int main(int argc, char *argv[]){
if(!argv[1]) {
printf("\n./cutTree <Tree Name> <Nr. Cuts> <Mask Name> <Output Name>\n");
return 0;
}
printf("\nLoading the dendrogram ... \n");
FILE *treeFile = fopen(argv[1], "r");
int goodValues;
fscanf(treeFile, "%i", &goodValues);
Node *tree = malloc((goodValues-1)*sizeof(Node));
for(int i=0; i<goodValues-1; i++){
fscanf(treeFile, "%i %i %lf", &(tree[i].left), &(tree[i].right), &(tree[i].distance));
}
fclose(treeFile);
printf("\nCutting the dendrogram ...\n");
int * clusterid;
int nr_clusters = atoi(argv[2]);
clusterid = (int*)malloc(goodValues*sizeof(int));
cuttree (goodValues, tree, nr_clusters, clusterid);
free(tree);
printf("\nLoading mask template ... \n");
FSLIO *fslio;
fslio = FslInit();
void *buffer = FslReadAllVolumes(fslio, argv[3]);
double ***mask = FslGetVolumeAsScaledDouble(fslio, 0);
FslClose(fslio);
printf("\nSaving the image ...\n");
nifti_image *nim = nifti_image_read(argv[3], 1);
int nx = nim->nx; int ny = nim->ny; int nz = nim->nz;
short *pData = (short *)nim->data;
int c = 0; int c2 = 0;
for(int k=0;k<nz;k++) {
for(int j=0;j<ny;j++) {
for(int i=0;i<nx;i++) {
if ( mask[k][j][i] != 0 ) {
pData[c2] = clusterid[c]+1;
c++; c2++;
}
else {
pData[c2] = 0;
c2++;
}
}}}
nim->data = (short *)pData;
int ret = nifti_set_filenames(nim, argv[4], 0, 1);
nifti_image_write( nim );
nifti_image_free( nim );
free(clusterid);
return 0;
}
int main(int argc, char * argv[])
{
FSLIO *fslio;
void *buffer;
char *f1name;
double ***vol;
int x,y,z,t;
/*** process commandline parameters */
if (argc < 2) {
pusage(argv[0]);
exit(1);
}
/************************* PRINT ***************************/
if (!strncmp(argv[1],"print",5)) {
if (argc != 3) {
fprintf(stderr, "\nError, print command takes one parameter: print <dataset>\n");
exit(1);
}
f1name = argv[2];
/** open nifti dataset */
fslio = FslInit();
buffer = FslReadAllVolumes(fslio,f1name);
if (buffer == NULL) {
fprintf(stderr, "\nError opening and reading %s.\n",f1name);
exit(1);
}
nifti_image_infodump(fslio->niftiptr);
exit(0);
}
/************************* PEEK ***************************/
if (!strncmp(argv[1],"peek",4)) {
if (argc != 7) {
fprintf(stderr, "\nError, peek command takes five parameters: peek <dataset> X Y Z T\n");
exit(1);
}
/**** get inputs */
f1name = argv[2];
x = atoi(argv[3]);
y = atoi(argv[4]);
z = atoi(argv[5]);
t = atoi(argv[6]);
/** open nifti dataset header */
fslio = FslReadHeader(f1name);
if (fslio == NULL) {
fprintf(stderr, "\nError, could not read header info for %s.\n",f1name);
exit(1);
}
/**** check inputs */
if ( (x<0) || (x>=fslio->niftiptr->nx) ) {
fprintf(stderr, "\nError: x index (%d) out of range [0..%d]\n",x,fslio->niftiptr->nx-1);
exit(1);
}
if ( (y<0) || (y>=fslio->niftiptr->ny) ) {
fprintf(stderr, "\nError: y index (%d) out of range [0..%d]\n",y,fslio->niftiptr->ny-1);
exit(1);
}
if ( (z<0) || (z>=fslio->niftiptr->nz) ) {
fprintf(stderr, "\nError: z index (%d) out of range [0..%d]\n",z,fslio->niftiptr->nz-1);
exit(1);
}
if ( (t<0) || (t>=fslio->niftiptr->nt) ) {
fprintf(stderr, "\nError: t index (%d) out of range [0..%d]\n",t,fslio->niftiptr->nt-1);
exit(1);
}
/*** get volume data as scaled doubles */
vol = FslGetVolumeAsScaledDouble(fslio,t);
if (vol == NULL) {
fprintf(stderr, "\nError accessing %s\n",f1name);
exit(1);
}
else {
fprintf(stderr, "\nLocation %d %d %d %d: %.4f\n",x,y,z,t,vol[z][y][x]);
exit(0);
}
}
fprintf(stderr, "\nError, unrecognized command %s\n",argv[1]);
pusage(argv[0]);
exit(1);
}
