int main(int argc, char **argv)
{
FSLIO* fslio;
void *buffer=NULL;
char *hdrxml, *filename;
int fileread=1, filetype=-1, existingimage=0;
size_t bufsize=0;
short x,y,z,v, dt=-1;
if (argc<2)
usage();
if ((argc==3) || (argc==4)) {
/* use the XML form of header specification */
filename = argv[2];
} else {
filename = argv[13];
}
/* check if file already exists and if so, read the image contents */
/* also store the size of this buffer for later in case it is wrong */
if (FslFileExists(filename)) {
/* buffer = FslReadAllVolumes(fslio,filename); */
existingimage = 1;
fslio = FslOpen(filename,"rb");
FslGetDim(fslio,&x,&y,&z,&v);
filetype = FslGetFileType(fslio);
bufsize = x * y * z * v * (FslGetDataType(fslio,&dt) / 8);
buffer = (void *) calloc(bufsize,1);
FslReadVolumes(fslio,buffer,v);
FslClose(fslio);
}
if (existingimage) {
fslio = FslXOpen(filename,"wb",filetype);
} else {
fslio = FslOpen(filename,"wb");
filetype = FslGetFileType(fslio);
}
if (FslBaseFileType(FslGetFileType(fslio))==FSL_TYPE_MINC) {
fprintf(stderr,"Minc file type is not supported yet\n");
exit(EXIT_FAILURE);
}
if (argc>3) {
/* set uninteresting defaults */
if (existingimage) {
FslSetDataType(fslio,dt);
} else {
FslSetDataType(fslio,atoi(argv[12]));
}
FslSetDim(fslio,atoi(argv[1]),atoi(argv[2]),atoi(argv[3]),atoi(argv[4]));
FslSetVoxDim(fslio,atof(argv[5]),atof(argv[6]),atof(argv[7]),atof(argv[8]));
{
short short_array[100];
short_array[0]=atoi(argv[9]);
short_array[1]=atoi(argv[10]);
short_array[2]=atoi(argv[11]);
if ( (short_array[0]!=0) || (short_array[1]!=0) || (short_array[2]!=0) )
{
FslSetAnalyzeSform(fslio,short_array,
atof(argv[5]),atof(argv[6]),atof(argv[7]));
}
}
} else {
/* read XML form */
char *newstr, *oldfname, *oldiname;
FILE *fileptr=NULL;
if (strcmp(argv[1],"-")==0) {fileread=0;}
newstr = (char *)calloc(10000,1);
oldfname = (char *)calloc(10000,1);
oldiname = (char *)calloc(10000,1);
hdrxml = (char *)calloc(65534,1); /* too long, to be safe */
if (fileread) {
fileptr = fopen(argv[1],"rb");
if (fileptr==NULL) {
fprintf(stderr,"Cannot open file %s\n",argv[1]);
exit(EXIT_FAILURE);
}
}
do {
/* read string from file or stdin */
if (fileread) {
if (fgets(newstr,9999,fileptr)==NULL) break;
} else {
if (fgets(newstr,9999,stdin)==NULL) break;
}
strcat(hdrxml,newstr);
} while (strcmp(newstr + strlen(newstr) - 2,"/>")!=0);
strcpy(oldfname,fslio->niftiptr->fname);
strcpy(oldiname,fslio->niftiptr->iname);
fslio->niftiptr = nifti_image_from_ascii(hdrxml);
if (fslio->niftiptr == NULL) {
fprintf(stderr,"Incomplete or incorrect text: could not form header info\n");
exit(EXIT_FAILURE);
}
fslio->niftiptr->fname = oldfname;
fslio->niftiptr->iname = oldiname;
free(hdrxml);
if (fileread) fclose(fileptr);
}
/* reset filetype and datatype in case it has been overwritten */
FslSetFileType(fslio,filetype);
if (existingimage) {
/* dt is only set if an image was previously read */
FslSetDataType(fslio,dt);
}
/* swap bytes */
fslio->niftiptr->byteorder = short_order();
/* if (strcmp(argv[argc-1],"-r")==0) { */
/* /\* swap *\/ */
/* if (short_order()==MSB_FIRST) fslio->niftiptr->byteorder = LSB_FIRST; */
/* else fslio->niftiptr->byteorder = MSB_FIRST; */
/* } */
/* write header */
FslWriteHeader(fslio);
/* if previously read buffer is wrong size then make a zero image here */
FslGetDim(fslio,&x,&y,&z,&v);
if ( bufsize != ( x * y * z * v * (FslGetDataType(fslio,&dt)/8)) ) {
if (bufsize>0) free(buffer); /* only if previously read */
buffer = (void *) calloc(x * y * z * v,FslGetDataType(fslio,&dt)/8);
}
/* write the data out - either from previous read or zeros */
FslWriteVolumes(fslio,buffer,fslio->niftiptr->dim[4]);
FslClose(fslio);
exit(0);
}
int main(int argc, char * argv[]) {
FSLIO *fslio;
FSLIO *fslioOutput;
void *buffer;
void *outputBuffer;
size_t buffsize;
char *inputpath = NULL;
char *outputpath = NULL;
char *maskpath = NULL;
int x=-1, y=-1, z=-1, t=0;
short xDim, yDim, zDim, vDim;
size_t pixtype;
short dt;
float inter = 0.0, slope = 1.0;
BOOL verbose = FALSE;
int threads = 1;
int ac;
if( argc < 2 ) {
rsMaskPrintHelp();
return 1;
}
/* parse parameters */
for( ac = 1; ac < argc; ac++ ) {
if( ! strncmp(argv[ac], "-h", 2) ) {
rsMaskPrintHelp();
return 1;
} else if ( ! strcmp(argv[ac], "-input") ) {
if( ++ac >= argc ) {
fprintf(stderr, "** missing argument for -input\n");
return 1;
}
inputpath = argv[ac]; /* no string copy, just pointer assignment */
} else if ( ! strncmp(argv[ac], "-m", 2) ) {
if( ++ac >= argc ) {
fprintf(stderr, "** missing argument for -m[ask]\n");
return 1;
}
maskpath = argv[ac]; /* no string copy, just pointer assignment */
} else if ( ! strncmp(argv[ac], "-v", 2) ) {
verbose = TRUE;
} else if ( ! strcmp(argv[ac], "-output") ) {
if( ++ac >= argc ) {
fprintf(stderr, "** missing argument for -output\n");
return 1;
}
outputpath = argv[ac]; /* no string copy, just pointer assignment */
} else if ( ! strcmp(argv[ac], "-threads") ) {
if( ++ac >= argc ) {
fprintf(stderr, "** missing argument for -threads\n");
return 1;
}
threads = atoi(argv[ac]); /* no string copy, just pointer assignment */
} else {
fprintf(stderr, "\nError, unrecognized command %s\n", argv[ac]);
}
}
rsSetThreadsNum(threads);
if ( inputpath == NULL ) {
fprintf(stderr, "No input volume specified!\n");
return 1;
}
if ( outputpath == NULL ) {
fprintf(stderr, "No output volume specified!\n");
return 1;
}
if ( maskpath == NULL ) {
fprintf(stderr, "A binary mask must be specified!\n");
return 1;
}
if ( verbose ) {
fprintf(stdout, "Input file: %s\n", inputpath);
fprintf(stdout, "Mask file: %s\n", maskpath);
fprintf(stdout, "Output file: %s\n", outputpath);
}
// Load file
/* open input file */
fslio = FslOpen(inputpath, "rb");
if (fslio == NULL) {
fprintf(stderr, "\nError, could not read header info for %s.\n", inputpath);
return 1;
}
/* determine dimensions */
FslGetDim(fslio, &xDim, &yDim, &zDim, &vDim);
if ( verbose ) {
fprintf(stdout, "Dim: %d %d %d (%d Volumes)\n", xDim, yDim, zDim, vDim);
}
if (fslio->niftiptr->scl_slope != 0) {
slope = fslio->niftiptr->scl_slope;
inter = fslio->niftiptr->scl_inter;
}
/* determine datatype and initalize buffer */
pixtype = FslGetDataType(fslio, &dt);
/* prepare centrality file */
fslioOutput = FslOpen(outputpath, "wb");
if (fslioOutput == NULL) {
fprintf(stderr, "\nError, could not read header info for %s.\n", outputpath);
return 1;
}
FslCloneHeader(fslioOutput, fslio);
FslSetDim(fslioOutput, xDim, yDim, zDim, vDim);
FslSetDimensionality(fslioOutput, 4);
FslSetDataType(fslioOutput, dt);
char *callString = rsMergeStringArray(argc, argv);
rsWriteNiftiHeader(fslioOutput, callString);
free(callString);
/* load mask */
unsigned long nPoints = 0L;
double ***mask = d3matrix(zDim-1, yDim-1, xDim-1);
Point3D *maskPoints = rsReadMask(maskpath, xDim, yDim, zDim, &nPoints, NULL, fslio, mask);
if ( maskPoints == NULL) {
fprintf(stderr, "\nError: Mask invalid.\n");
FslClose(fslio);
FslClose(fslioOutput);
return 1;
}
// Prepare buffer
buffsize = rsGetBufferSize(xDim, yDim, zDim, vDim, dt);
buffer = malloc(buffsize);
outputBuffer = malloc(buffsize);
if (buffer == NULL || outputBuffer == NULL) {
fprintf(stdout, "Not enough free memory :-(\n");
return 1;
}
FslReadVolumes(fslio, buffer, vDim);
rsResetBufferToValue(dt, outputBuffer, slope, inter, xDim, yDim, zDim, vDim, log(-1));
long p;
#pragma omp parallel num_threads(rsGetThreadsNum()) private(p) shared(buffer,fslio)
{
#pragma omp for schedule(guided, 1)
for (p = 0L; p<nPoints; p++) {
const Point3D *point = &maskPoints[p];
double *pointValues = (double*)malloc(sizeof(double)*vDim);
rsExtractTimecourseFromBuffer(dt, pointValues, buffer, slope, inter, point, xDim, yDim, zDim, vDim);
rsWriteTimecourseToBuffer(dt, pointValues, outputBuffer, slope, inter, point, xDim, yDim, zDim, vDim);
free(pointValues);
}
}
/* write output */
free(buffer);
FslWriteVolumes(fslioOutput, outputBuffer, vDim);
FslClose(fslioOutput);
free(outputBuffer);
free(fslioOutput);
free(maskPoints);
}
