Implementing the DICOM reader. (cfcd049e) · Commits · TNL / tnl-dev

CMakeLists.txt

+4 −0

Original line number	Diff line number	Diff line
		@@ -160,6 +160,10 @@ if( DCMTK_FOUND )
		set( HAVE_DCMTK_H "#define HAVE_DCMTK_H 1" )
		include_directories( ${DCMTK_INCLUDE_DIRS} )
		set( HAVE_DCMTK TRUE)
		set( DCMTK_LD_FLAGS "" )
		foreach( arg ${DCMTK_LIBRARIES} )
		set( DCMTK_LD_FLAGS "${DCMTK_LD_FLAGS} ${arg}" )
		endforeach( arg ${DCMTK_LIBRARIES} )
		else()
		set( HAVE_DCMTK_H "//#define HAVE_DCMTK_H 1" )
		endif()

src/core/images/tnlDicomSeries.h

+6 −2

Original line number	Diff line number	Diff line
		@@ -72,13 +72,17 @@ class tnlDicomSeries : public tnlImage< int >

		inline int getImagesCount();

		template< typename Vector >
		template< typename Real,
		typename Device,
		typename Index,
		typename Vector >
		bool getImage( const int imageIdx,
		const tnlGrid< 2, Real, Device, Index >& grid,
		const tnlRegionOfInterest< int > roi,
		Vector& vector );

		#ifdef HAVE_DCMTK_H
		inline const Uint16 *getData();
		inline const Uint16 *getData( int imageNumber = 0 );
		#endif

		inline int getColorCount();

src/core/images/tnlDicomSeries_impl.h

+94 −48

Original line number	Diff line number	Diff line
		@@ -78,20 +78,61 @@ inline tnlDicomSeries::~tnlDicomSeries()
		delete pixelData;
		}

		template< typename Real,
		typename Device,
		typename Index,
		typename Vector >
		bool
		tnlDicomSeries::
		getImage( const int imageIdx,
		const tnlGrid< 2, Real, Device, Index >& grid,
		const tnlRegionOfInterest< int > roi,
		Vector& vector )
		{
		const Uint16* imageData = this->getData( imageIdx );
		typedef tnlGrid< 2, Real, Device, Index > GridType;
		typedef typename GridType::CoordinatesType CoordinatesType;

		Index i, j;
		int position( 0 );
		for( i = 0; i < this->height; i ++ )
		{
		for( j = 0; j < this->width; j ++ )
		{
		if( roi.isIn( i, j ) )
		{
		Index cellIndex = grid.getCellIndex( CoordinatesType( j - roi.getLeft(),
		roi.getBottom() - 1 - i ) );
		Uint16 col = imageData[ position ];
		vector.setElement( cellIndex, ( Real ) col / ( Real ) this->getMaxColorValue() );
		cout << vector.getElement( cellIndex ) << " ";
		}
		position++;
		}
		cout << endl;
		}
		return true;
		}

		inline bool tnlDicomSeries::retrieveFileList( const tnlString& filePath)
		{
		tnlString filePathString(filePath);
		tnlString suffix(filePath.getString(), filePathString.getLength() - 3);
		//char *ima = "ima";
		//char *dcm = "dcm";

		//check DICOM files
		/***
		* Check DICOM files
		*/
		if( suffix != "ima" && suffix != "dcm" )
		{
		cerr << "The given file is not a DICOM file." << endl;
		return false;
		}

		int fileNamePosition = findLastIndexOf(filePathString,"/");

		//parse file path
		/***
		* Parse file path
		*/
		tnlString fileName(filePath.getString(), fileNamePosition);
		tnlString directoryPath(filePath.getString(), 0, filePathString.getLength() - fileNamePosition);

		@@ -271,9 +312,14 @@ inline bool tnlDicomSeries::loadImage( const tnlString& filePath, int number)

		inline bool tnlDicomSeries::loadDicomSeries( const tnlString& filePath )
		{
		//load list of files
		/***
		* Load list of files
		*/
		if( ! retrieveFileList( filePath ) )
		{
		cerr << "I am not able to retrieve the files of the DICOM series in " << filePath << "." << endl;
		return false;
		}

		//load images
		int imagesCountToLoad = fileList->getSize();
		@@ -292,9 +338,9 @@ inline int tnlDicomSeries::getImagesCount()
		return imagesInfo.imagesCount;
		}

		inline const Uint16 *tnlDicomSeries::getData()
		inline const Uint16 *tnlDicomSeries::getData( int imageNumber )
		{
		return pixelData;
		return &pixelData[ imageNumber * imagesInfo.frameUintsCount ];
		}

		inline int tnlDicomSeries::getColorCount()

tools/src/tnl-dicom-reader.cpp

+20 −6

Original line number	Diff line number	Diff line
		@@ -19,6 +19,7 @@
		#include <config/tnlConfigDescription.h>
		#include <config/tnlParameterContainer.h>
		#include <core/images/tnlDicomSeries.h>
		#include <core/mfilename.h>

		void setupConfig( tnlConfigDescription& config )
		{
		@@ -52,7 +53,12 @@ bool processDicomSeries( const tnlParameterContainer& parameters )
		for( int i = 0; i < dicomSeriesNames.getSize(); i++ )
		{
		const tnlString& seriesName = dicomSeriesNames[ i ];
		cout << "Reading a file " << seriesName << endl;
		tnlDicomSeries dicomSeries( seriesName.getString() );
		if( !dicomSeries.isDicomSeriesLoaded() )
		{
		cerr << "Loading of the DICOM series " << seriesName << " failed." << endl;
		}
		if( i == 0 )
		{
		if( ! roi.setup( parameters, &dicomSeries ) )
		@@ -61,9 +67,16 @@ bool processDicomSeries( const tnlParameterContainer& parameters )
		vector.setSize( grid.getNumberOfCells() );
		cout << "Writing grid to file " << meshFile << endl;
		grid.save( meshFile );

		}

		cout << "The series consists of " << dicomSeries.getImagesCount() << " images." << endl;
		for( int imageIdx = 0; imageIdx < dicomSeries.getImagesCount(); imageIdx++ )
		{
		dicomSeries.getImage( imageIdx, grid, roi, vector );
		tnlString fileName;
		FileNameBaseNumberEnding( seriesName.getString(), imageIdx, 2, ".tnl", fileName );
		cout << "Writing file " << fileName << " ... " << endl;
		vector.save( fileName );
		}
		}
		}
		#endif
		@@ -71,17 +84,18 @@ bool processDicomSeries( const tnlParameterContainer& parameters )
		int main( int argc, char* argv[] )
		{
		tnlParameterContainer parameters;
		tnlConfigDescription conf_desc;
		setupConfig( conf_desc );
		if( ! parseCommandLine( argc, argv, conf_desc, parameters ) )
		tnlConfigDescription configDescription;
		setupConfig( configDescription );
		if( ! parseCommandLine( argc, argv, configDescription, parameters ) )
		{
		conf_desc.printUsage( argv[ 0 ] );
		configDescription.printUsage( argv[ 0 ] );
		return EXIT_FAILURE;
		}
		if( ! parameters.checkParameter( "dicom-files" ) &&
		! parameters.checkParameter( "dicom-series") )
		{
		cerr << "Neither DICOM series nor DICOM files are given." << endl;
		configDescription.printUsage( argv[ 0 ] );
		return EXIT_FAILURE;
		}
		#ifdef HAVE_DCMTK_H

tools/src/tnl-image-converter.cpp

+7 −3

Original line number	Diff line number	Diff line
		@@ -195,14 +195,18 @@ bool processTNLFiles( const tnlParameterContainer& parameters )
		int main( int argc, char* argv[] )
		{
		tnlParameterContainer parameters;
		tnlConfigDescription conf_desc;
		configSetup( conf_desc );
		if( ! parseCommandLine( argc, argv, conf_desc, parameters ) )
		tnlConfigDescription configDescription;
		configSetup( configDescription );
		if( ! parseCommandLine( argc, argv, configDescription, parameters ) )
		{
		configDescription.printUsage( argv[ 0 ] );
		return EXIT_FAILURE;
		}
		if( ! parameters.checkParameter( "input-images" ) &&
		! parameters.checkParameter( "input-files") )
		{
		cerr << "Neither input images nor input .tnl files are given." << endl;
		configDescription.printUsage( argv[ 0 ] );
		return EXIT_FAILURE;
		}
		if( parameters.checkParameter( "input-images" ) && ! processImages( parameters ) )