Commit 2f0b73d8 authored by Tomáš Oberhuber's avatar Tomáš Oberhuber
Browse files

Implementing the DICOM reader.

parent afe05ef1

src/core/images/tnlDicomHeader.h

+1 −1
Original line number Diff line number Diff line
@@ -56,7 +56,7 @@ class tnlDicomHeader 
      

      inline tnlDicomSeriesInfo &getSeriesInfo();



      inline bool loadFromFile( const char* fileName );

      inline bool loadFromFile( const tnlString& fileName );



   protected:

src/core/images/tnlDicomHeader_impl.h

+2 −2
Original line number Diff line number Diff line
@@ -40,9 +40,9 @@ inline tnlDicomHeader::~tnlDicomHeader() 
    delete fileFormat;

}



inline bool tnlDicomHeader::loadFromFile(const char *fileName)

inline bool tnlDicomHeader::loadFromFile( const tnlString& fileName )

{

    OFCondition status = fileFormat->loadFile(fileName);

    OFCondition status = fileFormat->loadFile( fileName.getString() );

    if(status.good())

    {

        isLoaded = true;

src/core/images/tnlDicomSeries.h

+14 −10
Original line number Diff line number Diff line
@@ -26,7 +26,10 @@ 
#include <core/tnlList.h>

#include <core/tnlString.h>

#include <core/param-types.h>

#include <core/images/tnlImage.h>

#include <core/images/tnlDicomHeader.h>

#include <core/images/tnlRegionOfInterest.h>

#include <mesh/tnlGrid.h>

#include <tnlConfig.h>
@@ -49,7 +52,7 @@ struct WindowCenterWidth 


struct ImagesInfo

{

    int width, height, imagesCount, frameUintsCount, bps, colorsCount, mainFrameIndex,

    int imagesCount, frameUintsCount, bps, colorsCount, mainFrameIndex,

        frameSize, maxColorValue, minColorValue;

    WindowCenterWidth window;

};
@@ -59,24 +62,25 @@ struct ImagesInfo 
 * DICOM serie (searches the directory of the file). Call isDicomSeriesLoaded()

 * function to check if the load was successful.

 */

class tnlDicomSeries

class tnlDicomSeries : public tnlImage< int >

{

   public:

      

      inline tnlDicomSeries( const char *filePath );

      inline tnlDicomSeries( const tnlString& filePath );

       

      inline virtual ~tnlDicomSeries();



      inline int getImagesCount();

            

      template< typename Vector >

      bool getImage( const int imageIdx,

                     const tnlRegionOfInterest< int > roi,

                     Vector& vector );

       

#ifdef HAVE_DCMTK_H       

      inline const Uint16 *getData();

#endif       

       

      inline int getWidth();

       

      inline int getHeight();

       

      inline int getColorCount();

       

      inline int getBitsPerSampleCount();
@@ -95,11 +99,11 @@ class tnlDicomSeries 


   private:

      

      bool loadDicomSeries( const char *filePath );

      bool loadDicomSeries( const tnlString& filePath );

       

      bool retrieveFileList( const char *filePath );

      bool retrieveFileList( const tnlString& filePath );

       

      bool loadImage( char *filePath, int number );

      bool loadImage( const tnlString& filePath, int number );



      tnlList<tnlString *> *fileList;

src/core/images/tnlDicomSeries_impl.h

+59 −73
Original line number Diff line number Diff line
@@ -43,7 +43,7 @@ int filter(const struct dirent *dire) 
    return 1;

}



inline tnlDicomSeries::tnlDicomSeries( const char* filePath)

inline tnlDicomSeries::tnlDicomSeries( const tnlString& filePath)

{

    fileList = new tnlList<tnlString *>();

    dicomImage = 0;
@@ -78,10 +78,10 @@ inline tnlDicomSeries::~tnlDicomSeries() 
        delete pixelData;

}



inline bool tnlDicomSeries::retrieveFileList( const char *filePath)

inline bool tnlDicomSeries::retrieveFileList( const tnlString& filePath)

{

    tnlString filePathString(filePath);

    tnlString suffix(filePath, filePathString.getLength() - 3);

    tnlString suffix(filePath.getString(), filePathString.getLength() - 3);

    //char *ima = "ima";

    //char *dcm = "dcm";
@@ -92,8 +92,8 @@ inline bool tnlDicomSeries::retrieveFileList( const char *filePath) 
    int fileNamePosition = findLastIndexOf(filePathString,"/");



    //parse file path

    tnlString fileName(filePath, fileNamePosition);

    tnlString directoryPath(filePath, 0, filePathString.getLength() - fileNamePosition);

    tnlString fileName(filePath.getString(), fileNamePosition);

    tnlString directoryPath(filePath.getString(), 0, filePathString.getLength() - fileNamePosition);



    int separatorPosition = findLastIndexOf(fileName, "_");

    if (separatorPosition == -1)
@@ -135,29 +135,25 @@ inline bool tnlDicomSeries::retrieveFileList( const char *filePath) 
    return true;

}



inline bool tnlDicomSeries::loadImage(char *filePath, int number)

inline bool tnlDicomSeries::loadImage( const tnlString& filePath, int number)

{

   //load header

   tnlDicomHeader *header = new tnlDicomHeader();

   dicomSeriesHeaders.setSize( fileList->getSize() );

   dicomSeriesHeaders.setElement( number, header );

   if( !header->loadFromFile( filePath ) )

    {

      return false;

    }



   //check series UID

    const tnlString& seriesUID = dicomSeriesHeaders.operator [](0)->getSeriesInfo().getSeriesInstanceUID();

   const tnlString& seriesUID = dicomSeriesHeaders[ 0 ]->getSeriesInfo().getSeriesInstanceUID();

   if( seriesUID != header->getSeriesInfo().getSeriesInstanceUID() )

    {

      return false;

    }



   //load image

   if( dicomImage ) delete dicomImage;

   dicomImage = NULL;



    dicomImage = new DicomImage(filePath);

   dicomImage = new DicomImage( filePath.getString() );



   if(dicomImage->getFrameCount() > 1)

   {
@@ -198,18 +194,18 @@ inline bool tnlDicomSeries::loadImage(char *filePath, int number) 


    if(number == 0)

    {

        imagesInfo.height = dicomImage->getHeight();

        this->height = dicomImage->getHeight();

    }

    else if(dicomImage->getHeight() != imagesInfo.height)

    else if(dicomImage->getHeight() != this->height)

    {

        cerr << filePath <<" image has bad height value\n";

    }



    if(number == 0)

    {

        imagesInfo.width = dicomImage->getWidth ();

        this->width = dicomImage->getWidth ();

    }

    else if(dicomImage->getWidth() != imagesInfo.width)

    else if(dicomImage->getWidth() != this->width)

    {

        cerr << filePath <<" image has bad width value\n";

    }
@@ -266,14 +262,14 @@ inline bool tnlDicomSeries::loadImage(char *filePath, int number) 
    dicomImage->getOutputData(target,size,16);

    imagesInfo.imagesCount++;



    //delete image object - data are stored separatedly

    //delete image object - data are stored separately

    delete dicomImage;

    dicomImage = NULL;

    return true;

}





inline bool tnlDicomSeries::loadDicomSeries( const char *filePath )

inline bool tnlDicomSeries::loadDicomSeries( const tnlString& filePath )

{

   //load list of files

   if( !retrieveFileList( filePath ) )
@@ -283,9 +279,9 @@ inline bool tnlDicomSeries::loadDicomSeries( const char *filePath ) 
   int imagesCountToLoad = fileList->getSize();

   for( int i=0; i < imagesCountToLoad; i++ )

   {

         if(!loadImage((fileList->operator [](i))->getString(),i))

      if( !loadImage( ( ( *fileList )[ i ] )->getString(),i ) )

      {

             cerr << (fileList->operator [](i))->getString() << " skipped";

         cerr << ( ( *fileList )[ i ] )->getString() << " skipped";

      }

   }

   return true;
@@ -301,16 +297,6 @@ inline const Uint16 *tnlDicomSeries::getData() 
    return pixelData;

}



inline int tnlDicomSeries::getWidth()

{

    return imagesInfo.width;

}



inline int tnlDicomSeries::getHeight()

{

    return imagesInfo.height;

}



inline int tnlDicomSeries::getColorCount()

{

    return imagesInfo.colorsCount;

src/core/images/tnlRegionOfInterest.h

+4 −0
Original line number Diff line number Diff line
@@ -47,6 +47,10 @@ class tnlRegionOfInterest 
      

      Index getHeight() const;

      

      template< typename Grid >

         bool setGrid( Grid& grid,

                       bool verbose = false );

      

      bool isIn( const Index row, const Index column ) const;

      

   protected: