Further work on ECAT

rordenlab · Apr 26, 2017 · dfce355 · dfce355
1 parent 3aa614e
commit dfce355
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Showing 5 changed files with 312 additions and 41 deletions.
diff --git a/console/nii_dicom.cpp b/console/nii_dicom.cpp
@@ -1612,7 +1612,7 @@ size_t nii_SliceBytes(struct nifti_1_header hdr) {
         if (hdr.dim[i]  > 1)
             imgsz = imgsz * hdr.dim[i];
     return imgsz;
-} //nii_ImgBytes()
+} //nii_SliceBytes()
 
 size_t nii_ImgBytes(struct nifti_1_header hdr) {
     size_t imgsz = hdr.bitpix/8;

diff --git a/console/nii_dicom.h b/console/nii_dicom.h
@@ -95,6 +95,7 @@ static const int kCompress50 = 3; //obsolete JPEG lossy
     unsigned char * nii_planar2rgb(unsigned char* bImg, struct nifti_1_header *hdr, int isPlanar);
 	int isDICOMfile(const char * fname); //0=not DICOM, 1=DICOM, 2=NOTSURE(not part 10 compliant)
     int headerDcm2Nii2(struct TDICOMdata d, struct TDICOMdata d2, struct nifti_1_header *h);
+    int headerDcm2Nii(struct TDICOMdata d, struct nifti_1_header *h) ;
     //unsigned char * nii_loadImgX(char* imgname, struct nifti_1_header *hdr, struct TDICOMdata dcm, bool iVaries);
     unsigned char * nii_loadImgXL(char* imgname, struct nifti_1_header *hdr, struct TDICOMdata dcm, bool iVaries, int compressFlag, int isVerbose);
     //int foo (float vx);

diff --git a/console/nii_dicom_batch.cpp b/console/nii_dicom_batch.cpp
@@ -411,7 +411,7 @@ void nii_SaveBIDS(char pathoutname[], struct TDICOMdata d, struct TDCMopts opts,
 		//printf("-%02d-%02dT%02d:%02d:%02.6f\",\n", amonth, aday, ahour, amin, asec);
 		if (count) { // ISO 8601 specifies a sign must exist for distant years.
 			//report time of the day only format, https://www.cs.tut.fi/~jkorpela/iso8601.html
-			fprintf(fp, "\t\"AcquisitionTime\": %02d:%02d:%02.6f\",\n",ahour, amin, asec);
+			fprintf(fp, "\t\"AcquisitionTime\": \"%02d:%02d:%02.6f\",\n",ahour, amin, asec);
 			//report date and time together
 			if (!opts.isAnonymizeBIDS) {
 				fprintf(fp, "\t\"AcquisitionDateTime\": ");
@@ -722,7 +722,7 @@ bool intensityScaleVaries(int nConvert, struct TDCMsort dcmSort[],struct TDICOMd
  sliceOffsetR += sliceBytes8;
  } //for each slice
  return bImg;
- } //nii_ImgBytes()*/
+ } */
 
 bool niiExists(const char*pathoutname) {
     char niiname[2048] = {""};
@@ -1092,6 +1092,10 @@ void nii_saveAttributes (struct TDICOMdata &data, struct nifti_1_header &header,
 int nii_saveNII(char * niiFilename, struct nifti_1_header hdr, unsigned char* im, struct TDCMopts opts) {
     hdr.vox_offset = 352;
     size_t imgsz = nii_ImgBytes(hdr);
+    if (imgsz < 1) {
+    	printMessage("Error: Image size is zero bytes %s\n", niiFilename);
+    	return EXIT_FAILURE;
+    }
     #ifndef myDisableZLib
     if  ((opts.isGz) &&  (strlen(opts.pigzname)  < 1) &&  ((imgsz+hdr.vox_offset) <  2147483647) ) { //use internal compressor
         writeNiiGz (niiFilename, hdr,  im, imgsz, opts.gzLevel);
@@ -2111,8 +2115,8 @@ int nii_loadDir(struct TDCMopts* opts) {
     }*/
     getFileName(opts->indirParent, opts->indir);
     if (isFile && ( (isExt(indir, ".v"))) ) {
-    	//open_foreign(opts->indir);
-    	return open_foreign (indir);
+    	//return open_foreign (indir);
+		return open_foreign (indir, *opts);
 
     }
     if (isFile && ( (isExt(indir, ".par")) || (isExt(indir, ".rec"))) ) {