// clitk
#include "clitkImage2DicomRTStructFilter.h"
+#include "clitkBinaryImageToMeshFilter.h"
#include "clitkImageCommon.h"
#include "vvFromITK.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"
+
// itk
#include <itkImage.h>
#include <itkVTKImageToImageFilter.h>
+// gdcm
+#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;
}
//--------------------------------------------------------------------
template<class PixelType>
clitk::Image2DicomRTStructFilter<PixelType>::~Image2DicomRTStructFilter()
{
- DD("Image2DicomRTStructFilter Destructor");
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
template<class PixelType>
-void clitk::Image2DicomRTStructFilter<PixelType>::Update()
+void
+clitk::Image2DicomRTStructFilter<PixelType>::SetROIName(std::string name, std::string type)
{
- DD("Image2DicomRTStructFilter::GenerateData");
+ m_ROIName = name;
+ m_ROIType = type;
+}
+//--------------------------------------------------------------------
- // Read DicomRTStruct
- std::string filename = "RS.zzQAnotmt_french01_.dcm";
- clitk::DicomRT_StructureSet::Pointer structset = clitk::DicomRT_StructureSet::New();
- structset->Read(filename);
-
- DD(structset->GetName());
- clitk::DicomRT_ROI * roi = structset->GetROIFromROINumber(1); // Aorta
- DD(roi->GetName());
- DD(roi->GetROINumber());
-
- // Add an image to the roi
- vvImage::Pointer im = vvImageFromITK<3, PixelType>(m_Input);
- roi->SetImage(im);
-
- // Get one contour
- DD("Compute Mesh");
- roi->ComputeMeshFromImage();
- vtkSmartPointer<vtkPolyData> mesh = roi->GetMesh();
- DD("done");
+
+//--------------------------------------------------------------------
+template<class PixelType>
+void clitk::Image2DicomRTStructFilter<PixelType>::Update()
+{
+ // 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;
+ }
- // Change the mesh (shift by 10);
- // const vtkSmartPointer<vtkPoints> & points = mesh->GetPoints();
- // for(uint i=0; i<mesh->GetNumberOfVerts (); i++) {
- // DD(i);
- // double * p = points->GetPoint(i);
- // p[0] += 30;
- // points->SetPoint(i, p);
- // }
- roi->SetName("TOTO");
- roi->SetDicomUptodateFlag(false); // indicate that dicom info must be updated from the mesh.
-
- // Convert to dicom ?
- DD("TODO");
+ // Init writer
+ vtkGDCMPolyDataWriter * writer = vtkGDCMPolyDataWriter::New();
+ int numMasks = reader->GetNumberOfOutputPorts() + 1;//add one more
+ 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);
- // Write
- structset->Write("toto.dcm");
+ // Convert the image into a mesh
+ typedef clitk::BinaryImageToMeshFilter<ImageType> BinaryImageToMeshFilterType;
+ typename BinaryImageToMeshFilterType::Pointer convert = BinaryImageToMeshFilterType::New();
+ convert->SetThresholdValue(m_ThresholdValue);
+ convert->SetInput(m_Input);
+ convert->Update();
+ vtkPolyData* mesh = convert->GetOutputMesh();
+ if (GetVerboseFlag()) {
+ std::cout << "Mesh has " << mesh->GetNumberOfLines() << " lines." << std::endl;
+ }
+
+ // Copy previous contours
+ for (unsigned int i = 0; i < numMasks-1; ++i) {
+ writer->SetInput(i, reader->GetOutput(i));
+ 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 one
+ int last = numMasks-1;
+ writer->SetInput(last, mesh);
+ roiNames->InsertValue(last, m_ROIName);
+ roiAlgorithms->InsertValue(last, "CLITK_CREATED");
+ roiTypes->InsertValue(last, 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();
}
//--------------------------------------------------------------------