// clitk
#include "clitkImage2DicomRTStructFilter.h"
+#include "clitkBinaryImageToMeshFilter.h"
#include "clitkImageCommon.h"
+#include "vvFromITK.h"
// vtk
#include <vtkPolyDataToImageStencil.h>
#include <vtkLinearExtrusionFilter.h>
#include <vtkMetaImageWriter.h>
#include <vtkImageData.h>
+
+// FIXME to remove
+#include "vtkPolyDataMapper.h"
+#include "vtkPolyDataMapper2D.h"
+#include "vtkRenderWindowInteractor.h"
+#include "vtkPolyDataReader.h"
+#include "vtkRenderWindow.h"
+#include "vtkRenderer.h"
+#include "vtkCamera.h"
+#include "vtkProperty.h"
+#include "vtkProperty2D.h"
+#include <vtksys/SystemTools.hxx>
+
+// itk
#include <itkImage.h>
#include <itkVTKImageToImageFilter.h>
+// gdcm
+#include <vtkRTStructSetProperties.h>
+#include <vtkGDCMPolyDataReader.h>
+#include <vtkGDCMPolyDataWriter.h>
+
//--------------------------------------------------------------------
template<class PixelType>
clitk::Image2DicomRTStructFilter<PixelType>::Image2DicomRTStructFilter()
{
- DD("Image2DicomRTStructFilter Const");
+ m_StructureSetFilename = "";
+ m_DicomFolder = "";
+ m_OutputFilename = "default-output.dcm";
+ m_ThresholdValue = 0.5;
+ m_SkipInitialStructuresFlag = false;
}
//--------------------------------------------------------------------
template<class PixelType>
clitk::Image2DicomRTStructFilter<PixelType>::~Image2DicomRTStructFilter()
{
- DD("Image2DicomRTStructFilter Destructor");
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class PixelType>
+void
+clitk::Image2DicomRTStructFilter<PixelType>::SetROIType(std::string type)
+{
+ m_ROIType = type;
}
//--------------------------------------------------------------------
template<class PixelType>
void clitk::Image2DicomRTStructFilter<PixelType>::Update()
{
- DD("Image2DicomRTStructFilter::Update");
+ // Check this is a RT-Struct
+ gdcm::Reader gdcm_reader;
+ gdcm_reader.SetFileName(m_StructureSetFilename.c_str());
+ if (!gdcm_reader.Read()) {
+ clitkExceptionMacro("Error could not open the file '" << m_StructureSetFilename << std::endl);
+ }
+ gdcm::MediaStorage ms;
+ ms.SetFromFile(gdcm_reader.GetFile());
+ if (ms != gdcm::MediaStorage::RTStructureSetStorage) {
+ clitkExceptionMacro("File '" << m_StructureSetFilename << "' is not a DICOM-RT-Struct file." << std::endl);
+ }
+
+ // Read rt struct
+ vtkSmartPointer<vtkGDCMPolyDataReader> reader = vtkGDCMPolyDataReader::New();
+ reader->SetFileName(m_StructureSetFilename.c_str());
+ reader->Update();
+
+ // Get properties
+ vtkRTStructSetProperties * p = reader->GetRTStructSetProperties();
+ if (GetVerboseFlag()) {
+ std::cout << "Number of structures in the dicom-rt-struct : "
+ << p->GetNumberOfStructureSetROIs() << std::endl;
+ }
+
+ // number of additional contours
+ int m = m_InputFilenames.size();
+
+ // Init writer
+ vtkGDCMPolyDataWriter * writer = vtkGDCMPolyDataWriter::New();
+ int numMasks = reader->GetNumberOfOutputPorts() + m;
+
+ if (m_SkipInitialStructuresFlag) {
+ numMasks = m;
+ }
+
+ writer->SetNumberOfInputPorts(numMasks);
+ writer->SetFileName(m_OutputFilename.c_str());
+ writer->SetMedicalImageProperties(reader->GetMedicalImageProperties());
+
+ // List of already present rois
+ vtkStringArray* roiNames = vtkStringArray::New();
+ vtkStringArray* roiAlgorithms = vtkStringArray::New();
+ vtkStringArray* roiTypes = vtkStringArray::New();
+ roiNames->SetNumberOfValues(numMasks);
+ roiAlgorithms->SetNumberOfValues(numMasks);
+ roiTypes->SetNumberOfValues(numMasks);
+
+ // Convert the image into a mesh
+ std::vector<vtkSmartPointer<vtkPolyData> > meshes;
+ std::vector<std::string> m_ROINames;
+ meshes.resize(m);
+ m_ROINames.resize(m);
+ for(unsigned int i=0; i<m; i++) {
+
+ // read image
+ // typedef float PixelType;
+ //typedef itk::Image<PixelType, 3> ImageType;
+ ImagePointer input = clitk::readImage<ImageType>(m_InputFilenames[i], false);
+
+ std::ostringstream oss;
+ oss << vtksys::SystemTools::
+ GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(m_InputFilenames[i]));
+ std::string name = oss.str();
+ m_ROINames[i] = name;
+
+ // convert to mesh
+ typedef clitk::BinaryImageToMeshFilter<ImageType> BinaryImageToMeshFilterType;
+ typename BinaryImageToMeshFilterType::Pointer convert = BinaryImageToMeshFilterType::New();
+ convert->SetThresholdValue(m_ThresholdValue);
+ convert->SetInput(input);
+ convert->Update();
+ meshes[i] = convert->GetOutputMesh();
+ if (GetVerboseFlag()) {
+ std::cout << "Mesh has " << meshes[i]->GetNumberOfLines() << " lines." << std::endl;
+ }
+
+ /*
+ // debug mesh write FIXME
+ vtkSmartPointer<vtkPolyDataWriter> wr = vtkSmartPointer<vtkPolyDataWriter>::New();
+ wr->SetInputConnection(convert->GetOutputPort()); //psurface->GetOutputPort()
+ wr->SetFileName("bidon.obj");
+ wr->Update();
+ wr->Write();
+ */
+ }
+
+ // Copy previous contours
+ for (unsigned int i = 0; i < numMasks-m; ++i) {
+#if VTK_MAJOR_VERSION <= 5
+ writer->SetInput(i, reader->GetOutput(i));
+#else
+ writer->SetInputData(i, reader->GetOutput(i));
+#endif
+ std::string theString = reader->GetRTStructSetProperties()->GetStructureSetROIName(i);
+ roiNames->InsertValue(i, theString);
+ theString = reader->GetRTStructSetProperties()->GetStructureSetROIGenerationAlgorithm(i);
+ roiAlgorithms->InsertValue(i, theString);
+ theString = reader->GetRTStructSetProperties()->GetStructureSetRTROIInterpretedType(i);
+ roiTypes->InsertValue(i, theString);
+ }
+
+ // Add new ones
+ for (unsigned int i = numMasks-m; i < numMasks; ++i) {
+#if VTK_MAJOR_VERSION <= 5
+ writer->SetInput(i, meshes[i-numMasks+m]);
+#else
+ writer->SetInputData(i, meshes[i-numMasks+m]);
+#endif
+ roiNames->InsertValue(i, m_ROIType);
+ roiAlgorithms->InsertValue(i, "CLITK_CREATED");
+ roiTypes->InsertValue(i, m_ROIType);
+ }
+
+ /*
+ // Visu DEBUG
+ vtkPolyDataMapper *cubeMapper = vtkPolyDataMapper::New();
+ cubeMapper->SetInput( mesh );
+ cubeMapper->SetScalarRange(0,7);
+ vtkActor *cubeActor = vtkActor::New();
+ cubeActor->SetMapper(cubeMapper);
+ vtkProperty * property = cubeActor->GetProperty();
+ property->SetRepresentationToWireframe();
+
+ vtkRenderer *renderer = vtkRenderer::New();
+ vtkRenderWindow *renWin = vtkRenderWindow::New();
+ renWin->AddRenderer(renderer);
+
+ vtkRenderWindowInteractor *iren = vtkRenderWindowInteractor::New();
+ iren->SetRenderWindow(renWin);
+
+ renderer->AddActor(cubeActor);
+ renderer->ResetCamera();
+ renderer->SetBackground(1,1,1);
+
+ renWin->SetSize(300,300);
+ renWin->Render();
+ iren->Start();
+ */
+ // End visu
+ // Write (need to read dicom for slice id)
+ vtkRTStructSetProperties* theProperties = vtkRTStructSetProperties::New();
+ writer->SetRTStructSetProperties(theProperties);
+ if (GetVerboseFlag()) {
+ std::cout << "Looking for dicom info, study instance "
+ << p->GetStudyInstanceUID() << std::endl;
+ }
+ writer->InitializeRTStructSet(m_DicomFolder,
+ reader->GetRTStructSetProperties()->GetStructureSetLabel(),
+ reader->GetRTStructSetProperties()->GetStructureSetName(),
+ roiNames, roiAlgorithms, roiTypes);
+ writer->Write();
+ reader->Delete();
+ roiNames->Delete();
+ roiTypes->Delete();
+ roiAlgorithms->Delete();
+ writer->Delete();
}
//--------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff