#include "vtkCamera.h"
#include "vtkProperty.h"
#include "vtkProperty2D.h"
+#include <vtksys/SystemTools.hxx>
// itk
#include <itkImage.h>
m_DicomFolder = "";
m_OutputFilename = "default-output.dcm";
m_ThresholdValue = 0.5;
+ m_SkipInitialStructuresFlag = false;
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
template<class PixelType>
void
-clitk::Image2DicomRTStructFilter<PixelType>::SetROIName(std::string name, std::string type)
+clitk::Image2DicomRTStructFilter<PixelType>::SetROIType(std::string type)
{
- m_ROIName = name;
m_ROIType = type;
}
//--------------------------------------------------------------------
template<class PixelType>
void clitk::Image2DicomRTStructFilter<PixelType>::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();
+ reader->Update();
// Get properties
vtkRTStructSetProperties * p = reader->GetRTStructSetProperties();
<< 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
+ int numMasks = reader->GetNumberOfOutputPorts() + m;
+
+ if (m_SkipInitialStructuresFlag) {
+ numMasks = m;
+ }
+
writer->SetNumberOfInputPorts(numMasks);
writer->SetFileName(m_OutputFilename.c_str());
writer->SetMedicalImageProperties(reader->GetMedicalImageProperties());
roiTypes->SetNumberOfValues(numMasks);
// 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;
+ 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-1; ++i) {
+ for (unsigned int i = 0; i < numMasks-m; ++i) {
writer->SetInput(i, reader->GetOutput(i));
std::string theString = reader->GetRTStructSetProperties()->GetStructureSetROIName(i);
roiNames->InsertValue(i, theString);
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);
-
+ // Add new ones
+ for (unsigned int i = numMasks-m; i < numMasks; ++i) {
+ writer->SetInput(i, meshes[i-numMasks+m]);
+ roiNames->InsertValue(i, m_ROINames[i-numMasks+m]);
+ roiAlgorithms->InsertValue(i, "CLITK_CREATED");
+ roiTypes->InsertValue(i, m_ROIType);
+ }
+
/*
// Visu DEBUG
vtkPolyDataMapper *cubeMapper = vtkPolyDataMapper::New();