#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::GenerateData");
+ // 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();
- DD("reader done");
+ reader->Update();
// Get properties
vtkRTStructSetProperties * p = reader->GetRTStructSetProperties();
- DD(p->GetNumberOfStructureSetROIs());
- DD(p->GetStructureSetROIName(0));
- DD(p->GetStructureSetROINumber(0));
-
+ 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() + 1;//add one more
- DD(numMasks);
-
- // numMasks = 3; //FIXME temporary
+ int numMasks = reader->GetNumberOfOutputPorts() + m;
+
+ if (m_SkipInitialStructuresFlag) {
+ numMasks = m;
+ }
writer->SetNumberOfInputPorts(numMasks);
writer->SetFileName(m_OutputFilename.c_str());
roiNames->SetNumberOfValues(numMasks);
roiAlgorithms->SetNumberOfValues(numMasks);
roiTypes->SetNumberOfValues(numMasks);
-
- typedef clitk::BinaryImageToMeshFilter<ImageType> BinaryImageToMeshFilterType;
- typename BinaryImageToMeshFilterType::Pointer convert = BinaryImageToMeshFilterType::New();
- convert->SetInput(m_Input);
- DD("Update");
- convert->Update();
- DD("here");
- DD("end update");
- vtkPolyData* mesh = convert->GetOutputMesh();
- DD(mesh->GetNumberOfVerts());
- DD(mesh->GetNumberOfLines());
- DD(mesh->GetNumberOfPolys());
- DD(mesh->GetNumberOfStrips());
-
- // Add on (FIXME) to replace with binary image
- // vtkPolyData* blank = vtkPolyData::New();
- // writer->SetInput(0, blank);
- writer->SetInput(0, mesh);
- roiNames->InsertValue(0, "blank");
- roiAlgorithms->InsertValue(0, "blank");
- roiTypes->InsertValue(0, "ORGAN");
-
- for (unsigned int i = 1; i < numMasks; ++i) {
- // DD(i);
- writer->SetInput(i, reader->GetOutput(i-1));
- std::string theString = reader->GetRTStructSetProperties()->GetStructureSetROIName(i-1);
+
+ // 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-1);
+ theString = reader->GetRTStructSetProperties()->GetStructureSetROIGenerationAlgorithm(i);
roiAlgorithms->InsertValue(i, theString);
- theString = reader->GetRTStructSetProperties()->GetStructureSetRTROIInterpretedType(i-1);
+ 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
+ // Visu DEBUG
vtkPolyDataMapper *cubeMapper = vtkPolyDataMapper::New();
cubeMapper->SetInput( mesh );
cubeMapper->SetScalarRange(0,7);
renWin->Render();
iren->Start();
*/
-
-
// End visu
-
+ // Write (need to read dicom for slice id)
vtkRTStructSetProperties* theProperties = vtkRTStructSetProperties::New();
- DD(p->GetStudyInstanceUID());
writer->SetRTStructSetProperties(theProperties);
- /*writer->InitializeRTStructSet2(p,"./",
- reader->GetRTStructSetProperties()->GetStructureSetLabel(),
- reader->GetRTStructSetProperties()->GetStructureSetName(),
- roiNames, roiAlgorithms, roiTypes);*/
+ 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);
-
- DD("after init");
writer->Write();
- DD("write done");
-
reader->Delete();
roiNames->Delete();
roiTypes->Delete();
- //theProperties->Delete();
roiAlgorithms->Delete();
- //blank->Delete();
writer->Delete();
-
- ////////////////////
-
-
- /*
-
- // DicomRTStruct
- DD(m_StructureSet->GetName());
- clitk::DicomRT_ROI * roi = m_StructureSet->GetROIFromROINumber(1); // Aorta
- DD(roi->GetName());
- DD(roi->GetROINumber());
-
-
- // Get
-
-
-
-
- // Add an image to the roi
- vvImage::Pointer im = vvImageFromITK<3, PixelType>(m_Input);
- roi->SetImage(im);
-
- // Get one contour
- DD("Compute Mesh");
- roi->ComputeContoursFromImage(); // FIXME do the set mesh for the moment (to change)
- // roi->ComputeMeshFromContour();
- vtkSmartPointer<vtkPolyData> mesh = roi->GetMesh();
- DD("done");
-
- // 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(true); // indicate that dicom info must be updated from the mesh.
-
- // Convert to dicom ?
- DD("TODO");
-
- // Write
- structset->Write("toto.dcm");
- */
}
//--------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff