/*-----------------------------------------------------
Parameters:
Returns value:
Description
------------------------------------------------------*/
IMAGE *
ImageRead(const char*fname)
{
IMAGE *I = NULL ;
MATRIX *mat ;
FILE *fp ;
int type, frame ;
char buf[STRLEN] ;
strcpy(buf, fname) ; /* don't destroy callers string */
ImageUnpackFileName(buf, &frame, &type, buf) ;
switch (type)
{
case TIFF_IMAGE:
I = TiffReadImage(buf, frame) ;
if (I == NULL)
return(NULL) ;
break ;
case MATLAB_IMAGE:
DiagPrintf(DIAG_WRITE,
"ImageRead: buf=%s, frame=%d, type=%d (M=%d,H=%d)\n",
buf, frame, type , MATLAB_IMAGE, HIPS_IMAGE);
mat = MatlabRead(buf) ;
if (!mat)
ErrorReturn(NULL, (ERROR_NO_FILE, "ImageRead(%s) failed\n", buf)) ;
I = ImageFromMatrix(mat, NULL) ;
ImageInvert(I, I) ;
MatrixFree(&mat) ;
break ;
case HIPS_IMAGE:
fp = fopen(buf, "rb") ;
if (!fp)
ErrorReturn(NULL, (ERROR_NO_FILE, "ImageRead(%s, %d) failed\n",
buf, frame)) ;
I = ImageFRead(fp, buf, frame, 1) ;
fclose(fp) ;
break ;
case JPEG_IMAGE:
I = JPEGReadImage(buf);
break ;
case PGM_IMAGE:
I = PGMReadImage(buf);
break;
case PPM_IMAGE:
I = PPMReadImage(buf);
break;
case PBM_IMAGE:
I = PBMReadImage(buf);
break;
case RGBI_IMAGE:
I= RGBReadImage(buf);
default:
break ;
}
return(I) ;
}
/* --------------------------------------------- */
static int parse_commandline(int argc, char **argv) {
int nargc , nargsused;
char **pargv, *option ;
if (argc < 1) usage_exit();
nargc = argc;
pargv = argv;
while (nargc > 0) {
option = pargv[0];
if (debug) printf("%d %s\n",nargc,option);
nargc -= 1;
pargv += 1;
nargsused = 0;
if (!strcasecmp(option, "--help")) print_help() ;
else if (!strcasecmp(option, "--version")) print_version() ;
else if (!strcasecmp(option, "--debug")) debug = 1;
else if (!strcasecmp(option, "--checkopts")) checkoptsonly = 1;
else if (!strcasecmp(option, "--nocheckopts")) checkoptsonly = 0;
else if (!strcasecmp(option, "--synth")) synth = 1;
else if (!strcasecmp(option, "--nosynth")) synth = 0;
else if (!strcasecmp(option, "--mask-inv")) maskinv = 1;
else if (!strcasecmp(option, "--save-detrended")) SaveDetrended = 1;
else if (!strcasecmp(option, "--save-unmasked")) SaveUnmasked = 1;
else if (!strcasecmp(option, "--smooth-only")) SmoothOnly = 1;
else if (!strcasecmp(option, "--so")) SmoothOnly = 1;
else if (!strcasecmp(option, "--sqr")) DoSqr = 1;
else if (!strcasecmp(option, "--ispm")) InValsType = MRI_ANALYZE_FILE;
else if (!strcasecmp(option, "--ar2")) DoAR2 = 1;
else if (!strcasecmp(option, "--gdiag")) Gdiag_no = 1;
else if (!strcasecmp(option, "--i")) {
if (nargc < 1) CMDargNErr(option,1);
inpath = pargv[0];
nargsused = 1;
} else if (!strcasecmp(option, "--mask")) {
if (nargc < 1) CMDargNErr(option,1);
maskpath = pargv[0];
nargsused = 1;
} else if (!strcasecmp(option, "--mask-thresh")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%lf",&maskthresh);
nargsused = 1;
} else if (!strcasecmp(option, "--auto-mask")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%lf",&automaskthresh);
automask = 1;
nargsused = 1;
} else if (!strcasecmp(option, "--out-mask")) {
if (nargc < 1) CMDargNErr(option,1);
outmaskpath = pargv[0];
nargsused = 1;
} else if (!strcasecmp(option, "--sum")) {
if (nargc < 1) CMDargNErr(option,1);
sumfile = pargv[0];
nargsused = 1;
} else if (!strcasecmp(option, "--dat")) {
if (nargc < 1) CMDargNErr(option,1);
datfile = pargv[0];
nargsused = 1;
} else if (!strcasecmp(option, "--fwhm")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%lf",&infwhm);
ingstd = infwhm/sqrt(log(256.0));
nargsused = 1;
} else if (!strcasecmp(option, "--fwhmc")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%lf",&infwhmc);
ingstdc = infwhmc/sqrt(log(256.0));
nargsused = 1;
} else if (!strcasecmp(option, "--fwhmr")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%lf",&infwhmr);
ingstdr = infwhmr/sqrt(log(256.0));
nargsused = 1;
} else if (!strcasecmp(option, "--fwhms")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%lf",&infwhms);
ingstds = infwhms/sqrt(log(256.0));
nargsused = 1;
} else if (!strcasecmp(option, "--gstd")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%lf",&ingstd);
infwhm = ingstd*sqrt(log(256.0));
nargsused = 1;
} else if (!strcasecmp(option, "--to-fwhm")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%lf",&tofwhm);
nargsused = 1;
} else if (!strcasecmp(option, "--to-gstd")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%lf",&togstd);
tofwhm = togstd*sqrt(log(256.0));
nargsused = 1;
} else if (!strcasecmp(option, "--to-fwhm-tol")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%lf",&tofwhmtol);
nargsused = 1;
} else if (!strcasecmp(option, "--to-fwhm-nmax")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%d",&tofwhmnitersmax);
nargsused = 1;
} else if (!strcasecmp(option, "--to-fwhm-file")) {
if (nargc < 1) CMDargNErr(option,1);
tofwhmfile = pargv[0];
nargsused = 1;
} else if (!strcasecmp(option, "--nerode")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%d",&nerode);
nargsused = 1;
} else if (!strcasecmp(option, "--nframesmin")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%d",&nframesmin);
nargsused = 1;
} else if (!strcasecmp(option, "--synth-frames")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%d",&nframes);
synth = 1;
nargsused = 1;
} else if (!strcasecmp(option, "--seed")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%d",&SynthSeed);
synth = 1;
nargsused = 1;
} else if (!strcasecmp(option, "--tr")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%lf",&TR);
SetTR = 1;
nargsused = 1;
} else if (!strcasecmp(option, "--o")) {
if (nargc < 1) CMDargNErr(option,1);
outpath = pargv[0];
nargsused = 1;
} else if (!strcasecmp(option, "--ar1")) {
if (nargc < 1) CMDargNErr(option,1);
ar1path = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--sum2")) {
if (nargc < 1) CMDargNErr(option,1);
sum2file = pargv[0];
nargsused = 1;
} else if (!strcasecmp(option, "--X")) {
if (nargc < 1) CMDargNErr(option,1);
Xfile = pargv[0];
//X = MatrixReadTxt(Xfile, NULL);
X = MatlabRead(Xfile);
if (X == NULL) {
printf("ERROR: reading %s\n",Xfile);
exit(1);
}
nargsused = 1;
} else if (!strcasecmp(option, "--detrend")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%d",&DetrendOrder);
if (DetrendOrder > 2) {
printf("ERROR: cannot have detrending order > 2\n");
exit(1);
}
nargsused = 1;
} else if (!strcasecmp(option, "--in_nspmzeropad")) {
if (nargc < 1) CMDargNErr(option,1);
sscanf(pargv[0],"%d",&N_Zero_Pad_Input);
InValsType = MRI_ANALYZE_FILE;
nargsused = 1;
} else {
fprintf(stderr,"ERROR: Option %s unknown\n",option);
if (CMDsingleDash(option))
fprintf(stderr," Did you really mean -%s ?\n",option);
exit(-1);
}
nargc -= nargsused;
pargv += nargsused;
}
return(0);
}
