--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+#ifndef clitkImage2DicomGenericFilter_h
+#define clitkImage2DicomGenericFilter_h
+
+/* =================================================
+ * @file clitkImage2DicomGenericFilter.h
+ * @author
+ * @date
+ *
+ * @brief
+ *
+ ===================================================*/
+
+
+// clitk include
+#include "clitkIO.h"
+#include "clitkImageCommon.h"
+#include "clitkImage2Dicom_ggo.h"
+
+//itk include
+#include "itkLightObject.h"
+#include "itkGDCMImageIO.h"
+#include "itkMetaDataDictionary.h"
+#include "itkGDCMSeriesFileNames.h"
+#include "itkImageSeriesReader.h"
+#include "itkImageSeriesWriter.h"
+#include <vector>
+#include <itksys/SystemTools.hxx>
+
+#include "itkImage.h"
+#include "itkMinimumMaximumImageFilter.h"
+
+#include "itkGDCMImageIO.h"
+#include "itkGDCMSeriesFileNames.h"
+#include "itkNumericSeriesFileNames.h"
+
+#include "itkImageSeriesReader.h"
+#include "itkImageSeriesWriter.h"
+
+#include "itkResampleImageFilter.h"
+
+#if ( ( ITK_VERSION_MAJOR == 4 ) && ( ITK_VERSION_MINOR < 6 ) )
+#include "itkShiftScaleImageFilter.h"
+#endif
+
+#include "itkIdentityTransform.h"
+#include "itkLinearInterpolateImageFunction.h"
+
+#include <itksys/SystemTools.hxx>
+
+#if ITK_VERSION_MAJOR >= 4
+#include "gdcmUIDGenerator.h"
+#else
+#include "gdcm/src/gdcmFile.h"
+#include "gdcm/src/gdcmUtil.h"
+#endif
+
+#include <string>
+#include <sstream>
+
+namespace clitk
+{
+ template<class args_info_type>
+ class ITK_EXPORT Image2DicomGenericFilter : public itk::LightObject
+ {
+ public:
+ //----------------------------------------
+ // ITK
+ //----------------------------------------
+ typedef Image2DicomGenericFilter Self;
+ typedef itk::LightObject Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ // Method for creation through the object factory
+ itkNewMacro(Self);
+
+ // Run-time type information (and related methods)
+ itkTypeMacro( Image2DicomGenericFilter, LightObject );
+
+
+ //----------------------------------------
+ // Typedefs
+ //----------------------------------------
+
+
+ //----------------------------------------
+ // Set & Get
+ //----------------------------------------
+ void SetArgsInfo(const args_info_type & a)
+ {
+ m_ArgsInfo=a;
+ m_Verbose=m_ArgsInfo.verbose_flag;
+ m_InputFileName=m_ArgsInfo.input_arg;
+ }
+
+
+ //----------------------------------------
+ // Update
+ //----------------------------------------
+ void Update();
+
+ protected:
+
+ //----------------------------------------
+ // Constructor & Destructor
+ //----------------------------------------
+ Image2DicomGenericFilter();
+ ~Image2DicomGenericFilter() {};
+
+
+ //void CopyDictionary (itk::MetaDataDictionary &fromDict, itk::MetaDataDictionary &toDict);
+ //----------------------------------------
+ // Templated members
+ //----------------------------------------
+ template <unsigned int Dimension> void UpdateWithDim(std::string PixelType);
+ template <unsigned int Dimension, class PixelType> void UpdateWithDimAndPixelType();
+
+
+ //----------------------------------------
+ // Data members
+ //----------------------------------------
+ args_info_type m_ArgsInfo;
+ bool m_Verbose;
+ std::string m_InputFileName;
+
+ };
+
+
+} // end namespace clitk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "clitkImage2DicomGenericFilter.txx"
+#endif
+
+#endif // #define clitkImage2DicomGenericFilter_h
--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
+
+ This software is distributed WITHOUT ANY WARRANTY; without even
+ the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ PURPOSE. See the copyright notices for more information.
+
+ It is distributed under dual licence
+
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
+#ifndef clitkImage2DicomGenericFilter_txx
+#define clitkImage2DicomGenericFilter_txx
+
+/* =================================================
+ * @file clitkImage2DicomGenericFilter.txx
+ * @author
+ * @date
+ *
+ * @brief
+ *
+ ===================================================*/
+
+#include "itkVersion.h"
+#include "itkImage.h"
+#include "itkGDCMImageIO.h"
+#include "itkGDCMSeriesFileNames.h"
+#include "itkNumericSeriesFileNames.h"
+#include "itkImageSeriesReader.h"
+#include "itkImageSeriesWriter.h"
+
+#include "itkThresholdImageFilter.h"
+
+#if ( ( ITK_VERSION_MAJOR == 4 ) && ( ITK_VERSION_MINOR < 6 ) )
+#include "itkShiftScaleImageFilter.h"
+#endif
+
+#include <string>
+#include <sstream>
+#if GDCM_MAJOR_VERSION >= 2
+#include <gdcmUIDGenerator.h>
+#include <gdcmImageHelper.h>
+#include <gdcmAttribute.h>
+#include <gdcmReader.h>
+#include <gdcmWriter.h>
+#include <gdcmDataElement.h>
+#include <gdcmTag.h>
+#else
+#include "gdcmFile.h"
+#include "gdcmUtil.h"
+#endif
+
+namespace clitk
+{
+
+
+//-----------------------------------------------------------
+// Constructor
+//-----------------------------------------------------------
+template<class args_info_type>
+Image2DicomGenericFilter<args_info_type>::Image2DicomGenericFilter()
+{
+ m_Verbose=false;
+ m_InputFileName="";
+}
+
+
+//-----------------------------------------------------------
+// Update
+//-----------------------------------------------------------
+template<class args_info_type>
+void Image2DicomGenericFilter<args_info_type>::Update()
+{
+ // Read the Dimension and PixelType
+ int Dimension;
+ std::string PixelType;
+ ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType);
+
+
+ // Call UpdateWithDim
+ if(Dimension==2) UpdateWithDim<2>(PixelType);
+ else if(Dimension==3) UpdateWithDim<3>(PixelType);
+ // else if (Dimension==4)UpdateWithDim<4>(PixelType);
+ else {
+ std::cout<<"Error, Only for 2 or 3 Dimensions!!!"<<std::endl ;
+ return;
+ }
+}
+
+//-------------------------------------------------------------------
+// Update with the number of dimensions
+//-------------------------------------------------------------------
+template<class args_info_type>
+template<unsigned int Dimension>
+void
+Image2DicomGenericFilter<args_info_type>::UpdateWithDim(std::string PixelType)
+{
+ if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<"..."<<std::endl;
+
+ if(PixelType == "short") {
+ if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
+ UpdateWithDimAndPixelType<Dimension, signed short>();
+ }
+ else if(PixelType == "unsigned_short"){
+ if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
+ UpdateWithDimAndPixelType<Dimension, unsigned short>();
+ }
+
+ else if (PixelType == "unsigned_char") {
+ if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
+ UpdateWithDimAndPixelType<Dimension, unsigned char>();
+ }
+
+ // else if (PixelType == "char"){
+ // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
+ // UpdateWithDimAndPixelType<Dimension, signed char>();
+ // }
+ else if (PixelType == "double") {
+ if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and double..." << std::endl;
+ UpdateWithDimAndPixelType<Dimension, double>();
+ }
+ else {
+ if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
+ UpdateWithDimAndPixelType<Dimension, float>();
+ }
+}
+
+//-------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype read from
+// the dicom files. The MHD files may be resampled to match the
+// dicom spacing (and number of slices). Rounding errors in resampling
+// are handled by removing files when generating the output dicom
+// series.
+//-------------------------------------------------------------------
+template<class args_info_type>
+template <unsigned int Dimension, class PixelType>
+void
+Image2DicomGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
+{
+ // Validate input parameters
+
+ const unsigned int InputDimension = Dimension;
+ const unsigned int OutputDimension = Dimension-1;
+
+ typedef itk::Image< PixelType, InputDimension > InputImageType;
+ typedef itk::Image< PixelType, OutputDimension > OutputImageType;
+ typedef itk::ImageSeriesReader< InputImageType > ReaderType;
+ typedef itk::GDCMImageIO ImageIOType;
+#if ( ( ITK_VERSION_MAJOR == 4 ) && ( ITK_VERSION_MINOR < 6 ) )
+ typedef itk::ShiftScaleImageFilter< InputImageType, InputImageType > ShiftScaleType;
+#endif
+ typedef itk::ImageSeriesWriter< InputImageType, OutputImageType > SeriesWriterType;
+
+////////////////////////////////////////////////
+// 1) Read the input series
+
+// Read the input (MHD file)
+ typedef typename InputImageType::RegionType RegionType;
+ typedef typename RegionType::SizeType SizeType;
+ typedef itk::ImageFileReader<InputImageType> InputReaderType;
+ typename InputReaderType::Pointer volumeReader = InputReaderType::New();
+ volumeReader->SetFileName(m_ArgsInfo.input_arg);
+ volumeReader->Update();
+ typename InputImageType::Pointer input = volumeReader->GetOutput();
+ typedef itk::NumericSeriesFileNames OutputNamesGeneratorType;
+
+ ImageIOType::Pointer gdcmIO = ImageIOType::New();
+ gdcmIO->LoadPrivateTagsOn();
+ typename ReaderType::FileNamesContainer filenames;
+ filenames.push_back(m_ArgsInfo.inputDcm_arg);
+ typename ReaderType::Pointer reader = ReaderType::New();
+ reader->SetImageIO(gdcmIO);
+ reader->SetFileNames(filenames);
+ try {
+ reader->Update();
+ } catch (itk::ExceptionObject &excp) {
+ std::cerr << "Exception thrown while reading the series" << std::endl;
+ std::cerr << excp << std::endl;
+ return;
+ }
+
+ typename InputImageType::SpacingType outputSpacing;
+ typename InputImageType::SizeType outputSize;
+ for (unsigned int i = 0; i < 3; i++) {
+ outputSpacing[i] = input->GetSpacing()[i];
+ outputSize[i] = input->GetLargestPossibleRegion().GetSize()[i];
+ }
+
+////////////////////////////////////////////////
+// 2) Ensure to have value >= -1024
+
+ typedef itk::ThresholdImageFilter <InputImageType> ThresholdImageFilterType;
+ typename ThresholdImageFilterType::Pointer thresholdFilter = ThresholdImageFilterType::New();
+ thresholdFilter->SetInput(input);
+ thresholdFilter->ThresholdBelow(-1024);
+ thresholdFilter->SetOutsideValue(-1024);
+ thresholdFilter->Update();
+
+ input=thresholdFilter->GetOutput();
+
+////////////////////////////////////////////////
+// 3) Create a MetaDataDictionary for each slice.
+
+ // Copy the dictionary from the first image and override slice
+ // specific fields
+ typename ReaderType::DictionaryRawPointer inputDict = (*(reader->GetMetaDataDictionaryArray()))[0];
+ typename ReaderType::DictionaryArrayType outputArray;
+
+ // To keep the new series in the same study as the original we need
+ // to keep the same study UID. But we need new series and frame of
+ // reference UID's.
+#if ITK_VERSION_MAJOR >= 4
+ gdcm::UIDGenerator suid;
+ std::string seriesUID = suid.Generate();
+ gdcm::UIDGenerator fuid;
+ std::string frameOfReferenceUID = fuid.Generate();
+#else
+ std::string seriesUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
+ std::string frameOfReferenceUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
+#endif
+ std::string studyUID;
+ std::string sopClassUID;
+ itk::ExposeMetaData<std::string>(*inputDict, "0020|000d", studyUID);
+ itk::ExposeMetaData<std::string>(*inputDict, "0008|0016", sopClassUID);
+ gdcmIO->KeepOriginalUIDOn();
+ for (unsigned int f = 0; f < outputSize[2]; f++)
+ {
+ // Create a new dictionary for this slice
+ typename ReaderType::DictionaryRawPointer dict = new typename ReaderType::DictionaryType;
+
+ typedef itk::MetaDataDictionary DictionaryType;
+
+ DictionaryType::ConstIterator itrDic = (*inputDict).Begin();
+ DictionaryType::ConstIterator endDic = (*inputDict).End();
+ typedef itk::MetaDataObject< std::string > MetaDataStringType;
+
+ while( itrDic != endDic )
+ {
+ itk::MetaDataObjectBase::Pointer entry = itrDic->second;
+
+ MetaDataStringType::Pointer entryvalue =
+ dynamic_cast<MetaDataStringType *>( entry.GetPointer() ) ;
+ if( entryvalue )
+ {
+ std::string tagkey = itrDic->first;
+ std::string tagvalue = entryvalue->GetMetaDataObjectValue();
+ itk::EncapsulateMetaData<std::string>(*dict, tagkey, tagvalue);
+ }
+ ++itrDic;
+ }
+
+ // Set the UID's for the study, series, SOP and frame of reference
+ itk::EncapsulateMetaData<std::string>(*dict,"0020|000d", studyUID);
+ itk::EncapsulateMetaData<std::string>(*dict,"0020|000e", seriesUID);
+ itk::EncapsulateMetaData<std::string>(*dict,"0020|0052", frameOfReferenceUID);
+
+ #if ITK_VERSION_MAJOR >= 4
+ gdcm::UIDGenerator sopuid;
+ std::string sopInstanceUID = sopuid.Generate();
+ #else
+ std::string sopInstanceUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix());
+ #endif
+ itk::EncapsulateMetaData<std::string>(*dict,"0008|0018", sopInstanceUID);
+ itk::EncapsulateMetaData<std::string>(*dict,"0002|0003", sopInstanceUID);
+
+ // Change fields that are slice specific
+ std::ostringstream value;
+ value.str("");
+ value << f + 1;
+ // Image Number
+ itk::EncapsulateMetaData<std::string>(*dict,"0020|0013", value.str());
+
+ // Series Description - Append new description to current series
+ // description
+ std::string oldSeriesDesc;
+ itk::ExposeMetaData<std::string>(*inputDict, "0008|103e", oldSeriesDesc);
+
+ value.str("");
+ value << oldSeriesDesc
+ << ": Resampled with pixel spacing "
+ << outputSpacing[0] << ", "
+ << outputSpacing[1] << ", "
+ << outputSpacing[2];
+ // This is an long string and there is a 64 character limit in the
+ // standard
+ unsigned lengthDesc = value.str().length();
+
+ std::string seriesDesc( value.str(), 0,
+ lengthDesc > 64 ? 64
+ : lengthDesc);
+ itk::EncapsulateMetaData<std::string>(*dict,"0008|103e", seriesDesc);
+
+ // Series Number
+ value.str("");
+ value << 1001;
+ itk::EncapsulateMetaData<std::string>(*dict,"0020|0011", value.str());
+
+ // Derivation Description - How this image was derived
+ value.str("");
+
+
+
+
+
+ value << ": " << ITK_SOURCE_VERSION;
+
+ lengthDesc = value.str().length();
+ std::string derivationDesc( value.str(), 0,
+ lengthDesc > 1024 ? 1024
+ : lengthDesc);
+ itk::EncapsulateMetaData<std::string>(*dict,"0008|2111", derivationDesc);
+
+ // Image Position Patient: This is calculated by computing the
+ // physical coordinate of the first pixel in each slice.
+ typename InputImageType::PointType position;
+ typename InputImageType::IndexType index;
+ index[0] = 0;
+ index[1] = 0;
+ index[2] = f;
+ input->TransformIndexToPhysicalPoint(index, position);
+
+ value.str("");
+ value << position[0] << "\\" << position[1] << "\\" << position[2];
+ itk::EncapsulateMetaData<std::string>(*dict,"0020|0032", value.str());
+ // Slice Location: For now, we store the z component of the Image
+ // Position Patient.
+ value.str("");
+ value << position[2];
+ itk::EncapsulateMetaData<std::string>(*dict,"0020|1041", value.str());
+
+ // Slice Thickness: For now, we store the z spacing
+ value.str("");
+ value << outputSpacing[2];
+ itk::EncapsulateMetaData<std::string>(*dict,"0018|0050", value.str());
+ // Spacing Between Slices
+ itk::EncapsulateMetaData<std::string>(*dict,"0018|0088", value.str());
+ // Save the dictionary
+ outputArray.push_back(dict);
+ }
+
+#if ( ( ITK_VERSION_MAJOR == 4 ) && ( ITK_VERSION_MINOR < 6 ) )
+////////////////////////////////////////////////
+// 4) Shift data to undo the effect of a rescale intercept by the
+// DICOM reader
+ std::string interceptTag("0028|1052");
+ typedef itk::MetaDataObject<std::string> MetaDataStringType;
+ itk::MetaDataObjectBase::Pointer entry = (*inputDict)[interceptTag];
+
+ MetaDataStringType::ConstPointer interceptValue =
+ dynamic_cast<const MetaDataStringType *>(entry.GetPointer());
+
+ int interceptShift = 0;
+ if(interceptValue ) {
+ std::string tagValue = interceptValue->GetMetaDataObjectValue();
+ interceptShift = -atoi (tagValue.c_str());
+ }
+
+ ShiftScaleType::Pointer shiftScale = ShiftScaleType::New();
+ shiftScale->SetInput(resampler->GetOutput());
+ shiftScale->SetShift(interceptShift );
+#endif
+
+////////////////////////////////////////////////
+// 5) Write the new DICOM series
+ // Generate the file names
+ typename ReaderType::FileNamesContainer fileNamesOutput;
+
+ // Generate the file names
+ OutputNamesGeneratorType::Pointer outputNames = OutputNamesGeneratorType::New();
+ std::string seriesFormat(m_ArgsInfo.outputDcm_arg);
+ seriesFormat = seriesFormat + "/" + "IM%d.dcm";
+ outputNames->SetSeriesFormat(seriesFormat.c_str());
+ outputNames->SetStartIndex(1);
+ outputNames->SetEndIndex(outputSize[2]);
+
+ typename SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New();
+#if ( ( ITK_VERSION_MAJOR == 4 ) && ( ITK_VERSION_MINOR < 6 ) )
+ seriesWriter->SetInput(input);
+#else
+ seriesWriter->SetInput(input);
+#endif
+ seriesWriter->SetImageIO(gdcmIO);
+ seriesWriter->SetFileNames(outputNames->GetFileNames());
+ seriesWriter->SetMetaDataDictionaryArray(&outputArray);
+ try {
+ seriesWriter->Update();
+ } catch(itk::ExceptionObject & excp) {
+ std::cerr << "Exception thrown while writing the series " << std::endl;
+ std::cerr << excp << std::endl;
+ return;
+ }
+/*
+////////////////////////////////////////////////
+// 5) Read the new dicom data tag and copy it in the model data tag to have all dicom tags
+ gdcm::Reader readerModel, readerOutput;
+ readerModel.SetFileName(filenames[0].c_str());
+ readerOutput.SetFileName(fileNamesOutput[0].c_str());
+ readerModel.Read();
+ readerOutput.Read();
+ gdcm::File &fileModel = readerModel.GetFile();
+ gdcm::File &fileOutput = readerOutput.GetFile();
+ gdcm::DataSet &dsModel = fileModel.GetDataSet();
+ gdcm::DataSet &dsOutput = fileOutput.GetDataSet();
+ const unsigned int ptr_len = 42;
+ char *ptr = new char[ptr_len];
+ memset(ptr,0,ptr_len);
+
+ const gdcm::DataElement &dataOutput = dsOutput.GetDataElement(gdcm::Tag(0x7fe0, 0x10));
+ dsModel.Replace(dataOutput);
+ gdcm::Writer w;
+ w.SetFile(fileModel);
+ w.SetFileName(fileNamesOutput[0].c_str());
+ w.Write();
+ return;
+*/
+}
+}//end clitk
+
+#endif //#define clitkImage2DicomGenericFilter_txx
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff