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);
}
