Merge pull request #921 from yhuang43/development

neurolabusc · web-flow · commit e31488757a95 · 2025-02-28T08:45:44.000-08:00
DCM2NIIXFSLIB changes
diff --git a/console/dcm2niix_fswrapper.cpp b/console/dcm2niix_fswrapper.cpp
@@ -68,7 +68,7 @@ void dcm2niix_fswrapper::setOpts(const char *dcmindir, const char *dcm2niixopts)
 	// set the options for freesurfer mgz orientation
 	tdcmOpts.isRotate3DAcq = false;
 	tdcmOpts.isFlipY = false;
-	tdcmOpts.isIgnoreSeriesInstanceUID = true;
+	tdcmOpts.isIgnoreSeriesInstanceUID = true;  // Advanced feature: '-m 2' ignores Series Instance UID
 	tdcmOpts.isCreateBIDS = false;
 	tdcmOpts.isGz = false;
 	tdcmOpts.isForceStackSameSeries = 1; // merge 2D slice '-m y', tdcmOpts.isForceStackSameSeries = 1
@@ -153,7 +153,11 @@ void dcm2niix_fswrapper::__setDcm2niixOpts(const char *dcm2niixopts) {
 			else if (*v == 'y' || *v == 'Y' || *v == '1')
 				tdcmOpts.isForceStackSameSeries = 1;
 			else if (*v == '2')
+			{
 				tdcmOpts.isForceStackSameSeries = 2;
+				tdcmOpts.isIgnoreSeriesInstanceUID = true;
+				//printf("Advanced feature: '-m 2' ignores Series Instance UID.\n");
+			}
 			else if (*v == 'o' || *v == 'O')
 				tdcmOpts.isForceStackDCE = false;
 		} else if (strcmp(k, "v") == 0) {
@@ -194,7 +198,7 @@ bool dcm2niix_fswrapper::isDICOM(const char *file) {
  * interface to nii_loadDirCore() to search all dicom files from the directory input file is in,
  * and convert dicom files with the same series as given file.
  */
-int dcm2niix_fswrapper::dcm2NiiOneSeries(const char *dcmfile) {
+int dcm2niix_fswrapper::dcm2NiiOneSeries(const char *dcmfile, bool convert) {
 	// get seriesNo for given dicom file
 	struct TDICOMdata tdicomData = readDICOM((char *)dcmfile);
 
@@ -206,19 +210,55 @@ int dcm2niix_fswrapper::dcm2NiiOneSeries(const char *dcmfile) {
 	tdcmOpts.seriesNumber[0] = seriesNo;
 	tdcmOpts.numSeries = 1;
 
+	if (!convert)
+		tdcmOpts.isDumpNotConvert = true;  // retrieve dicom info only
+
 	return nii_loadDirCore(tdcmOpts.indir, &tdcmOpts);
 }
 
-// interface to nii_getMrifsStruct()
+/*
+ * interface to singleDICOM() to to convert only the single image provided.
+ */
+int dcm2niix_fswrapper::dcm2NiiSingleFile(const char* dcmfile)
+{
+  // get seriesNo for given dicom file
+  struct TDICOMdata tdicomData = readDICOM((char*)dcmfile);
+
+  double seriesNo = (double)tdicomData.seriesUidCrc;
+  if (tdcmOpts.isIgnoreSeriesInstanceUID)
+    seriesNo = (double)tdicomData.seriesNum;
+
+  // set TDCMopts to convert just one series
+  tdcmOpts.seriesNumber[0] = seriesNo;
+  tdcmOpts.numSeries = 1;
+
+  tdcmOpts.isOnlySingleFile = true;
+  
+  return singleDICOM(&tdcmOpts, (char*)dcmfile);
+}
+
+// interface to nii_dicom_batch.cpp::nii_getMrifsStruct()
 MRIFSSTRUCT *dcm2niix_fswrapper::getMrifsStruct(void) {
 	return nii_getMrifsStruct();
 }
 
-// interface to nii_getMrifsStructVector()
+// interface to nii_dicom_batch.cpp::nii_getMrifsStructVector()
 std::vector<MRIFSSTRUCT> *dcm2niix_fswrapper::getMrifsStructVector(void) {
 	return nii_getMrifsStructVector();
 }
 
+// interface to nii_dicom_batch.cpp::nii_clrMrifsStruct()
+void dcm2niix_fswrapper::clrMrifsStruct(void)
+{
+	nii_clrMrifsStruct();
+}
+  
+// interface to nii_dicom_batch.cpp::nii_clrMrifsStructVector()
+void dcm2niix_fswrapper::clrMrifsStructVector(void)
+{
+	nii_clrMrifsStructVector();
+}
+
 // return nifti header saved in MRIFSSTRUCT
 nifti_1_header *dcm2niix_fswrapper::getNiiHeader(void) {
 	MRIFSSTRUCT *mrifsStruct = getMrifsStruct();
diff --git a/console/dcm2niix_fswrapper.h b/console/dcm2niix_fswrapper.h
@@ -23,17 +23,26 @@ class dcm2niix_fswrapper {
 
 	// interface to nii_loadDirCore() to search all dicom files from the directory input file is in,
 	// and convert dicom files with the same series as given file.
-	static int dcm2NiiOneSeries(const char *dcmfile);
+	static int dcm2NiiOneSeries(const char *dcmfile, bool convert=true);
 
-	// interface to nii_getMrifsStruct()
+        // interface to singleDICOM() to convert only the single image provided
+        static int dcm2NiiSingleFile(const char* dcmfile);
+
+	// interface to nii_dicom_batch.cpp::nii_getMrifsStruct()
 	static MRIFSSTRUCT *getMrifsStruct(void);
 
+        // interface to nii_dicom_batch.cpp::nii_clrMrifsStruct()
+        static void clrMrifsStruct(void);
+
 	// return nifti header saved in MRIFSSTRUCT
 	static nifti_1_header *getNiiHeader(void);
 
-	// interface to nii_getMrifsStructVector()
+	// interface to nii_dicom_batch.cpp::nii_getMrifsStructVector()
 	static std::vector<MRIFSSTRUCT> *getMrifsStructVector(void);
 
+        // interface to nii_dicom_batch.cpp::nii_clrMrifsStructVector()
+        static void clrMrifsStructVector(void);
+
 	// return image data saved in MRIFSSTRUCT
 	static const unsigned char *getMRIimg(void);
 
diff --git a/console/nii_dicom_batch.cpp b/console/nii_dicom_batch.cpp
@@ -2650,6 +2650,18 @@ int *nii_saveDTI(char pathoutname[], int nConvert, struct TDCMsort dcmSort[], st
 		char sep = '\t';
 		if (opts.isCreateBIDS)
 			sep = ' ';
+
+#ifdef USING_DCM2NIIXFSWRAPPER
+		mrifsStruct.numDti = numVol;
+		mrifsStruct.tdti = (TDTI *)malloc(numVol * sizeof(TDTI));
+		for (int i = 0; i < numVol; i++)
+		{
+			mrifsStruct.tdti[i].V[0] = 0;
+			mrifsStruct.tdti[i].V[1] = 0;
+			mrifsStruct.tdti[i].V[2] = 0;
+			mrifsStruct.tdti[i].V[3] = 0;
+		}
+#else
 		// save bval
 		char txtname[2048] = {""};
 		strcpy(txtname, pathoutname);
@@ -2669,6 +2681,7 @@ int *nii_saveDTI(char pathoutname[], int nConvert, struct TDCMsort dcmSort[], st
 			fprintf(fp, "\n");
 		}
 		fclose(fp);
+#endif  // USING_DCM2NIIXFSWRAPPER
 #endif
 	}
 	if (numDti < 1)
@@ -8566,6 +8579,7 @@ int saveDcm2NiiCore(int nConvert, struct TDCMsort dcmSort[], struct TDICOMdata d
 			return EXIT_SUCCESS;
 	}
 #else
+	// opts.numSeries equals to 1
 	double seriesNum = (double)dcmList[dcmSort[0].indx].seriesUidCrc;
 	if (!isSameDouble(opts.seriesNumber[0], seriesNum))
 		return EXIT_SUCCESS;
@@ -9384,6 +9398,8 @@ int singleDICOM(struct TDCMopts *opts, char *fname) {
 	dcmList[0].converted2NII = 1;
 	dcmList[0] = readDICOMx(nameList.str[0], &prefs, dti4D); // ignore compile warning - memory only freed on first of 2 passes
 	// dcmList[0] = readDICOMv(nameList.str[0], opts->isVerbose, opts->compressFlag, dti4D); //ignore compile warning - memory only freed on first of 2 passes
+        if (opts->isIgnoreSeriesInstanceUID)
+	        dcmList[0].seriesUidCrc = dcmList[0].seriesNum;
 	fillTDCMsort(dcmSort[0], 0, dcmList[0]);
 	int ret = saveDcm2Nii(1, dcmSort, dcmList, &nameList, *opts, dti4D);
 	freeNameList(nameList);
@@ -10587,14 +10603,18 @@ void dcmListDump(int nConvert, struct TDCMsort dcmSort[], struct TDICOMdata dcmL
 		memset(mrifsStruct.dicomlst[i], 0, strlen(nameList->str[indx]) + 1);
 		memcpy(mrifsStruct.dicomlst[i], nameList->str[indx], strlen(nameList->str[indx]));
 
-		FILE *fp = stdout;
-		const char *imagelist = getenv("MGH_DCMUNPACK_IMAGELIST");
-		if (imagelist != NULL)
-			fp = fopen(imagelist, "a");
+                FILE *fp = stdout;
+                const char *imagelist = getenv("MGH_DCMUNPACK_IMAGELIST");
+                if (imagelist != NULL)
+                        fp = fopen(imagelist, "a");
+		
 		fprintf(fp, "%s %ld %s %s %f %f %f %f\\%f %c %f %s %s\n",
 				dcmList[indx].patientName, dcmList[indx].seriesNum, dcmList[indx].studyDate, dcmList[indx].studyTime,
 				dcmList[indx].TE, dcmList[indx].TR, dcmList[indx].flipAngle, dcmList[indx].xyzMM[1], dcmList[indx].xyzMM[2],
 				dcmList[indx].phaseEncodingRC, dcmList[indx].pixelBandwidth, nameList->str[indx], dcmList[indx].imageType);
+
+                if (fp != stdout)
+                        fclose(fp);
 	}
 }
 #endif
diff --git a/console/nii_dicom_batch.h b/console/nii_dicom_batch.h
@@ -96,6 +96,7 @@ void readIniFile(struct TDCMopts *opts, const char *argv[]);
 int nii_saveNIIx(char *niiFilename, struct nifti_1_header hdr, unsigned char *im, struct TDCMopts opts);
 int nii_loadDir(struct TDCMopts *opts);
 int nii_loadDirCore(char *indir, struct TDCMopts *opts);
+int singleDICOM(struct TDCMopts *opts, char *fname);
 void nii_SaveBIDS(char pathoutname[], struct TDICOMdata d, struct TDCMopts opts, struct nifti_1_header *h, const char *filename);
 int nii_createFilename(struct TDICOMdata dcm, char *niiFilename, struct TDCMopts opts);
 void nii_createDummyFilename(char *niiFilename, struct TDCMopts opts);
