DicomHandler Class Reference

#include <DicomHandler.hh>

Public Member Functions
	DicomHandler ()
	~DicomHandler ()
G4int	ReadFile (FILE *, char *)
G4int	ReadData (FILE *, char *)
void	CheckFileFormat ()

Static Public Member Functions
static DicomHandler *	Instance ()

Detailed Description

Definition at line 71 of file DicomHandler.hh.

Constructor & Destructor Documentation

DicomHandler::DicomHandler

(

)

Definition at line 79 of file DicomHandler.cc.

:   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), fNbrequali(0),
    fValueDensity(NULL),fValueCT(NULL),fReadCalibration(false),
    fMergedSlices(NULL),fDriverFile("Data.dat"),fCt2DensityFile("CT2Density.dat")
{
    fMergedSlices = new DicomPhantomZSliceMerged;
}

DicomHandler::~DicomHandler

(

)

Definition at line 96 of file DicomHandler.cc.

{

}

Member Function Documentation

void DicomHandler::CheckFileFormat

(

)

Definition at line 863 of file DicomHandler.cc.

{
  std::ifstream checkData(fDriverFile.c_str());
  char * oneLine = new char[128];
  
  if(!(checkData.is_open())) { //Check existance of Data.dat
    
    G4String message = 
      "\nDicomG4 needs Data.dat (or another driver file specified";
    message += " in command line):\n";
    message += "\tFirst line: number of image pixel for a voxel (G4Box)\n";
    message += "\tSecond line: number of images (CT slices) to read\n";
    message += "\tEach following line contains the name of a Dicom image";
    message += " except for the .dcm extension";
    G4Exception("DicomHandler::ReadFile",
                "DICOM001",
                FatalException,
                message.c_str());
  }
  
  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(fDriverFile.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);
      G4cout << "check 1: " << name << G4endl;
      //  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
    fMergedSlices->CheckSlices();
    
    delete [] fCompressionc;
    delete [] maxc;
    delete [] name;
    delete [] inputFile;
    if (rflag) return;
    
  }
  
  if(fValueDensity) { delete [] fValueDensity; }
  if(fValueCT) { delete [] fValueCT; }
  if(fMergedSlices) { delete fMergedSlices; }
  
}

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DicomHandler * DicomHandler::Instance ( void  )

static

Definition at line 72 of file DicomHandler.cc.

{
    return fInstance;
}

G4int DicomHandler::ReadData	(	FILE *	dicom,
		char *	filename2
	)

Definition at line 613 of file DicomHandler.cc.

{
  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;
}

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G4int DicomHandler::ReadFile	(	FILE *	dicom,
		char *	filename2
	)

Definition at line 103 of file DicomHandler.cc.

{
    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){
            G4Exception("DicomHandler::ReadFile",
                      "DICOM001",
                      FatalException,
                      "Function read_defined_nested() failed!");
            }
          }
        } 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) {
          G4Exception("DicomHandler::ReadFile",
                  "DICOM001",
                  FatalException,
                  "fseek failed");
        }
    
        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.);

    //===

    ReadData( dicom, filename2 );

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

    StoreData( zslice );

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

    fMergedSlices->AddZSlice(zslice);

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

    if (rflag) return returnvalue;
    return returnvalue;
}

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---

The documentation for this class was generated from the following files:

• source/geant4.10.03.p02/examples/extended/medical/DICOM/include/DicomHandler.hh
• source/geant4.10.03.p02/examples/extended/medical/DICOM/src/DicomHandler.cc