/*****************************************************************************
Major portions of this software are copyrighted by the Medical College
of Wisconsin, 1994-2000, and are released under the Gnu General Public
License, Version 2. See the file README.Copyright for details.
******************************************************************************/
/* Functional image is made by correlating refernce function from an ASCII
file with the series of images. All orthogonal ~ to a + b*x.
All is scaled accodingly to number of time points an independent
of referece function amplitude. Abs % change added.
Andre Jesmanowicz, MCW Milwaukee, 12.15.1992 */
#ifdef SPARKY
#undef _POSIX_SOURCE
#endif
#include <sys/types.h>
#include <stdio.h>
#include <math.h>
#include <ctype.h>
#include <sys/stat.h>
#include <stdlib.h>
#ifdef SYSV
#include <sys/fcntl.h>
#endif
#define min(a,b) ((a) < (b) ? (a) : (b))
#define max(a,b) ((a) > (b) ? (a) : (b))
#define EPX1 64 /* List of supported EPI image sizes */
#define EPY1 64 /* Each triple is: */
#define EPS1 (2*EPX1*EPY1) /* xsize, ysize, filesize */
#define EPX2 128
#define EPY2 128
#define EPS2 (2*EPX2*EPY2)
#define NOISE_THR 10. /* Minimum signal for delta comput */
#define SCALE 10000
#define D_COEF 1.
#define CORR ".CORR"
#define IM_HEIGHT 256
#define IM_ARR (IM_HEIGHT*IM_HEIGHT)
#define OFFSET (28*IM_HEIGHT) /* offset to data in 145408 bytes im */
#define H_SIZE (OFFSET+IM_ARR) /* 256x256 image with header */
#define IM_SIZE (2*H_SIZE)
#define SEQ_SIZE 1024 /* The length of reference sequence */
#define NF_MAX 1050 /* Max # of files */
#define EXT_FILES 1 /* Number of external func files */
extern double strtod();
char *ProgName, *SQ_name, *f_name[NF_MAX], **ptr, *file_out;
char *ort_name, file_CORR[256];
int ORT_ar[EXT_FILES][SEQ_SIZE], ORT_Nr[EXT_FILES], idot, isq;
float fORT[EXT_FILES][SEQ_SIZE], alpha, fdot, fsq, noise_thr;
int SQ_Nr, SQ_arr[SEQ_SIZE], n_ort;
int Im_frst = 0, npoints = 0, m_points;
int N_im, fsize, isize, ar_size, itmp;
short int *ar, tmp_ar[H_SIZE], corr_ar[H_SIZE];
float fSQ[SEQ_SIZE], ft[SEQ_SIZE], fSQ1[SEQ_SIZE], dt[SEQ_SIZE];
float fa, fb, fim[IM_ARR], amin, amax, ftmp, abmax, del_1, max_dev;
float pct = 30., pcc, fSQ_vl, fll, coef = D_COEF, fzz;
float fl_1ref, sq_1n, fcorr, max_cor, delr, next_cor = 0;;
FILE *fp;
int offs, normalize = 1, correl_im = 0, diff_im = 0;
int n_ess = 0;
/* --------------- */
main(argc,argv)
int argc;
char *argv[];
/* --------------- */
{
int i, j, m;
ProgName = argv[0];
if (argc < 2) Syntax();
noise_thr = NOISE_THR;
get_line_args(argc, argv);
if ( is_file(file_out) ) {
fprintf(stderr, "\n !!! Output file: %s exist. !!!\n", file_out);
Syntax();
}
/* Init to zero functional image */
for (i=0; i < IM_ARR; i++) fim[i] = 0.;
pcc = 1. - .01 * pct; /* Reference projection value (for rejecton) */
m_points = 0; /* considered time cours points */
idot = 0; /* set integral of ref to zero */
for (j=0; j < N_im; j++) {
if (SQ_arr[j] < 33333 ) {
idot += SQ_arr[j];
m_points++;
}
}
if ( m_points == 0) {
fprintf (stderr, "\n\n !!! Check reference file: %s !!!\n\n",SQ_name);
exit(-1);
}
sq_1n = 1./sqrt((double) m_points); /* points # normalizing coeff */
/* make reference function orthogonal to constant one */
fa = (float) idot / (float) m_points;
for (j=0; j < N_im; j++) {
if ( SQ_arr[j] < 33333 )
fSQ[j] = (float) SQ_arr[j] - fa;
else
fSQ[j] = 0.;
}
/* The same orthogoanlization to const for ref ort files */
for (m=0; m < n_ort; m++) {
idot = 0;
for (j=0; j < N_im; j++)
if (SQ_arr[j] < 33333 ) idot += ORT_ar[m][j];
fa = (float) idot / (float) m_points;
for (j=0; j < N_im; j++) {
if (SQ_arr[j] < 33333 )
fORT[m][j] = (float) ORT_ar[m][j] - fa;
else
fORT[m][j] = 0;
}
}
/* once othogonalized to const make orthogonalization to -ort files */
/* Temporarly single ort file case. AJ */
for (m=0; m < n_ort; m++) {
isq = 0; /* set integral to zero */
idot = 0;
for (j=0; j < N_im; j++) {
if (SQ_arr[j] < 33333 ) {
fdot += fSQ[j]*fORT[m][j];
fsq += fORT[m][j]*fORT[m][j];
}
}
if ( fsq == 0. ) {
fprintf (stderr, "\n\n !!! Orthogonal file #%d has zeros only !!!\n",
m+1);
exit(-3);
}
alpha = fdot / fsq;
for (j=0; j < N_im; j++)
if (SQ_arr[j] < 33333 ) fSQ[j] -= alpha * fORT[m][j];
}
/* normalize ref vector */
fSQ_vl = 0.;
for (j=0; j < N_im; j++) fSQ_vl += fSQ[j] * fSQ[j];
if (fSQ_vl < 1.e-10) {
fprintf (stderr, "\n\n !!! Too small variartion in reference file !!!\n\n");
exit(-1);
}
fl_1ref = 1./sqrt((double) fSQ_vl);
for (j=0; j < N_im; j++) fSQ1[j] = fSQ[j] * fl_1ref;
amin = 1.e37;
amax = -1.e37;
for (j=0; j < N_im; j++) {
if ( fSQ1[j] > amax ) amax = fSQ1[j];
if ( fSQ1[j] < amin ) amin = fSQ1[j];
}
del_1 = amax - amin; /* for reference of deviation */
max_dev = -1.e37; /* for max deviation of the function */
max_cor = 0.;
/* go over all pixels */
for (i=0; i < ar_size; i++) {
/* othogonalize (to const) data vector */
ftmp = 0; /* for average brightness */
for (j=0; j < N_im; j++) {
if ( SQ_arr[j] < 33333 ) {
dt[j] = ar[j*ar_size+i];
ftmp += dt[j];
}
}
fa = ftmp /(float) m_points; /* average value in data pixel */
if ( ftmp < 0 ) diff_im = 1; /* not regular images => no % of dev */
for (j=0; j < N_im; j++) {
if ( SQ_arr[j] < 33333 )
dt[j] -= fa;
else
dt[j] = 0.;
}
/* once data othogonalized to const make orthogonalization to ref files */
/* Temporarly single ort file case. AJ */
for (m=0; m < n_ort; m++) {
fdot = 0;
for (j=0; j < N_im; j++)
if ( SQ_arr[j] < 33333 ) fdot += dt[j] * fORT[m][j];
alpha = fdot / fsq;
for (j=0; j < N_im; j++)
if (SQ_arr[j] < 33333 ) dt[j] -= alpha * fORT[m][j];
}
/* normalize data vector */
fSQ_vl = 0.;
for (j=0; j < N_im; j++)
fSQ_vl += dt[j] * dt[j];
if (fSQ_vl < 1.e-10)
for (j=0; j < N_im; j++) ft[j] = 0.;
else {
fll = 1./sqrt(fSQ_vl);
for (j=0; j < N_im; j++)
ft[j] = dt[j] * fll;
}
/* make projection of normalized vectors */
fcorr = 0.;
for (j=0; j < N_im; j++) fcorr += ft[j] * fSQ1[j];
/* make correlation image */
corr_ar[i+offs] = fcorr * (float) SCALE;
/* make functional image for not too far data (correralte with normalized
vector) */
if ( (fb = fabs((double) fcorr)) > pcc ) {
for (j=0; j < N_im; j++) fim[i] += dt[j] * fSQ1[j];
if ( fa > noise_thr ) delr = del_1 * fim[i] / fa; /* rel change */
else delr = 0.;
if ( delr > max_dev ) max_dev = delr; /* max rel dev */
if ( fb > max_cor ) {
next_cor = max_cor;
max_cor = fb; /* max correl */
}
fim[i] *= fl_1ref; /* make a ratio rel to ref function */
n_ess++;
}
}
/* Make functional image independent of number of time course points.
Find min and max. */
amin = 1.e37;
amax = -1.e37;
for (i=0; i < ar_size; i++) {
if ( fim[i] > amax ) amax = fim[i];
if ( fim[i] < amin ) amin = fim[i];
}
fa = fabs((double) amax);
fb = fabs((double) amin);
abmax = max(fa, fb);
if (abmax < 1.e-10) {
fprintf (stderr, "\n !!! Check you reference and data files !!!");
fprintf (stderr, "\n !!! or increase value of -pcnt option. !!!");
fprintf (stderr, "\n !!! No variation in functional image. !!!");
fprintf (stderr, "\n !!! No output file created. !!!\n\n");
exit(-2);
}
if ( normalize ) fa = (float) SCALE / abmax;
else fa = coef;
printf ("\n Output file: %s\n", file_out);
printf (" Image data (relative to reference function):\n");
printf (" max value : %g , scaled : %g\n", amax, amax*fa);
printf (" min value : %g , scaled : %g\n", amin, amin*fa);
printf (" max variation : %g %%\n", max_dev*100.);
printf (" the best correlation: %g %%\n", max_cor*100.);
printf (" next to the best : %g %%\n", next_cor*100.);
printf (" number of essential pixels: %d\n", n_ess);
for (i=0; i < ar_size; i++) {
fzz = fim[i]*fa;
if ( fzz >= 0. ) tmp_ar[i+offs] = min((int) fzz, SCALE);
if ( fzz < 0. ) tmp_ar[i+offs] = max((int) fzz, -SCALE);
}
/* reload header (if present) to corr_ar */
for (i=0; i < offs; i++) corr_ar[i] = tmp_ar[i];
corr_ar[0+offs] = 0;
corr_ar[1+offs] = -SCALE;
corr_ar[2+offs] = SCALE; /* so color image will show zero as green */
tmp_ar[0+offs] = 0;
tmp_ar[1+offs] = -SCALE;
tmp_ar[2+offs] = SCALE; /* so color image will show zero as green */
/* Write functional image to file */
if (i = write_iqm(file_out, &fsize, tmp_ar) )
fprintf (stderr, "\n\n Error writing output_file: %s (will not overwrite) %d\n\n", file_out, i);
if (correl_im) {
strcpy(file_CORR, file_out);
strcat(file_CORR, CORR);
if (i = write_iqm(file_CORR, &fsize, corr_ar) )
fprintf (stderr, "\n\n Error writing output_file: %s (will not overwrite) %d\n\n", file_CORR, i);
}
exit(0) ;
}
/* ------------------------- */
get_line_args(argc, argv)
int argc;
char *argv[];
/* ------------------------- */
{
register int i, j, k, nopt, nnn;
int sp;
float ff;
n_ort = 0;
nopt = 0;
for (i = 1; i < argc; i++) { /* ------- Options ------- */
if (!strncmp(argv[i], "-h", 2)) { /* help */
Syntax();
}
if (strncmp(argv[i], "-non", 4) == 0) { /* don't normalize fim image */
normalize = 0;
nopt++;
continue;
}
if (strncmp(argv[i], "-corr", 4) == 0) { /* make correlation image */
correl_im = 1;
nopt++;
continue;
}
if (strncmp(argv [i], "-coe", 4) == 0) { /* extra coeff for im_out */
if (++i >= argc) { Syntax(); exit(2); }
ptr = argv;
coef = strtod(argv[i], ptr);
if ( **ptr ) {
fprintf (stderr, "\n !!! Wrong value in option -coef: %g !!!\n\n",
coef);
exit(1);
}
nopt++; nopt++;
continue;
}
if (strncmp(argv [i], "-im1", 4) == 0) { /* first image to count */
if (++i >= argc) { Syntax(); exit(2); }
ptr = argv;
Im_frst = strtod(argv[i], ptr) + .5;
if ( **ptr || (Im_frst < 1)) {
fprintf (stderr, "\n !!! First_image_# < 1 in -im1 !!!\n\n");
exit(1);
}
nopt++; nopt++;
continue;
}
if (strncmp(argv [i], "-ort", 4) == 0) { /* extra orthogonalize */
if (++i >= argc) { Syntax(); exit(2); }
ort_name = argv[i];
if ((fp = fopen(ort_name, "r")) == 0) {
fprintf(stderr,"\n !!! Problem opening ort file: %s !!!\n",
ort_name);
Syntax();
}
for(k=0; k < SEQ_SIZE; k++) /* Read sequence */
if (fscanf(fp, "%d", &ORT_ar[n_ort][k]) == EOF) break;
ORT_Nr[n_ort] = k;
if ( ORT_Nr[n_ort] == 0 ) {
fprintf(stderr,"\n !!! Problem reading %s file !!!\n", ort_name);
Syntax();
}
fclose(fp);
n_ort++;
nopt++; nopt++;
continue;
}
if (strncmp(argv [i], "-num", 4) == 0) {
if (++i >= argc) { Syntax(); exit(2); }
ptr = argv;
npoints = strtod(argv[i], ptr) + .5;
if ( **ptr || (npoints < 1)) {
fprintf (stderr, "\n !!! Too few images specified !!!\n\n");
exit(1); /* now symbolic for min npoints = 1 . AJ */
}
nopt++; nopt++;
continue;
}
if (strncmp(argv [i], "-pcnt", 5) == 0) {
if (++i >= argc) { Syntax(); exit(2); }
ptr = argv;
ff = strtod(argv[i], ptr);
if ( **ptr || (ff < .0) || (ff > 100.)) {
fprintf (stderr, "\n !!! %% accuracy in -pcnt out of range: %g !!!\n\n", ff);
exit(1);
}
pct = ff;
nopt++; nopt++;
continue;
}
if (strncmp(argv [i], "-list", 5) == 0) {
if (++i >= argc) { Syntax(); exit(2); }
ptr = argv;
ff = strtod(argv[i], ptr);
if ( **ptr || (ff < .0) ) {
fprintf (stderr, "\n !!! min_value in -list < 0 : %g !!!\n\n", ff);
exit(1);
}
noise_thr = ff;
nopt++; nopt++;
continue;
}
}
nopt++;
SQ_name = argv[nopt]; /* reference seqence file name */
if ((fp = fopen(SQ_name, "r")) == 0) {
fprintf(stderr,"\n !!! Problem opening sequence file: %s !!!\n", SQ_name);
Syntax();
}
for(k=0; k < SEQ_SIZE; k++) /* Read sequence */
if (fscanf(fp, "%d", &SQ_arr[k]) == EOF) break;
SQ_Nr = k;
if (SQ_Nr == 0) {
fprintf(stderr,"\n !!! Problem reading %s file !!!\n", SQ_name);
Syntax();
}
fclose(fp);
nopt++; /* Files to read (minimum one) */
if ( nopt > (argc-1) || nopt < (argc - NF_MAX) ) { /* Nr of files check */
fprintf (stderr, "\n Wrong # of files. %d files entered :\n", argc-nopt);
for(i=nopt, j=1; i < argc; i++, j++)
fprintf (stderr, " %3d - %s\n", j, argv[i]);
Syntax(); exit(2);
}
file_out = argv[argc-1];
N_im = argc-nopt-1; /* # of images */
if ( Im_frst > N_im ) {
fprintf (stderr, "\n !!! First_im_# %d in -im1 is bigger then number of images (%d) !!!\n\n", Im_frst, N_im);
Syntax(); exit(2);
}
for (i=0; i < N_im; i++) f_name[i] = argv[i+nopt];
for (i=0; i < Im_frst-1; i++) f_name[i] = f_name[Im_frst-1];
/* read and check the length of the first file for validity */
isize = 0;
fprintf(stderr, "\n\n Reading file %s\n", f_name[0]);
if (k = read_iqm(f_name[0], &isize, tmp_ar)) {
fprintf (stderr, "\n Problem with file: %s\n", f_name[0]);
Syntax(); exit(2);
}
if ( (isize != EPS1) && (isize != EPS2) && (isize != IM_SIZE) ) {
fprintf (stderr, "\n\n !!! File %s has wrong format !!!\n", f_name[0]);
Syntax(); exit(2);
}
fsize = isize;
if (fsize == IM_SIZE) {
ar_size = IM_ARR; /* 256x256 + header image */
offs = OFFSET;
}
else {
ar_size = fsize/2; /* AxA and no header */
offs = 0;
}
ar = (short int *) malloc((unsigned) ((ar_size*N_im)*sizeof(short int)));
for (i=0; i < ar_size; i++) ar[i] = tmp_ar[offs+i]; /* reload first image */
for (i=1; i < N_im; i++) { /* Read image files */
fprintf(stderr, " Reading file %s\n", f_name[i]);
isize = 0;
if ( k = read_iqm(f_name[i], &isize, tmp_ar) ) {
fprintf (stderr, "\n Problem with file: %s\n", f_name[i]);
Syntax(); exit(2);
}
if ( isize != fsize) { /* check lengthes of other files */
fprintf (stderr, "\n\n !!! File %s has different format !!!\n",
f_name[i]);
Syntax(); exit(2);
}
k = i*ar_size;
for (j=0; j < ar_size; j++) ar[k+j] = tmp_ar[offs+j]; /* reload data */
}
if (!npoints || npoints > N_im) npoints = N_im;
for (i=0; i < n_ort; i++) {
if ( ORT_Nr[i] < N_im ) {
fprintf(stderr,"\n !!! Orthogonal file # %d too short !!!\n", i);
exit(-4);
}
}
if ( SQ_Nr < N_im ) {
fprintf(stderr, "\n\n !!! Reference file to short. Add %d lines !!!\n\n",
N_im - SQ_Nr);
exit(-1);
}
}
/* ----------------------------------------------------------------
Read file subroutine fo use in C. A.Jesmanowicz, MCW 1991
return error : 0 - OK,
1 - opening problem,
2 - file longer then array.
fname : file name.
size : on input - max size of the arr or 0 for any length,
on output- real size of the file (and arr in bytes).
arr : returned file as array.
---------------------------------------------------------------- */
/* ----------------------------- */
int read_iqm(fname,size,arr)
int *size;
char fname[],arr[];
/* ----------------------------- */
{
int isize = *size;
int fp; /* file descriptor */
struct stat file_stat; /* status structure */
if ((fp = open(fname, O_RDONLY)) <= 0) /* file must exist */
return(1); /* or error = 1. */
fstat(fp, &file_stat); /* get file size in bytes */
if(file_stat.st_size > isize && isize) /* file can not be too long */
return(2); /* or error = 2. */
*size = file_stat.st_size; /* return file size */
read(fp, arr, file_stat.st_size); /* read whole file */
close(fp);
return(0); /* no error : 0 */
}
/* ----------------------------------------------------------------
Write file subroutine fo use in C. A.Jesmanowicz, MCW 1991
return error : 0 - OK,
1 - opening problem,
2 - negative length.
fname : file name.
size : size of the file.
arr : file array.
---------------------------------------------------------------- */
/* ----------------------------- */
int write_iqm(fname,size,arr)
int *size;
char fname[],arr[];
/* ----------------------------- */
{
int isize = *size;
int fp; /* file descriptor */
if(isize < 0) /* size has to be real */
return(2); /* or error = 2. */
if ((fp = open(fname, O_WRONLY|O_CREAT|O_EXCL,0444)) <= 0)
return(1); /* file must not exist */
/* or error = 1. */
write(fp, arr, isize); /* write whole file */
close(fp);
return(0);
}
/* ------------------ */ /* Check for unpleasant existence of output file */
int is_file(fname)
char *fname;
/* ------------------ */
{
FILE *fp;
if ( (fp = fopen(fname, "r")) != NULL ) { /* return = 1 if file exist */
fclose(fp);
return(1);
}
else
return(0);
}
/* ------------------- */
Syntax()
/* ------------------- */
{
fprintf (stderr, "\n\n %s makes functional image from time series of images and", ProgName);
fprintf (stderr, "\n reference (formated) functional-sequence file.");
fprintf (stderr, "\n Reference function is normalized before any correlation is done, so");
fprintf (stderr, "\n the results are proportional to the amplitude of functional changes.");
fprintf (stderr, "\n Additionally, output values are scaled to be independent of the number of");
fprintf (stderr, "\n used points in the reference functional-sequence file. Output data can");
fprintf (stderr, "\n be orthogonalized to additional external function using option -ort.");
fprintf (stderr, "\n Maximum number of external functios: %d", EXT_FILES);
fprintf (stderr, "\n Image resolusion: up to 256x256\n");
fprintf (stderr, "\n Usage: %s [options] func_seq_file file_1 [file_2 ... file_n] out_file\n", ProgName);
fprintf (stderr, "\n Where options are:\n");
fprintf (stderr, "\n -non - don't make normalization (def. normalize to %d)", SCALE);
fprintf (stderr, "\n -coef value - coefficient for output data (def. = %g)", D_COEF);
fprintf (stderr, "\n -im1 image_# - first image in time course. Previous images will be ");
fprintf (stderr, "\n filled with this one for proper timing of others.");
fprintf (stderr, "\n -num #_of_images - # of images in time course [2-%d].", NF_MAX);
fprintf (stderr, "\n -pcnt # - accuracy in %% of functional fit (def. = %g%%).", pct);
fprintf (stderr, "\n This value applies to the shape (not amplitude)");
fprintf (stderr, "\n and 30%% means that all data having correlation");
fprintf (stderr, "\n coefficient greater than .7 will be included.");
fprintf (stderr, "\n -ort file - additional function files to which data will be");
fprintf (stderr, "\n orthogonalized. Use one file with each option -ort .");
fprintf (stderr, "\n Maximum number of options -ort: %d .", EXT_FILES);
fprintf (stderr, "\n -corr - make image of correlation coefficients. Range -1 to 1");
fprintf (stderr, "\n is scaled to -/+ %d. The program will create second", SCALE);
fprintf (stderr, "\n output file with extention %s .", CORR);
fprintf (stderr, "\n -list min_value - make report for pixels brighter than min_value.");
fprintf (stderr, "\n Default min_value: %g", NOISE_THR);
fprintf (stderr, "\n\n Reference functional-sequence file can contain zero in each line for image");
fprintf (stderr, "\n with no action and value one for action. More complicated functions are OK.");
fprintf (stderr, "\n All values should be in the range -32768 to 32767. Any image can");
fprintf (stderr, "\n be discarded from computation by placing value 33,000 or more");
fprintf (stderr, "\n in equivalent line. Plot file of center pixel, made by program FD (using 'p')");
fprintf (stderr, "\n can be used as reference file too. AJ.");
fprintf (stderr, "\n\n");
exit(1);
}
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