = (isbig[0][0]) ? 'b' : 'l'; vdim = imgdim[0]*imgdim[1]*imgdim[2]; dimension = vdim*imgdim[3]; if (!(img1 = (float *) calloc (dimension, sizeof (float)))) errm (program); imgv = calloc_double2 (ngroup, dimension); /* variance accumulator */ imgs = calloc_double2 (ngroup, dimension); /* sum accumulator */ imgm = calloc_int2 (ngroup, dimension); /* voxel counter */ imgN = calloc_float2 (ngroup, vdim); /* input N image */ for (k = 0; k < ngroup; k++) { /****************/ /* read N image */ /****************/ printf ("Reading: %s\n", Nmgroot[k]); sprintf (imgfile, "%s.4dfp.img", Nmgroot[k]); if (!(fp = fopen (imgfile, "rb")) || eread (imgN[k], vdim, isbigN[k], fp) || fclose (fp)) errr (program, imgfile); /**********************************/ /* read and accumulate image data */ /**********************************/ for (j = 0; j < nimg[k]; j++) { printf ("Reading: %s\n", imgroot[k][j]); sprintf (imgfile, "%s.4dfp.img", imgroot[k][j]); if (!(fp = fopen (imgfile, "rb")) || eread (img1, dimension, isbig[k][j], fp) || fclose (fp)) errr (program, imgfile); for (i = 0; i < dimension; i++) { defined = isnormal (img1[i]) && img1[i] != (float) 1.e-37; if (!defined) continue; imgm[k][i]++; imgs[k][i] += img1[i]; imgv[k][i] += img1[i]*img1[i]; } } for (i = 0; i < dimension; i++) { u = (imgs[k][i] /= imgm[k][i]); imgv[k][i] -= u*u*imgm[k][i]; if (imgv[k][i] < 0.0) imgv[k][i] = 0.0; imgv[k][i] /= (imgm[k][i] - 1); } /***************************************/ /* divide variance estimate by N image */ /***************************************/ for (i = 0; i < vdim; i++) if (imgN[k][i]) for (j = 0; j < imgdim[3]; j++) { imgv[k][j*vdim + i] /= imgN[k][i]; } } /***************************************************************************/ /* compute voxelwize t statistic (Welch's approximate t' when ngroup == 2) */ /***************************************************************************/ for (i = 0; i < dimension; i++) { if (ngroup == 2) { imgs[0][i] -= imgs[1][i]; imgv[0][i] += imgv[1][i]; } if (isnormal (imgs[0][i]) && isnormal (imgv[0][i])) { img1[i] = imgs[0][i] / sqrt (imgv[0][i]); if (img1[i] > amax) amax = img1[i]; if (img1[i] < amin) amin = img1[i]; } else switch (NaN_flag) { case 'Z': img1[i] = 0.0; break; case 'E': img1[i] = (float) 1.e-37; break; case 'N': img1[i] = rnan (); break; } } if (!strlen (outroot)) { /*******************/ /* compute outroot */ /*******************/ strcpy (command, lstfile[0]); if (!(ptr = strrchr (command, '/'))) ptr = command; else ptr++; if (str = strrchr (ptr, '.')) *str = '\0'; sprintf (outroot, "RFX_%s", ptr); if (ngroup == 2) { strcat (outroot, "_vs_"); strcpy (command, lstfile[1]); if (!(ptr = strrchr (command, '/'))) ptr = command; else ptr++; if (str = strrchr (ptr, '.')) *str = '\0'; strcat (outroot, ptr); } strcat (outroot, "_tmap"); } sprintf (outfile, "%s.4dfp.img", outroot); /****************/ /* write result */ /****************/ printf ("Writing: %s\n", outfile); if (!(fp = fopen (outfile, "wb")) || ewrite (img1, dimension, control, fp) || fclose (fp)) errw (program, outfile); /*******/ /* ifh */ /*******/ Writeifh (program, outfile, &ifh, control); /*******/ /* hdr */ /*******/ sprintf (command, "ifh2hdr %s -r%.0fto%.0f", outroot, amin, amax); printf ("%s\n", command); status |= system (command); /*******/ /* rec */ /*******/ startrecle (outfile, argc, argv, rcsid, control); for (k = 0; k < ngroup; k++) { sprintf (command, "imglist %d\n", k + 1); printrec (command); catrec (lstfile[k]); printrec ("endimglist\n"); if (saverec) { sprintf (imgfile, "%s.4dfp.img", Nmgroot[k]); catrec (imgfile); for (j = 0; j < nimg[k]; j++) { sprintf (imgfile, "%s.4dfp.img", imgroot[k][j]); catrec (imgfile); } } } endrec (); free (img1); free_double2 (imgs); free_double2 (imgv); free_int2 (imgm); free_float2 (imgN); exit (status); }
int main (int argc, char *argv[]) { /*******/ /* i/o */ /*******/ FILE *fpimg, *fpout; IFH ifh; struct dsr hdr; /* ANALYZE hdr */ char imgroot[MAXL], imgfile[MAXL], outfile[MAXL]; char trailer[8] = ".4dint"; /****************/ /* image arrays */ /****************/ float *imgf, cscale = 1.0; short int *imgi=NULL; unsigned char *imgu=NULL; float voxsiz[3]; int imgdim[4], vdim, orient, isbig; int imin = 32767, imax = -32768; char control = '\0'; short int origin[3]; /* used in SPM99 conversions */ /***********/ /* utility */ /***********/ int c, i, j, k; char *str, command[MAXL], program[MAXL]; /*********/ /* flags */ /*********/ int uchar = 0; int debug = 0; int spm99 = 0; int swab_flag = 0; fprintf (stdout, "%s\n", rcsid); setprog (program, argv); /************************/ /* process command line */ /************************/ for (k = 0, i = 1; i < argc; i++) { if (*argv[i] == '-') { strcpy (command, argv[i]); str = command; while ((c = *str++)) switch (c) { case '8': uchar++; strcpy (trailer, "_8bit"); break; case 'd': debug++; break; case 'c': cscale = atof (str); *str = '\0'; break; case 'S': if (!strcmp (str, "PM99")) spm99++; *str = '\0'; break; case '@': control = *str++; *str = '\0'; break; } } else switch (k) { case 0: getroot (argv[i], imgroot); k++; break; } } if (k < 1) { printf ("Usage:\t%s <(4dfp) filename>\n", program); printf ("\toption\n"); printf ("\t-c<flt>\tscale output values by specified factor\n"); printf ("\t-8\toutput 8 bit unsigned char\n"); printf ("\t-SPM99\tinclude origin and scale in hdr (http:/wideman-one.com/gw/brain/analyze/format.doc)\n"); printf ("\t-@<b|l>\toutput big or little endian (default CPU endian)\n"); exit (1); } /*****************************/ /* get input 4dfp dimensions */ /*****************************/ if (get_4dfp_dimoe (imgroot, imgdim, voxsiz, &orient, &isbig)) errr (program, imgroot); vdim = imgdim[0] * imgdim[1] * imgdim[2]; if (uchar) { if (!(imgu = (unsigned char *) malloc (vdim * sizeof (char)))) errm (program); } else { if (!(imgi = (short *) malloc (vdim * sizeof (short)))) errm (program); } if (!(imgf = (float *) malloc (vdim * sizeof (float)))) errm (program); /*************************/ /* open input and output */ /*************************/ sprintf (imgfile, "%s.4dfp.img", imgroot); printf ("Reading: %s\n", imgfile); if (!(fpimg = fopen (imgfile, "rb"))) errr (program, imgfile); sprintf (outfile, "%s%s.img", imgroot, trailer); if (!(fpout = fopen (outfile, "wb"))) errw (program, outfile); printf ("Writing: %s\n", outfile); /**********************/ /* process all frames */ /**********************/ for (k = 0; k < imgdim[3]; k++) { if (eread (imgf, vdim, isbig, fpimg)) errr (program, imgfile); switch (orient) { case 4: flipx (imgf, imgdim + 0, imgdim + 1, imgdim + 2); /* sagittal */ case 3: flipz (imgf, imgdim + 0, imgdim + 1, imgdim + 2); /* coronal */ case 2: flipy (imgf, imgdim + 0, imgdim + 1, imgdim + 2); /* transverse */ break; default: fprintf (stderr, "%s: %s image orientation not recognized\n", program, imgfile); exit (-1); break; } for (i = 0; i < vdim; i++) { j = nint (cscale*imgf[i]); if (debug) printf ("%10.6f%10d\n", imgf[i], j); if (uchar) { if (j < 0) j = 0; if (j > 255) j = 255; imgu[i] = j; } else { imgi[i] = j; } if (j > imax) imax = j; if (j < imin) imin = j; } if (uchar) { if (fwrite ( imgu, sizeof (char), vdim, fpout) != vdim) errw (program, outfile); } else { if (gwrite ((char *) imgi, sizeof (short), vdim, fpout, control)) errw (program, outfile); } } fclose (fpimg); fclose (fpout); /**************************/ /* create ANALYZE 7.5 hdr */ /**************************/ Inithdr (&hdr, imgdim, voxsiz, ""); if (uchar) { hdr.dime.datatype = 2; /* unsigned char */ hdr.dime.bitpix = 8; } else { hdr.dime.datatype = 4; /* signed integer */ hdr.dime.bitpix = 16; } hdr.dime.glmax = imax; hdr.dime.glmin = imin; hdr.hist.orient = orient - 2; swab_flag = ((CPU_is_bigendian() != 0) && (control == 'l' || control == 'L')) || ((CPU_is_bigendian() == 0) && (control == 'b' || control == 'B')); if (spm99) { if (Getifh (imgroot, &ifh)) errr (program, imgroot); for (i = 0; i < 3; i++) origin[i] = 0.4999 + ifh.center[i]/ifh.mmppix[i]; /*************************************************/ /* flip 4dfp->analyze assuming transverse orient */ /*************************************************/ origin[1] = imgdim[1] + 1 - origin[1]; /*******************************************************************/ /* origin field officially text and so not affected by swab_hdr () */ /*******************************************************************/ if (swab_flag) for (i = 0; i < 3; i++) swab2 ((char *) (origin + i)); memcpy ((char *) &hdr + 253, (char *) origin, 3*sizeof (short int)); memcpy ((char *) &hdr + 112, (char *) &cscale, sizeof (float)); hdr.hk.extents = 0; } if (swab_flag) swab_hdr (&hdr); sprintf (outfile, "%s%s.hdr", imgroot, trailer); printf ("Writing: %s\n", outfile); if (!(fpout = fopen (outfile, "wb")) || fwrite (&hdr, sizeof (struct dsr), 1, fpout) != 1 || fclose (fpout)) errw (program, outfile); /*******************/ /* create rec file */ /*******************/ sprintf (outfile, "%s%s.img", imgroot, trailer); startrece (outfile, argc, argv, rcsid, control); sprintf (command, "Voxel values scaled by %f\n", cscale); printrec (command); catrec (imgfile); endrec (); free (imgf); if (uchar) { free (imgu); } else { free (imgi); } exit (0); }
int main (int argc, char *argv[]) { /************/ /* 4dfp I/O */ /************/ FILE *fp_img, *fp_out; IFH ifh; char outfile[MAXL], imgfile[MAXL]; char imgroot[MAXL], outroot[MAXL] = ""; char control = '\0'; /****************/ /* image arrays */ /****************/ float *img1, *imgc; float voxdim[3]; int imgdim[4], outdim[4], ix, iy, iz, index, vdim, isbig; int ix0 = 1, ix1 = 0, iy0 = 1, iy1 = 0, iz0 = 1, iz1 = 0; int vdim_crop, orient; /***********/ /* utility */ /***********/ int c, i, j, k; char *ptr, string[MAXL]; /*********/ /* flags */ /*********/ int doflip = 0; int docrop = 1; int scrollx = 0, scrolly = 0, scrollz = 0; printf ("%s\n", rcsid); setprog (program, argv); /************************/ /* process command line */ /************************/ for (k = 0, i = 1; i < argc; i++) { if (*argv[i] == '-') { strcpy (string, argv[i]); ptr = string; while (c = *ptr++) switch (c) { case 'f': doflip++; break; case 'Z': docrop = 0; break; case '@': control = *ptr++; *ptr = '\0'; break; case 'x': getirange (ptr, &ix0, &ix1); *ptr = '\0'; break; case 'y': getirange (ptr, &iy0, &iy1); *ptr = '\0'; break; case 'z': getirange (ptr, &iz0, &iz1); *ptr = '\0'; break; case 's': switch (*ptr++) { case 'x': scrollx = atoi (ptr); break; case 'y': scrolly = atoi (ptr); break; case 'z': scrollz = atoi (ptr); break; } *ptr = '\0'; break; } } else switch (k) { case 0: getroot (argv[i], imgroot); k++; break; case 1: getroot (argv[i], outroot); k++; break; } } if (k < 1) { printf ("Usage:\t%s <(4dfp) inroot> [(4dfp) outroot]\n", program); printf ("\toption\n"); printf ("\t-<x|y|z><int>[to[<int>]\tspecify x y z crop limits\n"); printf ("\t-s<x|y|z><int>\tscroll specified axis by specified number of pixels\n"); printf ("\t-f\tinterpret specifications under 4dfp<->analyze flips\n"); printf ("\t-Z\tzero voxels instead of physically cropping\n"); printf ("\t-@<b|l>\toutput big or little endian (default input endian)\n"); printf ("N.B.:\tcrop limit indices count from 1\n"); printf ("N.B.:\tscrolling is done after cropping\n"); printf ("N.B.:\tdefault (4dfp) output root is <(4dfp) inroot>\"_crop\"\n"); exit (1); } sprintf (imgfile, "%s.4dfp.img", imgroot); if (get_4dfp_dimoe (imgfile, imgdim, voxdim, &orient, &isbig) < 0 || Getifh (imgfile, &ifh)) errr (program, imgfile); if (!control) control = (isbig) ? 'b' : 'l'; printf ("input dimensions %10d%10d%10d%10d\n", imgdim[0], imgdim[1], imgdim[2], imgdim[3]); printf ("voxel dimensions %10.6f%10.6f%10.6f\n", voxdim[0], voxdim[1], voxdim[2]); if (ix1 > imgdim[0] || ix1 < 1) ix1 = imgdim[0]; if (iy1 > imgdim[1] || iy1 < 1) iy1 = imgdim[1]; if (iz1 > imgdim[2] || iz1 < 1) iz1 = imgdim[2]; if (ix0 > imgdim[0] || ix0 < 1) ix0 = 1; if (iy0 > imgdim[1] || iy0 < 1) iy0 = 1; if (iz0 > imgdim[2] || iz0 < 1) iz0 = 1; if (ix1 < ix0) {k = ix1; ix1 = ix0; ix0 = k;} if (iy1 < iy0) {k = iy1; iy1 = iy0; iy0 = k;} if (iz1 < iz0) {k = iz1; iz1 = iz0; iz0 = k;} printf ("crop limits x %3d to %3d\n", ix0, ix1); printf ("crop limits y %3d to %3d\n", iy0, iy1); printf ("crop limits z %3d to %3d\n", iz0, iz1); printf ("scroll x %3d\n", scrollx); printf ("scroll y %3d\n", scrolly); printf ("scroll z %3d\n", scrollz); outdim[0] = (docrop) ? ix1 - ix0 + 1 : imgdim[0]; outdim[1] = (docrop) ? iy1 - iy0 + 1 : imgdim[1]; outdim[2] = (docrop) ? iz1 - iz0 + 1 : imgdim[2]; outdim[3] = imgdim[3]; printf ("output dimensions %10d%10d%10d%10d\n", outdim[0], outdim[1], outdim[2], outdim[3]); vdim = imgdim[0] * imgdim[1] * imgdim[2]; if (!(img1 = (float *) malloc (vdim * sizeof (float)))) errm (program); if (!(fp_img = fopen (imgfile, "rb"))) errr (program, imgfile); printf ("Reading: %s\n", imgfile); if (!strlen (outroot)) sprintf (outroot, "%s_crop", imgroot); sprintf (outfile, "%s.4dfp.img", outroot); vdim_crop = outdim[0] * outdim[1] * outdim[2]; if (!(imgc = (float *) calloc (vdim_crop, sizeof (float)))) errm (program); if (!(fp_out = fopen (outfile, "wb"))) errw (program, outfile); printf ("Writing: %s\n", outfile); /***********/ /* process */ /***********/ printf ("processing volume"); for (k = 0; k < imgdim[3]; k++) {printf (" %d", k + 1); fflush (stdout); if (eread (img1, vdim, isbig, fp_img)) errr (program, imgfile); if (doflip) { if (x4dfp2analyze (img1, imgdim, ifh.orientation)) { fprintf (stderr, "%s: invalid %s orientation\n", program, imgroot); exit (-1); } } i = 0; for (iz = iz0 - 1; iz < iz1; iz++) { for (iy = iy0 - 1; iy < iy1; iy++) { for (ix = ix0 - 1; ix < ix1; ix++) { index = ix + imgdim[0]*(iy + imgdim[1]*iz); if (docrop) { imgc[i++] = img1[index]; } else { imgc[index] = img1[index]; } }}} if (scrollx) xscroll (img1, imgc, outdim, scrollx); if (scrolly) yscroll (img1, imgc, outdim, scrolly); if (scrollz) zscroll (img1, imgc, outdim, scrollz); if (doflip) x4dfp2analyze (imgc, outdim, ifh.orientation); if (ewrite (imgc, vdim_crop, control, fp_out)) errw (program, outfile); } printf ("\n"); fflush (stdout); fclose (fp_img); fclose (fp_out); /**************/ /* output ifh */ /**************/ if (docrop) { if (writeifhe (program, outroot, outdim, voxdim, ifh.orientation, control)) errw (program, outroot); } else { Writeifh (program, outroot, &ifh, control); } /***************/ /* run ifh2hdr */ /***************/ sprintf (string, "ifh2hdr %s", outroot); status |= system (string); /************/ /* rec file */ /************/ startrece (outfile, argc, argv, rcsid, control); if (doflip) printrec ("indices subjected to 4dfp<->analyze orientation dependent flips\n"); if (!docrop) printrec ("voxels zeroed instead of physically cropped\n"); sprintf (string, "crop limits x %3d to %3d\n", ix0, ix1); printrec (string); sprintf (string, "crop limits y %3d to %3d\n", iy0, iy1); printrec (string); sprintf (string, "crop limits z %3d to %3d\n", iz0, iz1); printrec (string); if (scrollx) {sprintf (string, "scroll x %3d\n", scrollx); printrec (string);} if (scrolly) {sprintf (string, "scroll y %3d\n", scrolly); printrec (string);} if (scrollz) {sprintf (string, "scroll z %3d\n", scrollz); printrec (string);} catrec (imgfile); endrec (); /************/ /* clean up */ /************/ free (img1); free (imgc); exit (status); }
int main (int argc, char **argv) { /*************/ /* image I/O */ /*************/ FILE *fp_img, *fp_out; IFH ifh; char imgfile[MAXL], imgroot[MAXL]; char outfile[MAXL], outroot[MAXL] = ""; /**************/ /* processing */ /**************/ int imgdim[4], dimension, orient, isbig; float voxdim[3]; float *imgr; float thresh=0.0; char control ='\0'; /***********/ /* utility */ /***********/ int c, i, k; char *ptr, command[MAXL], program[MAXL]; /*********/ /* flags */ /*********/ int status = 0; printf ("%s\n", rcsid); setprog (program, argv); /************************/ /* process command line */ /************************/ for (k = 0, i = 1; i < argc; i++) { if (i > 1 && *argv[i] == '-') { strcpy (command, argv[i]); ptr = command; while ((c = *ptr++)) switch (c) { case '@': control = *ptr++; *ptr = '\0'; break; } } else switch (k) { case 0: thresh = atof (argv[i]); k++; break; case 1: getroot (argv[i], imgroot); k++; break; case 2: getroot (argv[i], outroot); k++; break; } } if (k < 2) { printf ("Usage: %s <flt> <file_4dfp> [outroot]\n", program); printf (" option\n"); printf (" -@<b|l>\toutput big or little endian (default input endian)\n"); printf ("e.g., %s 90 pt349_study9to9\n", program); printf ("e.g., %s 90 pt349_study9to9 pt349_study9to9z\n", program); printf ("N.B.: default output 4dfp root is <file_4dfp>\"z\"\n"); exit (1); } sprintf (imgfile, "%s.4dfp.img", imgroot); /***************************************/ /* create output filename if not given */ /***************************************/ if (!strlen (outroot)) sprintf (outroot, "%sz", imgroot); sprintf (outfile, "%s.4dfp.img", outroot); /*****************************/ /* get 4dfp input dimensions */ /*****************************/ if (get_4dfp_dimoe (imgfile, imgdim, voxdim, &orient, &isbig) < 0) errr (program, imgroot); if (Getifh (imgfile, &ifh)) errr (program, imgroot); if (!control) control = (isbig) ? 'b' : 'l'; dimension = imgdim[0] * imgdim[1] * imgdim[2]; /*****************/ /* alloc buffers */ /*****************/ if (!(imgr = (float *) malloc (dimension * sizeof (float)))) errm (program); /***********/ /* process */ /***********/ if (!(fp_img = fopen (imgfile, "rb"))) errr (program, imgfile); if (!(fp_out = fopen (outfile, "wb"))) errw (program, outfile); fprintf (stdout, "Reading: %s\n", imgfile); fprintf (stdout, "Writing: %s\n", outfile); for (k = 0; k < imgdim[3]; k++) { if (gread ((char *) imgr, sizeof (float), dimension, fp_img, isbig)) errr (program, imgfile); for (i = 0; i < dimension; i++) if (imgr[i] < thresh) imgr[i] = 0.0; if (gwrite ((char *) imgr, sizeof (float), dimension, fp_out, control)) errw (program, outfile); } fclose (fp_img); fclose (fp_out); /***************/ /* ifh and hdr */ /***************/ if (Writeifh (program, outfile, &ifh, control)) errw (program, outfile); sprintf (command, "ifh2hdr %s", outroot); printf ("%s\n", command); status = system (command); /*******************/ /* create rec file */ /*******************/ startrece (outfile, argc, argv, rcsid, control); catrec (imgfile); endrec (); free (imgr); exit (status); }