/* ------------------------------------------------------------------ */
static int parse_commandline(int argc, char **argv) {
int nargc , nargsused;
char **pargv, *option ;
DVT *dvttmp;
float ftmp[2000];
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, "--keepid")) KeepSubjId = 1;
else if (!strcmp(option, "--gdf")) {
if (nargc < 1) argnerr(option,1);
GDFile = pargv[0];
fsgd0 = gdfRead(GDFile,0);
if (fsgd0 == NULL) exit(1);
nargsused = 1;
} else if (!strcmp(option, "--dvt")) {
if (nargc < 1) argnerr(option,1);
DVTFile = pargv[0];
dvttmp = DVTread(DVTFile);
dvt0 = DVTtranspose(dvttmp);
DVTfree(&dvttmp);
nargsused = 1;
} else if (!strcmp(option, "--classes")) {
if (nargc < 1) argnerr(option,1);
while (nth_is_arg(nargc, pargv, nargsused)) {
ClassList[nClassList] = pargv[nargsused];
nClassList++;
nargsused++;
}
} else if (!strcmp(option, "--covar")) {
if (nargc < 1) argnerr(option,1);
while (nth_is_arg(nargc, pargv, nargsused)) {
CovarList[nCovarList] = pargv[nargsused];
nCovarList++;
nargsused++;
}
} else if (!strcmp(option, "--covarprune")) {
if (nargc < 3) argnerr(option,3);
CovarPrune[nCovarPrune].Covar = pargv[0];
sscanf(pargv[1],"%f",&CovarPrune[nCovarPrune].Min);
sscanf(pargv[2],"%f",&CovarPrune[nCovarPrune].Max);
if (CovarPrune[nCovarPrune].Min > CovarPrune[nCovarPrune].Max) {
printf("ERROR: covarprune min > max\n");
exit(1);
}
nCovarPrune++;
nargsused = 3;
} else if (!strcmp(option, "--depvar")) {
if (nargc < 1) argnerr(option,1);
while (nth_is_arg(nargc, pargv, nargsused)) {
DepVarList[nDepVarList] = pargv[nargsused];
nDepVarList++;
nargsused++;
}
} else if (!strcmp(option, "--wdepvar")) {
if (nargc < 1) argnerr(option,1);
while (nth_is_arg(nargc, pargv, nargsused)) {
sscanf(pargv[nargsused],"%f",&ftmp[nwDepVar]);
nwDepVar++;
nargsused++;
}
wDepVar = (float *)calloc(sizeof(float),nwDepVar);
memmove(wDepVar,ftmp,sizeof(float)*nwDepVar);
} else if (!strcmp(option, "--wlms")) {
if (nargc < 1) argnerr(option,1);
WLMSDepVar = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--wclass")) {
if (nargc < 1) argnerr(option,1);
while (nth_is_arg(nargc, pargv, nargsused)) {
sscanf(pargv[nargsused],"%f",&ftmp[nwClass]);
nwClass++;
nargsused++;
}
wClass = (float *)calloc(sizeof(float),nwClass);
memmove(wClass,ftmp,sizeof(float)*nwClass);
} else if (!strcmp(option, "--wcovar")) {
if (nargc < 1) argnerr(option,1);
while (nth_is_arg(nargc, pargv, nargsused)) {
sscanf(pargv[nargsused],"%f",&ftmp[nwCovar]);
nwCovar++;
nargsused++;
}
wCovar = (float *)calloc(sizeof(float),nwCovar+1);
memmove(&wCovar[1],ftmp,sizeof(float)*nwCovar);
wCovar[0] = 0.0;
//Note: the first weight is for offset
} else if (!strcmp(option, "--testoffset")) TestOffset = 1;
else if (!strcmp(option, "--o")) {
if (nargc < 1) argnerr(option,1);
OutBase = pargv[0];
nargsused = 1;
} else {
fprintf(stderr,"ERROR: Option %s unknown\n",option);
if (singledash(option))
fprintf(stderr," Did you really mean -%s ?\n",option);
exit(-1);
}
nargc -= nargsused;
pargv += nargsused;
}
return(0);
}
/* ------------------------------------------------------------------ */
static int parse_commandline(int argc, char **argv) {
int i, nargc , nargsused;
char **pargv, *option ;
char tmpstr[1000];
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, "--abs")) DoAbs = 1;
else if (!strcasecmp(option, "--nogmnnorm")) gmnnorm = 0;
else if (!strcasecmp(option, "--rescale")) rescale=1;
else if (!strcasecmp(option, "--norescale")) rescale=0;
else if (!strcasecmp(option, "--no-output")) NoOutput = 1;
else if (!strcasecmp(option, "--fft")) UseFFT = 1;
else if (!strcasecmp(option, "--offset")) AddOffset=1;
else if (!strcasecmp(option, "--offset-mid")){
AddOffset = 1;
OffsetFrame = -1;
}
else if (!strcmp(option, "--hsc")) {
if (nargc < 2) argnerr(option,2);
sscanf(pargv[0],"%lf",&HSCMin);
sscanf(pargv[1],"%lf",&HSCMax);
DoHSC = 1;
nargsused = 2;
}
else if (!strcmp(option, "--sum2")) {
if (nargc < 1) argnerr(option,1);
sum2file = pargv[0];
pdfname = "delta";
//NoOutput = 1;
nframes = 1;
nargsused = 1;
}
else if (!strcmp(option, "--hsynth")) {
// eres mask DoTnorm out
if (nargc < 3) argnerr(option,3);
mri = MRIread(pargv[0]);
mask = MRIread(pargv[1]);
sscanf(pargv[2],"%d",&DoTNorm);
mri2 = fMRIhsynth(mri, mask, DoTNorm);
MRIwrite(mri2,pargv[3]);
exit(0);
nargsused = 2;
}
else if (!strcmp(option, "--vol") || !strcmp(option, "--o")) {
if (nargc < 1) argnerr(option,1);
volid = pargv[0];
nargsused = 1;
if (nth_is_arg(nargc, pargv, 1)) {
volfmt = pargv[1];
nargsused ++;
volfmtid = checkfmt(volfmt);
}
}
else if (!strcmp(option, "--temp") || !strcmp(option, "--template")) {
if(DoCurv){
printf("ERROR: cannot use --temp and --curv\n");
exit(1);
}
if(nargc < 1) argnerr(option,1);
tempid = pargv[0];
nargsused = 1;
if (nth_is_arg(nargc, pargv, 1)) {
tempfmt = pargv[1];
nargsused ++;
tempfmtid = checkfmt(tempfmt);
} else tempfmtid = getfmtid(tempid);
} else if (!strcmp(option, "--curv")) {
if(tempid != NULL){
printf("ERROR: cannot use --temp and --curv\n");
exit(1);
}
if(nargc < 2) argnerr(option,2);
subject = pargv[0];
hemi = pargv[1];
DoCurv = 1;
nargsused = 2;
sprintf(tmpstr,"%s/%s/surf/%s.thickness",getenv("SUBJECTS_DIR"),subject,hemi);
tempid = strcpyalloc(tmpstr);
} else if ( !strcmp(option, "--dim") ) {
if (nargc < 4) argnerr(option,4);
for (i=0;i<4;i++) sscanf(pargv[i],"%d",&dim[i]);
nargsused = 4;
dimSpeced = 1;
}
else if ( !strcmp(option, "--nframes") ) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%d",&nframes);
nargsused = 1;
}
else if ( !strcmp(option, "--TR") || !strcmp(option, "--tr") ) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%lf",&TR);
nargsused = 1;
}
else if ( !strcmp(option, "--res") ) {
if (nargc < 4) argnerr(option,4);
for (i=0;i<4;i++) sscanf(pargv[i],"%f",&res[i]);
nargsused = 4;
resSpeced = 1;
}
else if ( !strcmp(option, "--vox-size") ) {
if (nargc < 3) argnerr(option,3);
for (i=0;i<3;i++) sscanf(pargv[i],"%f",&res[i]);
nargsused = 4;
resSpeced = 1;
NewVoxSizeSpeced = 1;
}
else if ( !strcmp(option, "--c_ras") ) {
if (nargc < 3) argnerr(option,3);
for (i=0;i<3;i++) sscanf(pargv[i],"%f",&cras[i]);
nargsused = 3;
}
else if ( !strcmp(option, "--p0") ) {
if (nargc < 3) argnerr(option,3);
for (i=0;i<3;i++) sscanf(pargv[i],"%f",&p0[i]);
usep0 = 1;
nargsused = 3;
}
else if ( !strcmp(option, "--cdircos") ) {
if (nargc < 3) argnerr(option,3);
for (i=0;i<3;i++) sscanf(pargv[i],"%f",&cdircos[i]);
nargsused = 3;
} else if ( !strcmp(option, "--rdircos") ) {
if (nargc < 3) argnerr(option,3);
for (i=0;i<3;i++) sscanf(pargv[i],"%f",&rdircos[i]);
nargsused = 3;
} else if ( !strcmp(option, "--sdircos") ) {
if (nargc < 3) argnerr(option,3);
for (i=0;i<3;i++) sscanf(pargv[i],"%f",&sdircos[i]);
nargsused = 3;
} else if ( !strcmp(option, "--fwhm") ) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%f",&fwhm);
gstd = fwhm/sqrt(log(256.0));
nargsused = 1;
} else if (!strcmp(option, "--precision")) {
if (nargc < 1) argnerr(option,1);
precision = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--seed")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%ld",&seed);
nargsused = 1;
} else if (!strcmp(option, "--seedfile")) {
if (nargc < 1) argnerr(option,1);
seedfile = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--pdf")) {
if (nargc < 1) argnerr(option,1);
pdfname = pargv[0];
nargsused = 1;
} else if (!strcmp(option, "--bb")) {
if (nargc < 6) argnerr(option,6);
sscanf(pargv[0],"%d",&boundingbox.x);
sscanf(pargv[1],"%d",&boundingbox.y);
sscanf(pargv[2],"%d",&boundingbox.z);
sscanf(pargv[3],"%d",&boundingbox.dx);
sscanf(pargv[4],"%d",&boundingbox.dy);
sscanf(pargv[5],"%d",&boundingbox.dz);
pdfname = "boundingbox";
nargsused = 6;
}
else if (!strcasecmp(option, "--checker"))
pdfname = "checker";
else if (!strcmp(option, "--dof-num")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%d",&numdof);
nargsused = 1;
} else if (!strcmp(option, "--val-a")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%lf",&ValueA);
nargsused = 1;
} else if (!strcmp(option, "--val-b")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%lf",&ValueB);
nargsused = 1;
} else if (!strcmp(option, "--radius")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%lf",&voxradius);
nargsused = 1;
} else if (!strcmp(option, "--dof-den") || !strcmp(option, "--dof")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%d",&dendof);
nargsused = 1;
} else if (!strcmp(option, "--gmean")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%lf",&gausmean);
nargsused = 1;
} else if (!strcmp(option, "--gstd")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%lf",&gausstd);
nargsused = 1;
} else if (!strcmp(option, "--delta-crsf")) {
if (nargc < 4) argnerr(option,4);
sscanf(pargv[0],"%d",&delta_crsf[0]);
sscanf(pargv[1],"%d",&delta_crsf[1]);
sscanf(pargv[2],"%d",&delta_crsf[2]);
sscanf(pargv[3],"%d",&delta_crsf[3]);
delta_crsf_speced = 1;
nargsused = 4;
} else if (!strcmp(option, "--delta-val")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%lf",&delta_value);
nargsused = 1;
} else if (!strcmp(option, "--delta-val-off")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%lf",&delta_off_value);
nargsused = 1;
} else if (!strcmp(option, "--spike")) {
if (nargc < 1) argnerr(option,1);
sscanf(pargv[0],"%d",&SpikeTP);
nargsused = 1;
} else {
fprintf(stderr,"ERROR: Option %s unknown\n",option);
if (singledash(option))
fprintf(stderr," Did you really mean -%s ?\n",option);
exit(-1);
}
nargc -= nargsused;
pargv += nargsused;
}
return(0);
}
