DicomHandler.cc

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//
// $Id: DicomHandler.cc 81911 2014-06-06 14:06:19Z gcosmo $
//
//
// The code was written by :
//      *Louis Archambault louis.archambault@phy.ulaval.ca,
//      *Luc Beaulieu beaulieu@phy.ulaval.ca
//      +Vincent Hubert-Tremblay at tigre.2@sympatico.ca
//
//
// *Centre Hospitalier Universitaire de Quebec (CHUQ),
// Hotel-Dieu de Quebec, departement de Radio-oncologie
// 11 cote du palais. Quebec, QC, Canada, G1R 2J6
// tel (418) 525-4444 #6720
// fax (418) 691 5268
//
// + University Laval, Quebec (QC) Canada
//*******************************************************
//
//*******************************************************
//
//*******************************************************

#include "DicomHandler.hh"
#include "globals.hh"
#include "G4ios.hh"
#include <fstream>

#include <cctype>
#include <cstring>

#include "DicomPhantomZSliceHeader.hh"
#include "DicomPhantomZSliceMerged.hh"

//========================================================================================

DicomHandler* DicomHandler::fgInstance = 0;

//========================================================================================

DicomHandler* DicomHandler::Instance()
{
    return fgInstance;
}

//========================================================================================

DicomHandler::DicomHandler()
:   DATABUFFSIZE(8192), LINEBUFFSIZE(5020), FILENAMESIZE(512),
    fCompression(0), fNFiles(0), fRows(0), fColumns(0),
    fBitAllocated(0), fMaxPixelValue(0), fMinPixelValue(0),
    fPixelSpacingX(0.), fPixelSpacingY(0.),
    fSliceThickness(0.), fSliceLocation(0.),
    fRescaleIntercept(0), fRescaleSlope(0),
    fLittleEndian(true), fImplicitEndian(false),
    fPixelRepresentation(0), nbrequali(0),
    valuedensity(NULL),valueCT(NULL),readCalibration(false),
    mergedSlices(NULL),driverFile("Data.dat"),ct2densityFile("CT2Density.dat")
{
    mergedSlices = new DicomPhantomZSliceMerged;
}


//========================================================================================

DicomHandler::~DicomHandler()
{

}

//========================================================================================

G4int DicomHandler::ReadFile(FILE* dicom, char* filename2)
{
    G4cout << " ReadFile " << filename2 << G4endl;
    G4int returnvalue = 0; size_t rflag = 0;
    char * buffer = new char[LINEBUFFSIZE];

    fImplicitEndian = false;
    fLittleEndian = true;

    rflag = std::fread( buffer, 1, 128, dicom ); // The first 128 bytes
                                                 //are not important
                                                 // Reads the "DICOM" letters
    rflag = std::fread( buffer, 1, 4, dicom );
    // if there is no preamble, the FILE pointer is rewinded.
    if(std::strncmp("DICM", buffer, 4) != 0) {
        std::fseek(dicom, 0, SEEK_SET);
        fImplicitEndian = true;
    }

    short readGroupId;    // identify the kind of input data
    short readElementId;  // identify a particular type information
    short elementLength2; // deal with element length in 2 bytes
                          //unsigned int elementLength4; // deal with element length in 4 bytes
    unsigned long elementLength4; // deal with element length in 4 bytes

    char * data = new char[DATABUFFSIZE];


    // Read information up to the pixel data
    while(true) {

        //Reading groups and elements :
        readGroupId = 0;
        readElementId = 0;
        // group ID
        rflag = std::fread(buffer, 2, 1, dicom);
        GetValue(buffer, readGroupId);
        // element ID
        rflag = std::fread(buffer, 2, 1, dicom);
        GetValue(buffer, readElementId);

        // Creating a tag to be identified afterward
        G4int tagDictionary = readGroupId*0x10000 + readElementId;

        // beginning of the pixels
        if(tagDictionary == 0x7FE00010) {
            // Folling 2 fread's are modifications to original DICOM example (Jonathan Madsen)
            rflag = std::fread(buffer,2,1,dicom);   // Reserved 2 bytes (not used for pixels)
            rflag = std::fread(buffer,4,1,dicom);   // Element Length   (not used for pixels)
            break;      // Exit to ReadImageData()
        }

        // VR or element length
        rflag = std::fread(buffer,2,1,dicom);
        GetValue(buffer, elementLength2);

        // If value representation (VR) is OB, OW, SQ, UN, added OF and UT
        //the next length is 32 bits
        if((elementLength2 == 0x424f ||     // "OB"
            elementLength2 == 0x574f ||     // "OW"
            elementLength2 == 0x464f ||     // "OF"
            elementLength2 == 0x5455 ||     // "UT"
            elementLength2 == 0x5153 ||     // "SQ"
            elementLength2 == 0x4e55) &&    // "UN"
           !fImplicitEndian ) {             // explicit VR

            rflag = std::fread(buffer, 2, 1, dicom); // Skip 2 reserved bytes

            // element length
            rflag = std::fread(buffer, 4, 1, dicom);
            GetValue(buffer, elementLength4);

            if(elementLength2 == 0x5153)
            {
                if(elementLength4 == 0xFFFFFFFF)
                {
                    read_undefined_nested( dicom );
                    elementLength4=0;
                }  else{
                    if(read_defined_nested( dicom, elementLength4 )==0){
                        G4cerr << "Function read_defined_nested() failed!" << G4endl;
                        exit(-10);               }
                }
            } else  {
                // Reading the information with data
                rflag = std::fread(data, elementLength4,1,dicom);
            }


        }  else {

            //  explicit with VR different than previous ones
            if(!fImplicitEndian || readGroupId == 2) {

                //G4cout << "Reading  DICOM files with Explicit VR"<< G4endl;
                // element length (2 bytes)
                rflag = std::fread(buffer, 2, 1, dicom);
                GetValue(buffer, elementLength2);
                elementLength4 = elementLength2;

                rflag = std::fread(data, elementLength4, 1, dicom);

            } else {                                  // Implicit VR

                //G4cout << "Reading  DICOM files with Implicit VR"<< G4endl;

                // element length (4 bytes)
                if(std::fseek(dicom, -2, SEEK_CUR) != 0) {
                    G4cerr << "[DicomHandler] fseek failed" << G4endl;
                    exit(-10);}

                rflag = std::fread(buffer, 4, 1, dicom);
                GetValue(buffer, elementLength4);

                //G4cout <<  std::hex<< elementLength4 << G4endl;

                if(elementLength4 == 0xFFFFFFFF)
                {
                    read_undefined_nested(dicom);
                    elementLength4=0;
                }  else{
                    rflag = std::fread(data, elementLength4, 1, dicom);
                }

            }
        }

        // NULL termination
        data[elementLength4] = '\0';

        // analyzing information
        GetInformation(tagDictionary, data);
    }

    G4String fnameG4DCM = G4String(filename2) + ".g4dcm";

    // Perform functions originally written straight to file
    DicomPhantomZSliceHeader* zslice = new DicomPhantomZSliceHeader(fnameG4DCM);

    std::map<G4float,G4String>::const_iterator ite;
    for( ite = fMaterialIndices.begin(); ite != fMaterialIndices.end(); ++ite ){
        zslice->AddMaterial(ite->second);
    }

    zslice->SetNoVoxelX(fColumns/fCompression);
    zslice->SetNoVoxelY(fRows/fCompression);
    zslice->SetNoVoxelZ(1);

    zslice->SetMinX(-fPixelSpacingX*fColumns/2.);
    zslice->SetMaxX(fPixelSpacingX*fColumns/2.);

    zslice->SetMinY(-fPixelSpacingY*fRows/2.);
    zslice->SetMaxY(fPixelSpacingY*fRows/2.);

    zslice->SetMinZ(fSliceLocation-fSliceThickness/2.);
    zslice->SetMaxZ(fSliceLocation+fSliceThickness/2.);

    //=====================================================================
    // This is depreciated --> Handled by DicomPhantomZSliceHeader
    /*
     // Creating files to store information
     std::ofstream foutG4DCM;
     foutG4DCM.open(fnameG4DCM);
     G4cout << "### Writing of " << fnameG4DCM << " ### " << G4endl;

     foutG4DCM << fMaterialIndices.size() << G4endl;
     //--- Write materials
     unsigned int ii = 0;
     for( ite = fMaterialIndices.begin(); ite != fMaterialIndices.end(); ite++, ii++ ){
     foutG4DCM << ii << " " << (*ite).second << G4endl;
     }
     //--- Write number of voxels (assume only one voxel in Z)
     foutG4DCM << fColumns/fCompression << " " << fRows/fCompression << " 1 " << G4endl;
     //--- Write minimum and maximum extensions
     foutG4DCM << -fPixelSpacingX*fColumns/2. << " " << fPixelSpacingX*fColumns/2. << G4endl;
     foutG4DCM << -fPixelSpacingY*fRows/2. << " " << fPixelSpacingY*fRows/2. <<
     G4endl;
     foutG4DCM << fSliceLocation-fSliceThickness/2. << " "
     << fSliceLocation+fSliceThickness/2. << G4endl;
     //    foutG4DCM << fCompression << G4endl;
     */
    //=====================================================================

    ReadData( dicom, filename2 );

    // DEPRECIATED
    //StoreData( foutG4DCM );
    //foutG4DCM.close();

    StoreData( zslice );

    // Dumped 2 file after DicomPhantomZSliceMerged has checked for consistency
    //zslice->DumpToFile();

    mergedSlices->AddZSlice(zslice);

    //
    delete [] buffer;
    delete [] data;

    if (rflag) return returnvalue;
    return returnvalue;
}

//========================================================================================

void DicomHandler::GetInformation(G4int & tagDictionary, char * data)
{
    if(tagDictionary == 0x00280010 ) { // Number of Rows
        GetValue(data, fRows);
        std::printf("[0x00280010] Rows -> %i\n",fRows);

    } else if(tagDictionary == 0x00280011 ) { // Number of fColumns
        GetValue(data, fColumns);
        std::printf("[0x00280011] Columns -> %i\n",fColumns);

    } else if(tagDictionary == 0x00280102 ) { // High bits  ( not used )
        short highBits;
        GetValue(data, highBits);
        std::printf("[0x00280102] High bits -> %i\n",highBits);

    } else if(tagDictionary == 0x00280100 ) { // Bits allocated
        GetValue(data, fBitAllocated);
        std::printf("[0x00280100] Bits allocated -> %i\n", fBitAllocated);

    } else if(tagDictionary == 0x00280101 ) { //  Bits stored ( not used )
        short bitStored;
        GetValue(data, bitStored);
        std::printf("[0x00280101] Bits stored -> %i\n",bitStored);

    } else if(tagDictionary == 0x00280106 ) { //  Min. pixel value
        GetValue(data, fMinPixelValue);
        std::printf("[0x00280106] Min. pixel value -> %i\n", fMinPixelValue);

    } else if(tagDictionary == 0x00280107 ) { //  Max. pixel value
        GetValue(data, fMaxPixelValue);
        std::printf("[0x00280107] Max. pixel value -> %i\n", fMaxPixelValue);

    } else if(tagDictionary == 0x00281053) { //  Rescale slope
        fRescaleSlope = atoi(data);
        std::printf("[0x00281053] Rescale Slope -> %d\n", fRescaleSlope);

    } else if(tagDictionary == 0x00281052 ) { // Rescalse intercept
        fRescaleIntercept = atoi(data);
        std::printf("[0x00281052] Rescale Intercept -> %d\n", fRescaleIntercept );

    } else if(tagDictionary == 0x00280103 ) {
        //  Pixel representation ( functions not design to read signed bits )
        fPixelRepresentation = atoi(data); // 0: unsigned  1: signed
        std::printf("[0x00280103] Pixel Representation -> %i\n", fPixelRepresentation);
        if(fPixelRepresentation == 1 ) {
            std::printf("### PIXEL REPRESENTATION = 1, BITS ARE SIGNED, ");
            std::printf("DICOM READING SCAN FOR UNSIGNED VALUE, POSSIBLE ");
            std::printf("ERROR !!!!!! -> \n");
        }

    } else if(tagDictionary == 0x00080006 ) { //  Modality
        std::printf("[0x00080006] Modality -> %s\n", data);

    } else if(tagDictionary == 0x00080070 ) { //  Manufacturer
        std::printf("[0x00080070] Manufacturer -> %s\n", data);

    } else if(tagDictionary == 0x00080080 ) { //  Institution Name
        std::printf("[0x00080080] Institution Name -> %s\n", data);

    } else if(tagDictionary == 0x00080081 ) { //  Institution Address
        std::printf("[0x00080081] Institution Address -> %s\n", data);

    } else if(tagDictionary == 0x00081040 ) { //  Institution Department Name
        std::printf("[0x00081040] Institution Department Name -> %s\n", data);

    } else if(tagDictionary == 0x00081090 ) { //  Manufacturer's Model Name
        std::printf("[0x00081090] Manufacturer's Model Name -> %s\n", data);

    } else if(tagDictionary == 0x00181000 ) { //  Device Serial Number
        std::printf("[0x00181000] Device Serial Number -> %s\n", data);

    } else if(tagDictionary == 0x00080008 ) { //  Image type ( not used )
        std::printf("[0x00080008] Image Types -> %s\n", data);

    } else if(tagDictionary == 0x00283000 ) { //  Modality LUT Sequence ( not used )
        std::printf("[0x00283000] Modality LUT Sequence SQ 1 -> %s\n", data);

    } else if(tagDictionary == 0x00283002 ) { // LUT Descriptor ( not used )
        std::printf("[0x00283002] LUT Descriptor US or SS 3 -> %s\n", data);

    } else if(tagDictionary == 0x00283003 ) { // LUT Explanation ( not used )
        std::printf("[0x00283003] LUT Explanation LO 1 -> %s\n", data);

    } else if(tagDictionary == 0x00283004 ) { // Modality LUT ( not used )
        std::printf("[0x00283004] Modality LUT Type LO 1 -> %s\n", data);

    } else if(tagDictionary == 0x00283006 ) { // LUT Data ( not used )
        std::printf("[0x00283006] LUT Data US or SS -> %s\n", data);

    } else if(tagDictionary == 0x00283010 ) { // VOI LUT ( not used )
        std::printf("[0x00283010] VOI LUT Sequence SQ 1 -> %s\n", data);

    } else if(tagDictionary == 0x00280120 ) { // Pixel Padding Value ( not used )
        std::printf("[0x00280120] Pixel Padding Value US or SS 1 -> %s\n", data);

    } else if(tagDictionary == 0x00280030 ) { // Pixel Spacing
        G4String datas(data);
        int iss = datas.find('\\');
        fPixelSpacingX = atof( datas.substr(0,iss).c_str() );
        fPixelSpacingY = atof( datas.substr(iss+2,datas.length()).c_str() );

    } else if(tagDictionary == 0x00200037 ) { // Image Orientation ( not used )
        std::printf("[0x00200037] Image Orientation (Phantom) -> %s\n", data);

    } else if(tagDictionary == 0x00200032 ) { // Image Position ( not used )
        std::printf("[0x00200032] Image Position (Phantom,mm) -> %s\n", data);

    } else if(tagDictionary == 0x00180050 ) { // Slice Thickness
        fSliceThickness = atof(data);
        std::printf("[0x00180050] Slice Thickness (mm) -> %f\n", fSliceThickness);

    } else if(tagDictionary == 0x00201041 ) { // Slice Location
        fSliceLocation = atof(data);
        std::printf("[0x00201041] Slice Location -> %f\n", fSliceLocation);

    } else if(tagDictionary == 0x00280004 ) { // Photometric Interpretation ( not used )
        std::printf("[0x00280004] Photometric Interpretation -> %s\n", data);

    } else if(tagDictionary == 0x00020010) { // Endian
        if(strcmp(data, "1.2.840.10008.1.2") == 0)
            fImplicitEndian = true;
        else if(strncmp(data, "1.2.840.10008.1.2.2", 19) == 0)
            fLittleEndian = false;
        //else 1.2.840..10008.1.2.1 (explicit little endian)

        std::printf("[0x00020010] Endian -> %s\n", data);
    }

    // others
    else {
        //std::printf("[0x%x] -> %s\n", tagDictionary, data);
        ;
    }

}

//========================================================================================

void DicomHandler::StoreData(DicomPhantomZSliceHeader* dcmPZSH)
{
    G4int mean;
    G4double density;
    G4bool overflow = false;

    if(!dcmPZSH) { return; }

    dcmPZSH->SetSliceLocation(fSliceLocation);

    //----- Print indices of material
    if(fCompression == 1) { // no fCompression: each pixel has a density value)
        for( G4int ww = 0; ww < fRows; ww++) {
            dcmPZSH->AddRow();
            for( G4int xx = 0; xx < fColumns; xx++) {
                mean = fTab[ww][xx];
                density = Pixel2density(mean);
                dcmPZSH->AddValue(density);
                dcmPZSH->AddMateID(GetMaterialIndex(density));
            }
        }

    } else {
        // density value is the average of a square region of
        // fCompression*fCompression pixels
        for(G4int ww = 0; ww < fRows ;ww += fCompression ) {
            dcmPZSH->AddRow();
            for(G4int xx = 0; xx < fColumns ;xx +=fCompression ) {
                overflow = false;
                mean = 0;
                for(int sumx = 0; sumx < fCompression; sumx++) {
                    for(int sumy = 0; sumy < fCompression; sumy++) {
                        if(ww+sumy >= fRows || xx+sumx >= fColumns) overflow = true;
                        mean += fTab[ww+sumy][xx+sumx];
                    }
                    if(overflow) break;
                }
                mean /= fCompression*fCompression;

                if(!overflow) {
                    density = Pixel2density(mean);
                    dcmPZSH->AddValue(density);
                    dcmPZSH->AddMateID(GetMaterialIndex(density));
                }
            }
        }
    }

    dcmPZSH->FlipData();
}

//========================================================================================
// This function is depreciated as it is handled by DicomPhantomZSliceHeader::DumpToFile
void DicomHandler::StoreData(std::ofstream& foutG4DCM)
{
    G4int mean;
    G4double density;
    G4bool overflow = false;

    //----- Print indices of material
    if(fCompression == 1) { // no fCompression: each pixel has a density value)
        for( G4int ww = 0; ww < fRows; ww++) {
            for( G4int xx = 0; xx < fColumns; xx++) {
                mean = fTab[ww][xx];
                density = Pixel2density(mean);
                foutG4DCM << GetMaterialIndex( density ) << " ";
            }
            foutG4DCM << G4endl;
        }

    } else {
        // density value is the average of a square region of
        // fCompression*fCompression pixels
        for(G4int ww = 0; ww < fRows ;ww += fCompression ) {
            for(G4int xx = 0; xx < fColumns ;xx +=fCompression ) {
                overflow = false;
                mean = 0;
                for(int sumx = 0; sumx < fCompression; sumx++) {
                    for(int sumy = 0; sumy < fCompression; sumy++) {
                        if(ww+sumy >= fRows || xx+sumx >= fColumns) overflow = true;
                        mean += fTab[ww+sumy][xx+sumx];
                    }
                    if(overflow) break;
                }
                mean /= fCompression*fCompression;

                if(!overflow) {
                    density = Pixel2density(mean);
                    foutG4DCM << GetMaterialIndex( density ) << " ";
                }
            }
            foutG4DCM << G4endl;
        }

    }

    //----- Print densities
    if(fCompression == 1) { // no fCompression: each pixel has a density value)
        for( G4int ww = 0; ww < fRows; ww++) {
            for( G4int xx = 0; xx < fColumns; xx++) {
                mean = fTab[ww][xx];
                density = Pixel2density(mean);
                foutG4DCM << density << " ";
                if( xx%8 == 3 ) foutG4DCM << G4endl; // just for nicer reading
            }
        }

    } else {
        // density value is the average of a square region of
        // fCompression*fCompression pixels
        for(G4int ww = 0; ww < fRows ;ww += fCompression ) {
            for(G4int xx = 0; xx < fColumns ;xx +=fCompression ) {
                overflow = false;
                mean = 0;
                for(int sumx = 0; sumx < fCompression; sumx++) {
                    for(int sumy = 0; sumy < fCompression; sumy++) {
                        if(ww+sumy >= fRows || xx+sumx >= fColumns) overflow = true;
                        mean += fTab[ww+sumy][xx+sumx];
                    }
                    if(overflow) break;
                }
                mean /= fCompression*fCompression;

                if(!overflow) {
                    density = Pixel2density(mean);
                    foutG4DCM << density  << " ";
                    if( xx/fCompression%8 == 3 ) foutG4DCM << G4endl; // just for nicer reading
                }
            }
        }

    }

}

//========================================================================================

void DicomHandler::ReadMaterialIndices( std::ifstream& finData)
{
    unsigned int nMate;
    G4String mateName;
    G4float densityMax;
    finData >> nMate;
    if( finData.eof() ) return;

    G4cout << " ReadMaterialIndices " << nMate << G4endl;
    for( unsigned int ii = 0; ii < nMate; ii++ ){
        finData >> mateName >> densityMax;
        fMaterialIndices[densityMax] = mateName;
        G4cout << ii << " ReadMaterialIndices " << mateName << " " << densityMax << G4endl;
    }

}

//========================================================================================

unsigned int DicomHandler::GetMaterialIndex( G4float density )
{
    std::map<G4float,G4String>::reverse_iterator ite;
    G4int ii = fMaterialIndices.size();
    for( ite = fMaterialIndices.rbegin(); ite != fMaterialIndices.rend(); ite++, ii-- ) {
        if( density >= (*ite).first ) {
            break;
        }
    }
    //-  G4cout << " GetMaterialIndex " << density << " = " << ii << G4endl;

    if(static_cast<unsigned int>(ii) == fMaterialIndices.size())
    { ii = fMaterialIndices.size()-1; }

    return  ii;

}

//========================================================================================

G4int DicomHandler::ReadData(FILE *dicom,char * filename2)
{
    G4int returnvalue = 0; size_t rflag = 0;

    //  READING THE PIXELS :
    G4int w = 0;

    fTab = new G4int*[fRows];
    for ( G4int i = 0; i < fRows; i ++ ) {
        fTab[i] = new G4int[fColumns];
    }

    if(fBitAllocated == 8) { // Case 8 bits :

        std::printf("@@@ Error! Picture != 16 bits...\n");
        std::printf("@@@ Error! Picture != 16 bits...\n");
        std::printf("@@@ Error! Picture != 16 bits...\n");

        unsigned char ch = 0;

        for(G4int j = 0; j < fRows; j++) {
            for(G4int i = 0; i < fColumns; i++) {
                w++;
                rflag = std::fread( &ch, 1, 1, dicom);
                fTab[j][i] = ch*fRescaleSlope + fRescaleIntercept;
            }
        }
        returnvalue = 1;

    } else { //  from 12 to 16 bits :
        char sbuff[2];
        short pixel;
        for( G4int j = 0; j < fRows; j++) {
            for( G4int i = 0; i < fColumns; i++) {
                w++;
                rflag = std::fread(sbuff, 2, 1, dicom);
                GetValue(sbuff, pixel);
                fTab[j][i] = pixel*fRescaleSlope + fRescaleIntercept;
            }
        }
    }

    // Creation of .g4 files wich contains averaged density data
    char * nameProcessed = new char[FILENAMESIZE];
    FILE* fileOut;

    std::sprintf(nameProcessed,"%s.g4dcmb",filename2);
    fileOut = std::fopen(nameProcessed,"w+b");
    std::printf("### Writing of %s ###\n",nameProcessed);

    unsigned int nMate = fMaterialIndices.size();
    rflag = std::fwrite(&nMate, sizeof(unsigned int), 1, fileOut);
    //--- Write materials
    std::map<G4float,G4String>::const_iterator ite;
    for( ite = fMaterialIndices.begin(); ite != fMaterialIndices.end(); ite++ ){
        G4String mateName = (*ite).second;
        for( G4int ii = (*ite).second.length(); ii < 40; ii++ ) {
            mateName += " ";
        }         //mateName = const_cast<char*>(((*ite).second).c_str());

        const char* mateNameC = mateName.c_str();
        rflag = std::fwrite(mateNameC, sizeof(char),40, fileOut);
    }

    unsigned int fRowsC = fRows/fCompression;
    unsigned int fColumnsC = fColumns/fCompression;
    unsigned int planesC = 1;
    G4float pixelLocationXM = -fPixelSpacingX*fColumns/2.;
    G4float pixelLocationXP = fPixelSpacingX*fColumns/2.;
    G4float pixelLocationYM = -fPixelSpacingY*fRows/2.;
    G4float pixelLocationYP = fPixelSpacingY*fRows/2.;
    G4float fSliceLocationZM = fSliceLocation-fSliceThickness/2.;
    G4float fSliceLocationZP = fSliceLocation+fSliceThickness/2.;
    //--- Write number of voxels (assume only one voxel in Z)
    rflag = std::fwrite(&fRowsC, sizeof(unsigned int), 1, fileOut);
    rflag = std::fwrite(&fColumnsC, sizeof(unsigned int), 1, fileOut);
    rflag = std::fwrite(&planesC, sizeof(unsigned int), 1, fileOut);
    //--- Write minimum and maximum extensions
    rflag = std::fwrite(&pixelLocationXM, sizeof(G4float), 1, fileOut);
    rflag = std::fwrite(&pixelLocationXP, sizeof(G4float), 1, fileOut);
    rflag = std::fwrite(&pixelLocationYM, sizeof(G4float), 1, fileOut);
    rflag = std::fwrite(&pixelLocationYP, sizeof(G4float), 1, fileOut);
    rflag = std::fwrite(&fSliceLocationZM, sizeof(G4float), 1, fileOut);
    rflag = std::fwrite(&fSliceLocationZP, sizeof(G4float), 1, fileOut);
    // rflag = std::fwrite(&fCompression, sizeof(unsigned int), 1, fileOut);

    std::printf("%8i   %8i\n",fRows,fColumns);
    std::printf("%8f   %8f\n",fPixelSpacingX,fPixelSpacingY);
    std::printf("%8f\n", fSliceThickness);
    std::printf("%8f\n", fSliceLocation);
    std::printf("%8i\n", fCompression);

    G4int compSize = fCompression;
    G4int mean;
    G4float density;
    G4bool overflow = false;

    //----- Write index of material for each pixel
    if(compSize == 1) { // no fCompression: each pixel has a density value)
        for( G4int ww = 0; ww < fRows; ww++) {
            for( G4int xx = 0; xx < fColumns; xx++) {
                mean = fTab[ww][xx];
                density = Pixel2density(mean);
                unsigned int mateID = GetMaterialIndex( density );
                rflag = std::fwrite(&mateID, sizeof(unsigned int), 1, fileOut);
            }
        }

    } else {
        // density value is the average of a square region of
        // fCompression*fCompression pixels
        for(G4int ww = 0; ww < fRows ;ww += compSize ) {
            for(G4int xx = 0; xx < fColumns ;xx +=compSize ) {
                overflow = false;
                mean = 0;
                for(int sumx = 0; sumx < compSize; sumx++) {
                    for(int sumy = 0; sumy < compSize; sumy++) {
                        if(ww+sumy >= fRows || xx+sumx >= fColumns) overflow = true;
                        mean += fTab[ww+sumy][xx+sumx];
                    }
                    if(overflow) break;
                }
                mean /= compSize*compSize;

                if(!overflow) {
                    density = Pixel2density(mean);
                    unsigned int mateID = GetMaterialIndex( density );
                    rflag = std::fwrite(&mateID, sizeof(unsigned int), 1, fileOut);
                }
            }

        }
    }

    //----- Write density for each pixel
    if(compSize == 1) { // no fCompression: each pixel has a density value)
        for( G4int ww = 0; ww < fRows; ww++) {
            for( G4int xx = 0; xx < fColumns; xx++) {
                mean = fTab[ww][xx];
                density = Pixel2density(mean);
                rflag = std::fwrite(&density, sizeof(G4float), 1, fileOut);
            }
        }

    } else {
        // density value is the average of a square region of
        // fCompression*fCompression pixels
        for(G4int ww = 0; ww < fRows ;ww += compSize ) {
            for(G4int xx = 0; xx < fColumns ;xx +=compSize ) {
                overflow = false;
                mean = 0;
                for(int sumx = 0; sumx < compSize; sumx++) {
                    for(int sumy = 0; sumy < compSize; sumy++) {
                        if(ww+sumy >= fRows || xx+sumx >= fColumns) overflow = true;
                        mean += fTab[ww+sumy][xx+sumx];
                    }
                    if(overflow) break;
                }
                mean /= compSize*compSize;

                if(!overflow) {
                    density = Pixel2density(mean);
                    rflag = std::fwrite(&density, sizeof(G4float), 1, fileOut);
                }
            }

        }
    }

    rflag = std::fclose(fileOut);

    delete [] nameProcessed;

    /*    for ( G4int i = 0; i < fRows; i ++ ) {
     delete [] fTab[i];
     }
     delete [] fTab;
     */

    if (rflag) return returnvalue;
    return returnvalue;
}


//========================================================================================
// Separated out of Pixel2density
// No need to read in same calibration EVERY time
// Increases the speed of reading file by several orders of magnitude
void DicomHandler::ReadCalibration()
{
    nbrequali = 0;

    // CT2Density.dat contains the calibration curve to convert CT (Hounsfield)
    // number to physical density
    std::ifstream calibration(ct2densityFile.c_str());
    calibration >> nbrequali;

    valuedensity = new G4double[nbrequali];
    valueCT = new G4double[nbrequali];

    if(!calibration) {
        G4cerr << "@@@ No value to transform pixels in density!" << G4endl;
        exit(1);

    } else { // calibration was successfully opened
        for(G4int i = 0; i < nbrequali; i++) { // Loop to store all the pts in CT2Density.dat
            calibration >> valueCT[i] >> valuedensity[i];
        }
    }
    calibration.close();

    readCalibration = true;
}

//========================================================================================

G4float DicomHandler::Pixel2density(G4int pixel)
{
    if(!readCalibration) { ReadCalibration(); }

    G4float density = -1.;
    G4double deltaCT = 0;
    G4double deltaDensity = 0;


    for(G4int j = 1; j < nbrequali; j++) {
        if( pixel >= valueCT[j-1] && pixel < valueCT[j]) {

            deltaCT = valueCT[j] - valueCT[j-1];
            deltaDensity = valuedensity[j] - valuedensity[j-1];

            // interpolating linearly
            density = valuedensity[j] - ((valueCT[j] - pixel)*deltaDensity/deltaCT );
            break;
        }
    }

    if(density < 0.) {
        std::printf("@@@ Error density = %f && Pixel = %i \
        (0x%x) && deltaDensity/deltaCT = %f\n",density,pixel,pixel, deltaDensity/deltaCT);
    }

    return density;
}

//========================================================================================

void DicomHandler::CheckFileFormat()
{
    std::ifstream checkData(driverFile.c_str());
    char * oneLine = new char[128];

    if(!(checkData.is_open())) { //Check existance of Data.dat

        std::ostringstream message;
        message << "\nDicomG4 needs Data.dat (or another driver file specified"
                << " in command line):\n"
                << "\tFirst line: number of image pixel for a voxel (G4Box)\n"
                << "\tSecond line: number of images (CT slices) to read\n"
                << "\tEach following line contains the name of a Dicom image"
                << " except for the .dcm extension";
        G4cout << message.str() << G4endl;
        exit(0);
    }

    checkData >> fCompression;
    checkData >> fNFiles;
    G4String oneName;
    checkData.getline(oneLine,100);
    std::ifstream testExistence;
    G4bool existAlready = true;
    for(G4int rep = 0; rep < fNFiles; rep++) {
        checkData.getline(oneLine,100);
        oneName = oneLine;
        oneName += ".g4dcm"; // create dicomFile.g4dcm
        G4cout << fNFiles << " test file " << oneName << G4endl;
        testExistence.open(oneName.data());
        if(!(testExistence.is_open())) {
            existAlready = false;
            testExistence.clear();
            testExistence.close();
        }
        testExistence.clear();
        testExistence.close();
    }

    ReadMaterialIndices( checkData );

    checkData.close();
    delete [] oneLine;

    if( existAlready == false  ) { // The files *.g4dcm have to be created

        G4cout << "\nAll the necessary images were not found in processed form, starting "
        << "with .dcm images\n";

        FILE * dicom;
        FILE * lecturePref;
        char * fCompressionc = new char[LINEBUFFSIZE];
        char * maxc = new char[LINEBUFFSIZE];
        //char name[300], inputFile[300];
        char * name = new char[FILENAMESIZE];
        char * inputFile = new char[FILENAMESIZE];
        G4int rflag;

        lecturePref = std::fopen(driverFile.c_str(),"r");
        rflag = std::fscanf(lecturePref,"%s",fCompressionc);
        fCompression = atoi(fCompressionc);
        rflag = std::fscanf(lecturePref,"%s",maxc);
        fNFiles = atoi(maxc);
        G4cout << " fNFiles " << fNFiles << G4endl;

        for( G4int i = 1; i <= fNFiles; i++ ) { // Begin loop on filenames

            rflag = std::fscanf(lecturePref,"%s",inputFile);
            std::sprintf(name,"%s.dcm",inputFile);
            std::cout << "check 1: " << name << std::endl;
            //  Open input file and give it to gestion_dicom :
            std::printf("### Opening %s and reading :\n",name);
            dicom = std::fopen(name,"rb");
            // Reading the .dcm in two steps:
            //      1.  reading the header
            //        2. reading the pixel data and store the density in Moyenne.dat
            if( dicom != 0 ) {
                ReadFile(dicom,inputFile);
            } else {
                G4cout << "\nError opening file : " << name << G4endl;
            }
            rflag = std::fclose(dicom);
        }
        rflag = std::fclose(lecturePref);

        // Checks the spacing is correct. Dumps to files
        mergedSlices->CheckSlices();

        delete [] fCompressionc;
        delete [] maxc;
        delete [] name;
        delete [] inputFile;
        if (rflag) return;

    }

    if(valuedensity) { delete [] valuedensity; }
    if(valueCT) { delete [] valueCT; }
    if(mergedSlices) { delete mergedSlices; }


}

//========================================================================================

G4int DicomHandler::read_defined_nested(FILE * nested,G4int SQ_Length)
{
    //      VARIABLES
    unsigned short item_GroupNumber;
    unsigned short item_ElementNumber;
    G4int item_Length;
    G4int items_array_length=0;
    char * buffer= new char[LINEBUFFSIZE];
    size_t rflag = 0;

    while(items_array_length < SQ_Length)
    {
        rflag = std::fread(buffer, 2, 1, nested);
        GetValue(buffer, item_GroupNumber);

        rflag = std::fread(buffer, 2, 1, nested);
        GetValue(buffer, item_ElementNumber);

        rflag = std::fread(buffer, 4, 1, nested);
        GetValue(buffer, item_Length);

        rflag = std::fread(buffer, item_Length, 1, nested);

        items_array_length= items_array_length+8+item_Length;
    }

    delete [] buffer;

    if( SQ_Length>items_array_length )
        return 0;
    else
        return 1;
    if (rflag) return 1;
}

//========================================================================================

void DicomHandler::read_undefined_nested(FILE * nested)
{
    //      VARIABLES
    unsigned short item_GroupNumber;
    unsigned short item_ElementNumber;
    unsigned int item_Length;
    char * buffer= new char[LINEBUFFSIZE];
    size_t rflag = 0;

    do
    {
        rflag = std::fread(buffer, 2, 1, nested);
        GetValue(buffer, item_GroupNumber);

        rflag = std::fread(buffer, 2, 1, nested);
        GetValue(buffer, item_ElementNumber);

        rflag = std::fread(buffer, 4, 1, nested);
        GetValue(buffer, item_Length);

        if(item_Length!=0xffffffff)
            rflag = std::fread(buffer, item_Length, 1, nested);
        else
            read_undefined_item(nested);


    } while(item_GroupNumber!=0xFFFE || item_ElementNumber!=0xE0DD || item_Length!=0);

    delete [] buffer;
    if (rflag) return;
}

//========================================================================================

void DicomHandler::read_undefined_item(FILE * nested)
{
    //      VARIABLES
    unsigned short item_GroupNumber;
    unsigned short item_ElementNumber;
    G4int item_Length; size_t rflag = 0;
    char *buffer= new char[LINEBUFFSIZE];

    do
    {
        rflag = std::fread(buffer, 2, 1, nested);
        GetValue(buffer, item_GroupNumber);

        rflag = std::fread(buffer, 2, 1, nested);
        GetValue(buffer, item_ElementNumber);

        rflag = std::fread(buffer, 4, 1, nested);
        GetValue(buffer, item_Length);


        if(item_Length!=0)
            rflag = std::fread(buffer,item_Length,1,nested);

    }
    while(item_GroupNumber!=0xFFFE || item_ElementNumber!=0xE00D || item_Length!=0);

    delete [] buffer;
    if (rflag) return;
}

//========================================================================================

template <class Type>
void DicomHandler::GetValue(char * _val, Type & _rval) {

#if BYTE_ORDER == BIG_ENDIAN
    if(fLittleEndian) {      // little endian
#else // BYTE_ORDER == LITTLE_ENDIAN
        if(!fLittleEndian) {     // big endian
#endif
            const int SIZE = sizeof(_rval);
            char ctemp;
            for(int i = 0; i < SIZE/2; i++) {
                ctemp = _val[i];
                _val[i] = _val[SIZE - 1 - i];
                _val[SIZE - 1 - i] = ctemp;
            }
        }
        _rval = *(Type *)_val;
    }

//========================================================================================