Merge pull request #813 from CGSchwarzMayo/DeIdentificationMethod_json

Add DeidentificationMethod and DeidentificationMethodCodeSequence to json

console/dcm2niix_fswrapper.cpp

@@ -476,4 +476,8 @@ void dcm2niix_fswrapper::seriesInfoDump(FILE *fpdump, const MRIFSSTRUCT *pmrifsS
 
   // dcm2niix doesn't seem to retrieve this  0x51, 0x1016
   //fprintf(fpdump, "SiemensCrit %s\n",e->d.string);
+
+  // kDeidentificationMethod 0x0012 + (0x0063 << 16) // '0012' '0063' 'LO' 'DeidentificationMethod'
+  fprintf(fpdump, "DeidentificationMethod %s\n", tdicomData->deidentificationMethod);
+
 }

console/nii_dicom.cpp

@@ -4391,6 +4391,11 @@ struct TDICOMdata readDICOMx(char *fname, struct TDCMprefs *prefs, struct TDTI4D
 #define kPatientWeight 0x0010 + (0x1030 << 16)
 #define kAnatomicalOrientationType 0x0010 + (0x2210 << 16)
 #define kDeidentificationMethod 0x0012 + (0x0063 << 16) //[DICOMANON, issue 383
+#define kDeidentificationMethodCodeSequence 0x0012 + (0x0064 << 16)
+#define kCodeValue 0x0008 + (0x0100 << 16)
+#define kCodingSchemeDesignator 0x0008 + (0x0102 << 16)
+#define kCodingSchemeVersion 0x0008 + (0x0103 << 16)
+#define kCodeMeaning 0x0008 + (0x0104 << 16)
 #define kBodyPartExamined 0x0018 + (0x0015 << 16)
 #define kBodyPartExamined 0x0018 + (0x0015 << 16)
 #define kScanningSequence 0x0018 + (0x0020 << 16)
@@ -4791,6 +4796,7 @@ const uint32_t kEffectiveTE = 0x0018 + uint32_t(0x9082 << 16); //FD
 	bool isPaletteColor = false;
 	bool isInterpolated = false;
 	bool isIconImageSequence = false;
+	bool isDeidentificationMethodCodeSequence = false;
 	int sqDepthIcon = -1;
 	bool isSwitchToImplicitVR = false;
 	bool isSwitchToBigEndian = false;
@@ -5311,6 +5317,8 @@ const uint32_t kEffectiveTE = 0x0018 + uint32_t(0x9082 << 16); //FD
 			//return d;
 		}
 		if (lLength > 0) //issue695: skip empty tags, "gdcmanon --dumb --empty 0018,0089 good.dcm bad.dcm"
+		if(sqDepth < 1 && isDeidentificationMethodCodeSequence && groupElement != kItemDelimitationTag && groupElement != kItemTag )
+			isDeidentificationMethodCodeSequence = false;
 		switch (groupElement) {
 		case kMediaStorageSOPClassUID: {
 			char mediaUID[kDICOMStr];
@@ -5671,15 +5679,41 @@ const uint32_t kEffectiveTE = 0x0018 + uint32_t(0x9082 << 16); //FD
 			break;
 		}
 		case kDeidentificationMethod: { //issue 383
-			char anonTxt[kDICOMStr];
-			dcmStr(lLength, &buffer[lPos], anonTxt);
-			int slen = (int)strlen(anonTxt);
-			if ((slen < 10) || (strstr(anonTxt, "DICOMANON") == NULL))
+			dcmStr(lLength, &buffer[lPos], d.deidentificationMethod);
+			int slen = (int)strlen(d.deidentificationMethod);
+			if ((slen < 10) || (strstr(d.deidentificationMethod, "DICOMANON") == NULL))
 				break;
 			isDICOMANON = true;
 			printWarning("Matlab DICOMANON can scramble SeriesInstanceUID (0020,000e) and remove crucial data (see issue 383). \n");
 			break;
 		}
+		case kDeidentificationMethodCodeSequence: {
+			isDeidentificationMethodCodeSequence = true;
+			break;
+		}
+		case kCodeValue: {
+			if(isDeidentificationMethodCodeSequence && d.deID_CS_n < MAX_DEID_CS)
+				dcmStr(lLength, &buffer[lPos], d.deID_CS[d.deID_CS_n].CodeValue);
+			break;
+		}
+		case kCodingSchemeDesignator: {
+			if(isDeidentificationMethodCodeSequence && d.deID_CS_n < MAX_DEID_CS)
+				dcmStr(lLength, &buffer[lPos], d.deID_CS[d.deID_CS_n].CodingSchemeDesignator);
+			break;
+		}
+		case kCodingSchemeVersion: {
+			if(isDeidentificationMethodCodeSequence && d.deID_CS_n < MAX_DEID_CS)
+				dcmStr(lLength, &buffer[lPos], d.deID_CS[d.deID_CS_n].CodingSchemeVersion);
+			break;
+		}
+		case kCodeMeaning: {
+			if(isDeidentificationMethodCodeSequence && d.deID_CS_n < MAX_DEID_CS)
+			{
+				dcmStr(lLength, &buffer[lPos], d.deID_CS[d.deID_CS_n].CodeMeaning);
+				d.deID_CS_n++;
+			}
+			break;
+		}
 		case kPatientID:
 			if (strlen(d.patientID) > 1)
 				break;

console/nii_dicom.h

@@ -184,6 +184,9 @@ static const int kMaxOverlay = 16; //even group values 0x6000..0x601E
 // Maximum number of dimensions for .dimensionIndexValues, i.e. possibly the
 // number of axes in the output .nii.
 static const uint8_t MAX_NUMBER_OF_DIMENSIONS = 8;
+// Maximum supported number of entries in DeidentificationMethodCodeSequence
+// Any additional will be ignored
+static const uint8_t MAX_DEID_CS = 10;
     struct TDTI {
         float V[4];
         //int totalSlicesIn4DOrder;
@@ -235,9 +238,16 @@ static const uint8_t MAX_NUMBER_OF_DIMENSIONS = 8;
         char bidsEntitySuffix[kDICOMStrLarge]; //anat, func, dwi
         char bidsTask[kDICOMStr]; //rest, naming40
     };
+    struct TDeIDCodeSequence {
+      char CodeValue[kDICOMStr];
+      char CodeMeaning[kDICOMStrLarge];
+      char CodingSchemeDesignator[kDICOMStr];
+      char CodingSchemeVersion[kDICOMStr];
+    };
     struct TDICOMdata {
         long seriesNum;
         int xyzDim[5];
+        int deID_CS_n = 0;
         uint32_t coilCrc, seriesUidCrc, instanceUidCrc;
         int overlayStart[kMaxOverlay];
         int postLabelDelay, shimGradientX, shimGradientY, shimGradientZ, phaseNumber, spoiling, mtState, partialFourierDirection, interp3D, aslFlags, durationLabelPulseGE, epiVersionGE, internalepiVersionGE, maxEchoNumGE, rawDataRunNumber, numberOfTR, numberOfImagesInGridUIH, numberOfDiffusionT2GE, numberOfDiffusionDirectionGE, tensorFileGE, diffCyclingModeGE, phaseEncodingGE, protocolBlockStartGE, protocolBlockLengthGE, modality, dwellTime, effectiveEchoSpacingGE, phaseEncodingLines, phaseEncodingSteps, frequencyEncodingSteps, phaseEncodingStepsOutOfPlane, echoTrainLength, echoNum, sliceOrient, manufacturer, converted2NII, acquNum, imageNum, imageStart, imageBytes, bitsStored, bitsAllocated, samplesPerPixel,locationsInAcquisition, locationsInAcquisitionConflict, compressionScheme;
@@ -248,12 +258,13 @@ static const uint8_t MAX_NUMBER_OF_DIMENSIONS = 8;
         float pixelPaddingValue;  // used for both FloatPixelPaddingValue (0028, 0122) and PixelPaddingValue (0028, 0120); NaN if not present.
         double imagingFrequency, acquisitionDuration, triggerDelayTime, RWVScale, RWVIntercept, dateTime, acquisitionTime, acquisitionDate, bandwidthPerPixelPhaseEncode;
         char parallelAcquisitionTechnique[kDICOMStr], radiopharmaceutical[kDICOMStr], convolutionKernel[kDICOMStr], unitsPT[kDICOMStr], tracerRadionuclide[kDICOMStr], decayCorrection[kDICOMStr], attenuationCorrectionMethod[kDICOMStr],reconstructionMethod[kDICOMStr], transferSyntax[kDICOMStr];
-        char prescanReuseString[kDICOMStr], imageOrientationText[kDICOMStr], pulseSequenceName[kDICOMStr], coilElements[kDICOMStr], coilName[kDICOMStr], phaseEncodingDirectionDisplayedUIH[kDICOMStr], imageBaseName[kDICOMStr], stationName[kDICOMStr], studyDescription[kDICOMStr],  softwareVersions[kDICOMStr], deviceSerialNumber[kDICOMStr], institutionName[kDICOMStr], referringPhysicianName[kDICOMStr], instanceUID[kDICOMStr], seriesInstanceUID[kDICOMStr], studyInstanceUID[kDICOMStr], bodyPartExamined[kDICOMStr], procedureStepDescription[kDICOMStr], imageTypeText[kDICOMStr], imageType[kDICOMStr], institutionalDepartmentName[kDICOMStr], manufacturersModelName[kDICOMStr], patientID[kDICOMStr], patientOrient[kDICOMStr], patientName[kDICOMStr], accessionNumber[kDICOMStr], seriesDescription[kDICOMStr], studyID[kDICOMStr], sequenceName[kDICOMStr], protocolName[kDICOMStr],sequenceVariant[kDICOMStr],scanningSequence[kDICOMStr], patientBirthDate[kDICOMStr], patientAge[kDICOMStr],  studyDate[kDICOMStr],studyTime[kDICOMStr];
+        char prescanReuseString[kDICOMStr], imageOrientationText[kDICOMStr], pulseSequenceName[kDICOMStr], coilElements[kDICOMStr], coilName[kDICOMStr], phaseEncodingDirectionDisplayedUIH[kDICOMStr], imageBaseName[kDICOMStr], stationName[kDICOMStr], studyDescription[kDICOMStr],  softwareVersions[kDICOMStr], deviceSerialNumber[kDICOMStr], institutionName[kDICOMStr], referringPhysicianName[kDICOMStr], instanceUID[kDICOMStr], seriesInstanceUID[kDICOMStr], studyInstanceUID[kDICOMStr], bodyPartExamined[kDICOMStr], procedureStepDescription[kDICOMStr], imageTypeText[kDICOMStr], imageType[kDICOMStr], institutionalDepartmentName[kDICOMStr], manufacturersModelName[kDICOMStr], patientID[kDICOMStr], patientOrient[kDICOMStr], patientName[kDICOMStr], accessionNumber[kDICOMStr], seriesDescription[kDICOMStr], studyID[kDICOMStr], sequenceName[kDICOMStr], protocolName[kDICOMStr],sequenceVariant[kDICOMStr],scanningSequence[kDICOMStr], patientBirthDate[kDICOMStr], patientAge[kDICOMStr],  studyDate[kDICOMStr],studyTime[kDICOMStr], deidentificationMethod[kDICOMStr];
         char deepLearningText[kDICOMStrLarge], scanOptions[kDICOMStrLarge], institutionAddress[kDICOMStrLarge], imageComments[kDICOMStrLarge];
         uint32_t dimensionIndexValues[MAX_NUMBER_OF_DIMENSIONS];
         struct TCSAdata CSA;
         bool isDeepLearning, isVariableFlipAngle, isQuadruped, isRealIsPhaseMapHz, isPrivateCreatorRemap, isHasOverlay, isEPI, isIR, isPartialFourier, isDiffusion, isVectorFromBMatrix, isRawDataStorage, isGrayscaleSoftcopyPresentationState, isStackableSeries, isCoilVaries, isNonParallelSlices, isBVecWorldCoordinates, isSegamiOasis, isXA10A, isScaleOrTEVaries, isScaleVariesEnh, isDerived, isXRay, isMultiEcho, isValid, is3DAcq, is2DAcq, isExplicitVR, isLittleEndian, isPlanarRGB, isSigned, isHasPhase, isHasImaginary, isHasReal, isHasMagnitude,isHasMixed, isFloat, isResampled, isLocalizer;
         char phaseEncodingRC, patientSex;
+        struct TDeIDCodeSequence deID_CS[MAX_DEID_CS];
     };
     struct TDCMprefs {
         int isVerbose, compressFlag, isIgnoreTriggerTimes;

console/nii_dicom_batch.cpp

@@ -1465,6 +1465,24 @@ tse3d: T2*/
 			fprintf(fp, "\t\"NonlinearGradientCorrection\": false,\n");
 	if (d.isDerived) //DICOM is derived image or non-spatial file (sounds, etc)
 		fprintf(fp, "\t\"RawImage\": false,\n");
+	json_Str(fp, "\t\"DeidentificationMethod\": \"%s\",\n", d.deidentificationMethod);
+if(d.deID_CS_n>0)
+{
+	fprintf(fp, "\t\"DeidentificationMethodCodeSequence\": [ \n");
+	for (int i = 0; i < d.deID_CS_n && i < MAX_DEID_CS; i++)
+	{
+		fprintf(fp, "\t  { \n");
+		json_Str(fp, "\t\t\"CodeValue\": \"%s\",\n", d.deID_CS[i].CodeValue);
+		json_Str(fp, "\t\t\"CodingSchemeDesignator\": \"%s\",\n", d.deID_CS[i].CodingSchemeDesignator);
+		json_Str(fp, "\t\t\"CodingSchemeVersion\": \"%s\",\n", d.deID_CS[i].CodingSchemeVersion);
+		json_Str(fp, "\t\t\"CodeMeaning\": \"%s\"\n", d.deID_CS[i].CodeMeaning);
+		if(i+1 < d.deID_CS_n)
+			fprintf(fp, "\t  },\n");
+		else
+			fprintf(fp, "\t  }\n");
+	}
+	fprintf(fp, "\t],\n");
+}
 	if (d.seriesNum > 0)
 		fprintf(fp, "\t\"SeriesNumber\": %ld,\n", d.seriesNum);
 	//Chris Gorgolewski: BIDS standard specifies ISO8601 date-time format (Example: 2016-07-06T12:49:15.679688)