--- /dev/null
+/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+ Main authors : XX XX XX
+
+ Authors belongs 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 http://www.opensource.org/licenses/bsd-license.php
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+
+ =========================================================================*/
+
+// clitk
+#include "clitkXml2DicomRTStructFilter.h"
+
+// xml parser
+#include "../utilities/pugixml/pugixml.hpp"
+
+// vtk
+#include <vtkSmartPointer.h>
+#include <vtkMetaImageWriter.h>
+#include <vtkImageData.h>
+#include <vtkPolygon.h>
+#include <vtkAppendPolyData.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>
+
+// gdcm
+#include <vtkRTStructSetProperties.h>
+#include <vtkGDCMPolyDataReader.h>
+#include <vtkGDCMPolyDataWriter.h>
+
+//--------------------------------------------------------------------
+template<class PixelType>
+clitk::Xml2DicomRTStructFilter<PixelType>::Xml2DicomRTStructFilter()
+{
+ m_StructureSetFilename = "";
+ m_DicomFolder = "";
+ m_OutputFilename = "default-output.dcm";
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class PixelType>
+clitk::Xml2DicomRTStructFilter<PixelType>::~Xml2DicomRTStructFilter()
+{
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class PixelType>
+void clitk::Xml2DicomRTStructFilter<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();
+
+ // Get properties
+ vtkRTStructSetProperties * p = reader->GetRTStructSetProperties();
+ if (GetVerboseFlag()) {
+ std::cout << "Number of structures in the dicom-rt-struct : "
+ << p->GetNumberOfStructureSetROIs() << std::endl;
+ }
+
+ std::map<std::string, vtkSmartPointer<vtkAppendPolyData> > mapName2Data;
+
+ pugi::xml_document doc;
+ pugi::xml_parse_result result = doc.load_file(m_InputFilename.c_str());
+ if (!result) {
+ std::cout << "ERROR: no result" << std::endl;
+ return;
+ }
+
+ //Take the main dict and look for point_mm in each struct in each slice
+ pugi::xml_node mainDict = doc.child("plist").child("dict").child("array");
+ for (pugi::xml_node_iterator mainDictIt = mainDict.begin(); mainDictIt != mainDict.end(); ++mainDictIt) { //Look for all slice (one slice per dict)
+ if (!std::strcmp(mainDictIt->name(), "dict")) {
+ for (pugi::xml_node_iterator sliceIt = mainDictIt->child("array").begin(); sliceIt != mainDictIt->child("array").end(); ++sliceIt) { //Look for all struct in the current slice (one struct per dict)
+ if (!std::strcmp(sliceIt->name(), "dict")) {
+ pugi::xml_node_iterator structureIt = sliceIt->begin();
+ while (structureIt != sliceIt->end() && std::abs(std::strcmp(structureIt->child_value(), "Name"))) //Look for the name for the current struct
+ ++structureIt;
+ if (structureIt != sliceIt->end()) { //take the following node to have the values
+ ++structureIt;
+ std::string name(structureIt->child_value());
+ while (structureIt != sliceIt->end() && std::abs(std::strcmp(structureIt->child_value(), "Point_mm"))) //Look for the Point_mm for the current struct
+ ++structureIt;
+ if (structureIt != sliceIt->end()) { //take the following node to have the values
+ ++structureIt;
+ // Insert all points for 1 struct into vtkPoints
+ vtkSmartPointer<vtkPoints> points = vtkSmartPointer<vtkPoints>::New();
+ for (pugi::xml_node_iterator pointIt = structureIt->begin(); pointIt != structureIt->end(); ++pointIt) { //Look for all points in mm in the current struct (one point per string)
+ if (!std::strcmp(pointIt->name(), "string")) {
+ // Split the string to save the 3 values (remove the useless char) as double
+ char* copy = (char*)pointIt->child_value();
+ std::vector<char*> v;
+ char* chars_array = strtok(copy, ", ");
+ while(chars_array) {
+ v.push_back(chars_array);
+ chars_array = strtok(NULL, ", ");
+ }
+ v[0] = v[0] + 1;
+ v[2][strlen(v[2])-1] = '\0';
+ double x, y, z;
+ x = std::atof(v[0]);
+ y = std::atof(v[1]);
+ z = std::atof(v[2]);
+ points->InsertNextPoint(x, y, z);
+ }
+ }
+
+ //Create the polygon attached to the points
+ vtkSmartPointer<vtkPolygon> polygon = vtkSmartPointer<vtkPolygon>::New();
+ polygon->GetPointIds()->SetNumberOfIds(points->GetNumberOfPoints()); //make a quad
+ for (int pointIdx=0; pointIdx<points->GetNumberOfPoints(); ++pointIdx)
+ polygon->GetPointIds()->SetId(pointIdx, pointIdx);
+ // Add the polygon to a list of polygons
+ vtkSmartPointer<vtkCellArray> polygons = vtkSmartPointer<vtkCellArray>::New();
+ polygons->InsertNextCell(polygon);
+ // Create a PolyData
+ vtkSmartPointer<vtkPolyData> polygonPolyData = vtkSmartPointer<vtkPolyData>::New();
+ polygonPolyData->SetPoints(points);
+ polygonPolyData->SetPolys(polygons);
+
+ //Append the polyData into the map at the correct stuct name entry
+ std::map<std::string, vtkSmartPointer<vtkAppendPolyData> >::const_iterator it = mapName2Data.find(name);
+ if (it == mapName2Data.end())
+ mapName2Data[name] = vtkSmartPointer<vtkAppendPolyData>::New();
+#if VTK_MAJOR_VERSION <= 5
+ mapName2Data[name]->AddInput(polygonPolyData);
+#else
+ mapName2Data[name]->AddInputData(polygonPolyData);
+#endif
+ }
+ }
+ }
+ }
+ }
+ }
+
+ for (std::map<std::string, vtkSmartPointer<vtkAppendPolyData> >::iterator it = mapName2Data.begin(); it != mapName2Data.end(); ++it)
+ it->second->Update();
+
+ // number of contours
+ int numMasks = mapName2Data.size();
+
+ // Init writer
+ vtkGDCMPolyDataWriter * writer = vtkGDCMPolyDataWriter::New();
+ 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);
+
+ // Add new structures
+ std::map<std::string, vtkSmartPointer<vtkAppendPolyData> >::iterator it = mapName2Data.begin();
+ for (unsigned int i = 0; i < numMasks; ++i) {
+#if VTK_MAJOR_VERSION <= 5
+ writer->SetInput(i, it->second->GetOutput());
+#else
+ writer->SetInputData(i, it->second->GetOutput());
+#endif
+ roiNames->InsertValue(i, it->first);
+ roiAlgorithms->InsertValue(i, "CLITK_CREATED");
+ roiTypes->InsertValue(i, "coucou"); //Roi type instead of coucou
+ ++it;
+ }
+
+ /*
+ // Visu DEBUG
+ vtkPolyDataMapper *cubeMapper = vtkPolyDataMapper::New();
+ cubeMapper->SetInputData( mapName2Data[0]->GetOutput() );
+ 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