nii_dicom.h

#include <stdbool.h> //requires VS 2015 or later
#include <string.h>
#include <stdint.h>
#include "nifti1_io_core.h"
#ifndef USING_R
#include "nifti1.h"
#endif

#ifndef MRIpro_nii_dcm_h

#define MRIpro_nii_dcm_h

#ifdef  __cplusplus
extern "C" {
#endif

#define STR_HELPER(x) #x
#define STR(x) STR_HELPER(x)

 #if defined(myEnableJPEGLS) || defined(myEnableJPEGLS1)
   #define kLSsuf " (JP-LS:CharLS)"
 #else
   #define kLSsuf ""
 #endif
 #ifdef myEnableJasper
  #define kJP2suf " (JP2:JasPer)"
 #else
  #ifdef myDisableOpenJPEG
    #define kJP2suf ""
  #else
    #define kJP2suf " (JP2:OpenJPEG)"
  #endif
 #endif
#if defined(__ICC) || defined(__INTEL_COMPILER)
	#define kCCsuf  " IntelCC" STR(__INTEL_COMPILER)
#elif defined(_MSC_VER)
	#define kCCsuf  " MSC" STR(_MSC_VER)
#elif defined(__clang__)
	#define kCCsuf  " Clang" STR(__clang_major__) "." STR(__clang_minor__) "." STR(__clang_patchlevel__)
#elif defined(__GNUC__) || defined(__GNUG__)
    #define kCCsuf  " GCC" STR(__GNUC__) "." STR(__GNUC_MINOR__) "." STR(__GNUC_PATCHLEVEL__)
#else
	#define kCCsuf " CompilerNA" //unknown compiler!
#endif
#if defined(__arm__) || defined(__ARM_ARCH)
    #define kCPUsuf " ARM"
#elif defined(__x86_64)
    #define kCPUsuf " x86-64"
#else
    #define kCPUsuf " " //unknown CPU
#endif

#define kDCMdate "v1.0.20211220"
#define kDCMvers kDCMdate " " kJP2suf kLSsuf kCCsuf kCPUsuf

static const int kMaxEPI3D = 1024; //maximum number of EPI images in Siemens Mosaic
static const int kMaxSlice2D = 65535; //issue460 maximum number of 2D slices in 4D (Philips) images
static const int kMaxDTI4D = kMaxSlice2D; //issue460: maximum number of DTI directions for 4D (Philips) images, also maximum number of 2D slices for Enhanced DICOM and PAR/REC

#define kDICOMStr 66 //64 characters plus NULL https://github.com/rordenlab/dcm2niix/issues/268
#define kDICOMStrLarge 256

#define kMANUFACTURER_UNKNOWN  0
#define kMANUFACTURER_SIEMENS  1
#define kMANUFACTURER_GE  2
#define kMANUFACTURER_PHILIPS  3
#define kMANUFACTURER_TOSHIBA  4
#define kMANUFACTURER_UIH  5
#define kMANUFACTURER_BRUKER  6
#define kMANUFACTURER_HITACHI  7
#define kMANUFACTURER_CANON  8
#define kMANUFACTURER_MEDISO  9

//note: note a complete modality list, e.g. XA,PX, etc
#define kMODALITY_UNKNOWN  0
#define kMODALITY_CR  1
#define kMODALITY_CT  2
#define kMODALITY_MR  3
#define kMODALITY_PT  4
#define kMODALITY_US  5

// PartialFourierDirection 0018,9036
#define kPARTIAL_FOURIER_DIRECTION_UNKNOWN  0
#define kPARTIAL_FOURIER_DIRECTION_PHASE  1
#define kPARTIAL_FOURIER_DIRECTION_FREQUENCY  2
#define kPARTIAL_FOURIER_DIRECTION_SLICE_SELECT  3
#define kPARTIAL_FOURIER_DIRECTION_COMBINATION  4

//GE EPI settings
#define kGE_EPI_UNKNOWN  -1
#define kGE_EPI_EPI  0
#define kGE_EPI_EPIRT  1
#define kGE_EPI_EPI2  2
#define kGE_EPI_PEPOLAR_FWD  3
#define kGE_EPI_PEPOLAR_REV  4
#define kGE_EPI_PEPOLAR_REV_FWD  5
#define kGE_EPI_PEPOLAR_FWD_REV  6
#define kGE_EPI_PEPOLAR_REV_FWD_FLIP  7
#define kGE_EPI_PEPOLAR_FWD_REV_FLIP  8


//GE phase encoding
#define kGE_PHASE_ENCODING_POLARITY_UNKNOWN  -1
#define kGE_PHASE_ENCODING_POLARITY_UNFLIPPED  0
#define kGE_PHASE_ENCODING_POLARITY_FLIPPED  4
#define kGE_SLICE_ORDER_UNKNOWN -1
#define kGE_SLICE_ORDER_TOP_DOWN  0
#define kGE_SLICE_ORDER_BOTTOM_UP  2


//#define kGE_PHASE_DIRECTION_CENTER_OUT_REV  3
//#define kGE_PHASE_DIRECTION_CENTER_OUT  4

//EXIT_SUCCESS 0
//EXIT_FAILURE 1
#define kEXIT_NO_VALID_FILES_FOUND  2
#define kEXIT_REPORT_VERSION  3
#define kEXIT_CORRUPT_FILE_FOUND  4
#define kEXIT_INPUT_FOLDER_INVALID  5
#define kEXIT_OUTPUT_FOLDER_INVALID  6
#define kEXIT_OUTPUT_FOLDER_READ_ONLY  7
#define kEXIT_SOME_OK_SOME_BAD  8
#define kEXIT_RENAME_ERROR  9
#define kEXIT_INCOMPLETE_VOLUMES_FOUND  10 //issue 515
#define kEXIT_NOMINAL  11 //did not expect to convert files

//0043,10A3  ---: PSEUDOCONTINUOUS
//0043,10A4  ---: 3D pulsed continuous ASL technique
#define kASL_FLAG_NONE 0
#define kASL_FLAG_GE_3DPCASL 1
#define kASL_FLAG_GE_3DCASL 2
#define kASL_FLAG_GE_PSEUDOCONTINUOUS 4
#define kASL_FLAG_GE_CONTINUOUS 8
#define kASL_FLAG_PHILIPS_CONTROL 16
#define kASL_FLAG_PHILIPS_LABEL 32


//for spoiling 0018,9016
#define kSPOILING_UNKOWN -1
#define kSPOILING_NONE 0
#define kSPOILING_RF 1
#define kSPOILING_GRADIENT 2
#define kSPOILING_RF_AND_GRADIENT 3

static const int kSliceOrientUnknown = 0;
static const int kSliceOrientTra = 1;
static const int kSliceOrientSag = 2;
static const int kSliceOrientCor = 3;
static const int kSliceOrientMosaicNegativeDeterminant = 4;
static const int kCompressNone = 0;
static const int kCompressYes = 1;
static const int kCompressC3 = 2; //obsolete JPEG lossless
static const int kCompress50 = 3; //obsolete JPEG lossy
static const int kCompressRLE = 4; //run length encoding
static const int kCompressPMSCT_RLE1 = 5; //see rle2img: Philips/ELSCINT1 run-length compression 07a1,1011= PMSCT_RLE1
static const int kCompressJPEGLS = 6; //LoCo JPEG-LS
static const int kMaxOverlay = 16; //even group values 0x6000..0x601E
#ifdef myEnableJasper
    static const int kCompressSupport = kCompressYes; //JASPER for JPEG2000
#else
    #ifdef myDisableOpenJPEG
        static const int kCompressSupport = kCompressNone; //no decompressor
    #else
        static const int kCompressSupport = kCompressYes; //OPENJPEG for JPEG2000
    #endif
#endif

// 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;
    struct TDTI {
        float V[4];
        //int totalSlicesIn4DOrder;
    };
    struct TDTI4D {
        struct TDTI S[kMaxDTI4D];
        int sliceOrder[kMaxSlice2D]; // [7,3,2] means the first slice on disk should be moved to 7th position
        int gradDynVol[kMaxDTI4D]; //used to parse dimensions of Philips data, e.g. file with multiple dynamics, echoes, phase+magnitude
        //int fragmentOffset[kMaxDTI4D], fragmentLength[kMaxDTI4D]; //for images with multiple compressed fragments
        float frameDuration[kMaxDTI4D], decayFactor[kMaxDTI4D], volumeOnsetTime[kMaxDTI4D], triggerDelayTime[kMaxDTI4D], TE[kMaxDTI4D], RWVScale[kMaxDTI4D], RWVIntercept[kMaxDTI4D], intenScale[kMaxDTI4D], intenIntercept[kMaxDTI4D], intenScalePhilips[kMaxDTI4D];
        bool isReal[kMaxDTI4D];
        bool isImaginary[kMaxDTI4D];
        bool isPhase[kMaxDTI4D];
        float repetitionTimeExcitation, repetitionTimeInversion;
    };

#ifdef _MSC_VER //Microsoft nomenclature for packed structures is different...
    #pragma pack(2)
    typedef struct {
        char name[64]; //null-terminated
        int32_t vm;
        char vr[4]; //  possibly nul-term string
        int32_t syngodt;//  ??
        int32_t nitems;// number of items in CSA
        int32_t xx;// maybe == 77 or 205
    } TCSAtag; //Siemens csa tag structure
    typedef struct {
        int32_t xx1, xx2_Len, xx3_77, xx4;
    } TCSAitem; //Siemens csa item structure
    #pragma pack()
#else
    typedef struct __attribute__((packed)) {
        char name[64]; //null-terminated
        int32_t vm;
        char vr[4]; //  possibly nul-term string
        int32_t syngodt;//  ??
        int32_t nitems;// number of items in CSA
        int32_t xx;// maybe == 77 or 205
    } TCSAtag; //Siemens csa tag structure
    typedef struct __attribute__((packed)) {
        int32_t xx1, xx2_Len, xx3_77, xx4;
    } TCSAitem; //Siemens csa item structure
#endif
    struct TCSAdata {
    	float sliceTiming[kMaxEPI3D], dtiV[4], sliceNormV[4], bandwidthPerPixelPhaseEncode, sliceMeasurementDuration;
        int numDti, SeriesHeader_offset, SeriesHeader_length, multiBandFactor, sliceOrder, slice_start, slice_end, mosaicSlices, protocolSliceNumber1, phaseEncodingDirectionPositive;
    	bool isPhaseMap;

    };
    struct TDICOMdata {
        long seriesNum;
        int xyzDim[5];
        uint32_t coilCrc, seriesUidCrc, instanceUidCrc;
        int overlayStart[kMaxOverlay];
        int phaseNumber, spoiling, mtState, partialFourierDirection, interp3D, aslFlags, durationLabelPulseGE, epiVersionGE, internalepiVersionGE, maxEchoNumGE, rawDataRunNumber, numberOfImagesInGridUIH, numberOfDiffusionDirectionGE, phaseEncodingGE, protocolBlockStartGE, protocolBlockLengthGE, modality, dwellTime, effectiveEchoSpacingGE, phaseEncodingLines, phaseEncodingSteps, echoTrainLength, echoNum, sliceOrient, manufacturer, converted2NII, acquNum, imageNum, imageStart, imageBytes, bitsStored, bitsAllocated, samplesPerPixel,locationsInAcquisition, locationsInAcquisitionConflict, compressionScheme;
        float 	xRayTubeCurrent, exposureTimeMs, numberOfExcitations, numberOfArms, numberOfPointsPerArm, groupDelay, decayFactor, percentSampling,waterFatShift, numberOfAverages, imagingFrequency, patientWeight, zSpacing, zThick, pixelBandwidth, SAR, phaseFieldofView, accelFactPE, accelFactOOP, flipAngle, fieldStrength, TE, TI, TR, intenScale, intenIntercept, intenScalePhilips, gantryTilt, lastScanLoc, angulation[4];
        float orient[7], patientPosition[4], patientPositionLast[4], xyzMM[4], stackOffcentre[4];
        float rtia_timerGE, radionuclidePositronFraction, radionuclideTotalDose, radionuclideHalfLife, doseCalibrationFactor; //PET ISOTOPE MODULE ATTRIBUTES (C.8-57)
		float frameDuration, ecat_isotope_halflife, ecat_dosage;
		float pixelPaddingValue;  // used for both FloatPixelPaddingValue (0028, 0122) and PixelPaddingValue (0028, 0120); NaN if not present.
        double acquisitionDuration, triggerDelayTime, RWVScale, RWVIntercept, dateTime, acquisitionTime, acquisitionDate, bandwidthPerPixelPhaseEncode;
        char parallelAcquisitionTechnique[kDICOMStr], radiopharmaceutical[kDICOMStr], convolutionKernel[kDICOMStr], unitsPT[kDICOMStr], decayCorrection[kDICOMStr], attenuationCorrectionMethod[kDICOMStr],reconstructionMethod[kDICOMStr];
        char imageOrientationText[kDICOMStr], coilElements[kDICOMStr], coilName[kDICOMStr], phaseEncodingDirectionDisplayedUIH[kDICOMStr], imageBaseName[kDICOMStr], scanOptions[kDICOMStr], stationName[kDICOMStr], softwareVersions[kDICOMStr], deviceSerialNumber[kDICOMStr], institutionName[kDICOMStr], referringPhysicianName[kDICOMStr], instanceUID[kDICOMStr], seriesInstanceUID[kDICOMStr], studyInstanceUID[kDICOMStr], bodyPartExamined[kDICOMStr], procedureStepDescription[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 institutionAddress[kDICOMStrLarge], imageComments[kDICOMStrLarge];
        uint32_t dimensionIndexValues[MAX_NUMBER_OF_DIMENSIONS];
        struct TCSAdata CSA;
        bool 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 TDCMprefs {
        int isVerbose, compressFlag, isIgnoreTriggerTimes;
	};

    size_t nii_ImgBytes(struct nifti_1_header hdr);
	void setDefaultPrefs (struct TDCMprefs *prefs);
    int isSameFloatGE (float a, float b);
    void getFileNameX( char *pathParent, const char *path, int maxLen);
    struct TDICOMdata readDICOMv(char * fname, int isVerbose, int compressFlag, struct TDTI4D *dti4D);
    struct TDICOMdata readDICOMx(char * fname, struct TDCMprefs* prefs, struct TDTI4D *dti4D);

	struct TDICOMdata readDICOM(char * fname);
    struct TDICOMdata clear_dicom_data(void);
    struct TDICOMdata  nii_readParRec (char * parname, int isVerbose, struct TDTI4D *dti4D, bool isReadPhase);
    unsigned char * nii_flipY(unsigned char* bImg, struct nifti_1_header *h);
    unsigned char *nii_flipImgY(unsigned char *bImg, struct nifti_1_header *hdr);
    unsigned char * nii_flipZ(unsigned char* bImg, struct nifti_1_header *h);
    //*unsigned char * nii_reorderSlices(unsigned char* bImg, struct nifti_1_header *h, struct TDTI4D *dti4D);
    void changeExt (char *file_name, const char* ext);
    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)
    void setQSForm(struct nifti_1_header *h, mat44 Q44i, bool isVerbose);
    int headerDcm2Nii2(struct TDICOMdata d, struct TDICOMdata d2, struct nifti_1_header *h, int isVerbose);
    int headerDcm2Nii(struct TDICOMdata d, struct nifti_1_header *h, bool isComputeSForm) ;
    unsigned char * nii_loadImgXL(char* imgname, struct nifti_1_header *hdr, struct TDICOMdata dcm, bool iVaries, int compressFlag, int isVerbose, struct TDTI4D *dti4D);
#ifdef  __cplusplus
}
#endif

#endif