rsZeropaddingParameters *rsZeropaddingParseParams(int argc, char * argv[]) {
rsZeropaddingParameters *p = rsZeropaddingInitParameters();
p->callString = rsMergeStringArray(argc, argv);
rsZeropaddingBuildInterface(p);
// parse
BOOL parsingSuccessful = rsUIParse(p->interface, argc, argv, (void*)p);
if ( ! parsingSuccessful ) {
return p;
}
// check if the required arguments have been provided
if ( p->inputpath == NULL ) {
fprintf(stderr, "No input volume specified!\n");
return p;
}
if ( p->outputpath == NULL ) {
fprintf(stderr, "An output volume must be specified!\n");
return p;
}
p->parametersValid = parsingSuccessful;
return p;
}
rsFitParameters *rsFitParseParams(int argc, char * argv[])
{
rsFitParameters *p = rsFitInitParameters();
p->callString = rsMergeStringArray(argc, argv);
rsFitBuildInterface(p);
// parse
BOOL parsingSuccessful = rsUIParse(p->interface, argc, argv, (void*)p);
if ( ! parsingSuccessful ) {
return p;
}
if ( p->inputpath == NULL ) {
fprintf(stderr, "No input volume specified(--input)!\n");
return p;
}
if ( p->targetpath == NULL ) {
fprintf(stderr, "No target volume specified(--target)!\n");
return p;
}
if ( p->betaspath == NULL ) {
fprintf(stderr, "No betas volume specified(--betas)!\n");
return p;
}
p->parametersValid = parsingSuccessful;
return p;
}
rsApplyTransformationParameters *rsApplyTransformationParseParams(int argc, char * argv[]) {
rsApplyTransformationParameters *p = rsApplyTransformationInitParameters();
p->callString = rsMergeStringArray(argc, argv);
rsApplyTransformationBuildInterface(p);
// parse
BOOL parsingSuccessful = rsUIParse(p->interface, argc, argv, (void*)p);
if ( ! parsingSuccessful ) {
return p;
}
// check if the required arguments have been provided
if (p->inputpath == NULL) {
fprintf(stderr, "No input volume specified!\n");
return p;
}
if (p->outputpath == NULL) {
fprintf(stderr, "An output volume must be specified!\n");
return p;
}
if (p->referencepath == NULL) {
fprintf(stderr, "A reference volume must be specified!\n");
return p;
}
if (p->transformations == NULL || g_strv_length(p->transformations) < 1) {
fprintf(stderr, "At least one transformation needs to be specified!\n");
return p;
}
if (p->coordinateSpaceTypeInput == NULL || strstr(p->coordinateSpaceTypeInput, "input") != NULL) {
p->coordinateSpaceType = -1;
} else if (strstr(p->coordinateSpaceTypeInput, "unknown") != NULL) {
p->coordinateSpaceType = NIFTI_XFORM_UNKNOWN;
} else if (strstr(p->coordinateSpaceTypeInput, "scanner") != NULL) {
p->coordinateSpaceType = NIFTI_XFORM_SCANNER_ANAT;
} else if (strstr(p->coordinateSpaceTypeInput, "aligned") != NULL) {
p->coordinateSpaceType = NIFTI_XFORM_ALIGNED_ANAT;
} else if (strstr(p->coordinateSpaceTypeInput, "talairach") != NULL) {
p->coordinateSpaceType = NIFTI_XFORM_TALAIRACH;
} else if (strstr(p->coordinateSpaceTypeInput, "mni") != NULL) {
p->coordinateSpaceType = NIFTI_XFORM_MNI_152;
} else {
fprintf(stderr, "'%s' is not a valid value for the coordinate space\n");
return p;
}
p->nTransformations = g_strv_length(p->transformations);
p->parametersValid = parsingSuccessful;
return p;
}
rsInfoParameters* rsInfoParseParams(int argc, char * argv[])
{
rsInfoParameters *p = rsInfoInitParameters();
rsInfoBuildInterface(p);
// parse
BOOL parsingSuccessful = rsUIParse(p->interface, argc, argv, (void*)p);
if ( ! parsingSuccessful ) {
return p;
}
// check if the required arguments have been provided
if ( p->inputpath == NULL ) {
fprintf(stderr, "No input volume specified(--input)!\n");
return p;
}
p->parametersValid = parsingSuccessful;
return p;
}
rsOrientationParameters *rsOrientationParseParams(int argc, char * argv[]) {
rsOrientationParameters *p = rsOrientationInitParameters();
p->callString = rsMergeStringArray(argc, argv);
rsOrientationBuildInterface(p);
// parse
BOOL parsingSuccessful = rsUIParse(p->interface, argc, argv, (void*)p);
if ( ! parsingSuccessful ) {
return p;
}
// check if the required arguments have been provided
if ( p->inputpath == NULL ) {
fprintf(stderr, "No input volume specified!\n");
return p;
}
if ( p->outputpath == NULL ) {
fprintf(stderr, "An output volume must be specified!\n");
return p;
}
if (p->orientation == NULL) {
p->orientation = "LPI";
}
BOOL validOrientation = strlen(p->orientation) == 3;
// validate and normalize orientation code
if (validOrientation) {
BOOL LRpresent = FALSE;
BOOL PApresent = FALSE;
BOOL ISpresent = FALSE;
// make all uppercase
p->orientation = rsString(p->orientation);
for(short i = 0; p->orientation[i]; i++){
p->orientation[i] = toupper(p->orientation[i]);
}
// check if we got a letter for each direction
for (short i=0; i<3; i++) {
const char code = p->orientation[i];
if (code=='L' || code=='R') {
LRpresent = TRUE;
} else if (code=='P' || code=='A') {
PApresent = TRUE;
} else if (code=='I' || code=='S') {
ISpresent = TRUE;
}
}
validOrientation = LRpresent && PApresent && ISpresent;
}
if (!validOrientation) {
fprintf(stderr, "The parameter --orientation (-a) needs to be a three letter code containing the letters (L, R, P, A, I, S)!\n");
return p;
}
p->parametersValid = parsingSuccessful;
return p;
}
