/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
- Program: vv
- Language: C++
- Author : Joel Schaerer (joel.schaerer@insa-lyon.fr)
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
-Copyright (C) 2008
-Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
-CREATIS-LRMN 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.
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, version 3 of the License.
+ It is distributed under dual licence
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-=========================================================================*/
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+======================================================================-====*/
#include <algorithm>
#include <QApplication>
+#include <gdcmFile.h>
+#if GDCM_MAJOR_VERSION == 2
+#else
#include <gdcm.h>
#include <gdcmSQItem.h>
+#endif
#include <vtkSmartPointer.h>
#include <vtkAppendPolyData.h>
#include "clitkCommon.h"
#include "vvMeshReader.h"
#include "vvProgressDialog.h"
+#include <clitkCommon.h>
vvMeshReader::vvMeshReader() :
- vtk_mode(false)
+ vtk_mode(false)
{}
void vvMeshReader::Update()
{
- //Show a progress bar only when opening a DC-struct (ie. multiple contours)
- vvProgressDialog progress("Opening " + filename,(not vtk_mode) and (selected_contours.size()>1));
- this->start();
- while (this->isRunning())
- {
- progress.SetProgress(result.size(),selected_contours.size());
- this->wait(50);
- qApp->processEvents();
- }
+ //Show a progress bar only when opening a DC-struct (ie. multiple contours)
+ vvProgressDialog progress("Opening " + filename,(!vtk_mode) && (selected_contours.size()>1));
+ this->start();
+ while (this->isRunning()) {
+ progress.SetProgress(result.size(),selected_contours.size());
+ this->wait(50);
+ qApp->processEvents();
+ }
}
void vvMeshReader::run()
{
- ///Verify the important stuff has been set
- assert(filename != "");
- if (vtk_mode) //Read vtkPolyData
- {
- vvMesh::Pointer m=vvMesh::New();
- m->ReadFromVTK(filename.c_str());
- if (vf) m->propagateContour(vf);
- result.push_back(m);
- }
- else //Read a Dicom-struct file
- {
- assert(selected_contours.size() > 0);
- assert(image);
- std::vector<vvMesh::Pointer> contour_stacks=readSelectedContours();
- for (std::vector<vvMesh::Pointer>::iterator i=contour_stacks.begin();
- i!=contour_stacks.end();i++)
- {
- (*i)->ComputeMasks(image->GetVTKImages()[0],true); //Remesh the contour
- (*i)->ComputeMeshes();
- if (vf) (*i)->propagateContour(vf);
- result.push_back(*i);
- }
- }
-}
-
-template<class ElementType>
-ElementType parse_value(std::string str)
-{
- std::istringstream parser(str);
- ElementType value;
- parser >> value;
- assert(!parser.fail());
- return value;
-}
-
-template<class ElementType>
-std::vector<ElementType> parse_string(std::string str,char delim)
-{
- std::istringstream ss(str);
- std::string token;
- std::vector<ElementType> result;
- while (getline(ss,token,delim))
- {
- result.push_back(parse_value<ElementType>(token));
+ ///Verify the important stuff has been set
+ assert(filename != "");
+ if (vtk_mode) { //Read vtkPolyData
+ vvMesh::Pointer m=vvMesh::New();
+ m->ReadFromVTK(filename.c_str());
+ if (vf) m->propagateContour(vf);
+ m->ComputeMasks(image->GetVTKImages()[0],false); //don't extrude the contour
+ result.push_back(m);
+ } else { //Read a Dicom-struct file
+ assert(selected_contours.size() > 0);
+ assert(image);
+ std::vector<vvMesh::Pointer> contour_stacks=readSelectedContours();
+ for (std::vector<vvMesh::Pointer>::iterator i=contour_stacks.begin();
+ i!=contour_stacks.end(); i++) {
+ (*i)->ComputeMasks(image->GetVTKImages()[0],true); //Remesh the contour
+ (*i)->ComputeMeshes();
+ if (vf) (*i)->propagateContour(vf);
+ result.push_back(*i);
}
- return result;
+ }
}
std::vector<std::pair<int,std::string> > vvMeshReader::GetROINames()
{
- assert(filename!="");
- gdcm::File reader;
- reader.SetFileName(filename.c_str());
- reader.SetMaxSizeLoadEntry(16384);
- reader.Load();
-
- gdcm::SeqEntry * roi_info=reader.GetSeqEntry(0x3006,0x0020);
- assert(roi_info);
- std::vector<std::pair<int, std::string> > roi_names;
- // DD("ici");
- //int n=0;
- for (gdcm::SQItem* i=roi_info->GetFirstSQItem();i!=0;i=roi_info->GetNextSQItem())
- if (i->GetEntryValue(0x3006,0x0022)!= gdcm::GDCM_UNFOUND)
- roi_names.push_back(make_pair(atoi(i->GetEntryValue(0x3006,0x0022).c_str()),i->GetEntryValue(0x3006,0x0026)));
- return roi_names;
+ assert(filename!="");
+ std::vector<std::pair<int, std::string> > roi_names;
+#if GDCM_MAJOR_VERSION == 2
+#else
+ gdcm::File reader;
+ reader.SetFileName(filename.c_str());
+ reader.SetMaxSizeLoadEntry(16384);
+ reader.Load();
+
+ gdcm::SeqEntry * roi_info=reader.GetSeqEntry(0x3006,0x0020);
+ assert(roi_info);
+ // DD("ici");
+ //int n=0;
+ for (gdcm::SQItem* i=roi_info->GetFirstSQItem(); i!=0; i=roi_info->GetNextSQItem())
+ if (i->GetEntryValue(0x3006,0x0022)!= gdcm::GDCM_UNFOUND)
+ roi_names.push_back(make_pair(atoi(i->GetEntryValue(0x3006,0x0022).c_str()),i->GetEntryValue(0x3006,0x0026)));
+#endif
+ return roi_names;
}
std::vector<vvMesh::Pointer> vvMeshReader::readSelectedContours()
{
- gdcm::File reader;
- reader.SetFileName(filename.c_str());
- reader.SetMaxSizeLoadEntry(16384);
- reader.Load();
-
- std::vector<vvMesh::Pointer> result;
- gdcm::SeqEntry * rois=reader.GetSeqEntry(0x3006,0x0039);
- ///We need to iterate both on the contours themselves, and on the contour info
- gdcm::SeqEntry * roi_info=reader.GetSeqEntry(0x3006,0x0020);
- gdcm::SQItem* k=roi_info->GetFirstSQItem();
- for(gdcm::SQItem* i=rois->GetFirstSQItem();i!=0;i=rois->GetNextSQItem()) //loop over ROIS
- {
- assert(k!=0);
- vtkSmartPointer<vtkAppendPolyData> append=vtkSmartPointer<vtkAppendPolyData>::New();
- std::istringstream ss(i->GetEntryValue(0x3006,0x0084));
- int roi_number;ss >> roi_number;
- if (std::find(selected_contours.begin(),selected_contours.end(),roi_number) != selected_contours.end())//Only read selected ROIs
- {
- vvMesh::Pointer current_roi=vvMesh::New();
- std::vector<double> rgb=parse_string<double>(i->GetEntryValue(0x3006,0x002a),'\\');
- assert(rgb.size()==3);
- current_roi->r=rgb[0]/255; current_roi->g=rgb[1]/255; current_roi->b=rgb[2]/255;
- current_roi->structure_name=k->GetEntryValue(0x3006,0x0026);
- gdcm::SeqEntry * contours=i->GetSeqEntry(0x3006,0x0040);
- double z0=-1; //Used to determine spacing between slices, assumed to be constant
- for(gdcm::SQItem* j=contours->GetFirstSQItem();j!=0;j=contours->GetNextSQItem()) //loop over 2D contours
- {
- std::string contour_type=j->GetEntryValue(0x3006,0x0042);
- if (contour_type=="CLOSED_PLANAR ")
- {
- int point_number=parse_value<int>(j->GetEntryValue(0x3006,0x0046));
- std::vector<float> points=parse_string<float>(j->GetEntryValue(0x3006,0x0050),'\\');
- assert(points.size() == static_cast<unsigned int>(point_number)*3);
- if (z0 == -1) //First contour
- z0=points[2];
- //2nd contour, spacing not yet set. Need to be sure we are on a different slice,
- //sometimes there is more than one closed contour per slice
- else if (current_roi->GetSpacing()==-1 && points[2] != z0 )
- current_roi->SetSpacing(points[2]-z0);
- vtkPolyData * contour=vtkPolyData::New();
- contour->Allocate(); //for cell structures
- contour->SetPoints(vtkPoints::New());
- vtkIdType ids[2];
- for (unsigned int idx=0;idx<points.size();idx+=3)
- {
- contour->GetPoints()->InsertNextPoint(points[idx],points[idx+1],points[idx+2]);
- ids[0]=idx/3;ids[1]=(ids[0]+1)%point_number; //0-1,1-2,...,n-1-0
- contour->GetLines()->InsertNextCell(2,ids);
- }
- append->AddInput(contour);
- }
- else if (contour_type == "POINT ")
- ; // silently ignore POINT type since we don't need them at the moment
- else
- std::cerr << "Warning: contour type " << contour_type << " not handled!" << std::endl;
- }
- append->Update();
- current_roi->AddMesh(append->GetOutput());
- result.push_back(current_roi);
- }
+ std::vector<vvMesh::Pointer> result;
+#if GDCM_MAJOR_VERSION == 2
+#else
+ gdcm::File reader;
+ reader.SetFileName(filename.c_str());
+ reader.SetMaxSizeLoadEntry(16384);
+ reader.Load();
+
+ gdcm::SeqEntry * rois=reader.GetSeqEntry(0x3006,0x0039);
+ ///We need to iterate both on the contours themselves, and on the contour info
+ gdcm::SeqEntry * roi_info=reader.GetSeqEntry(0x3006,0x0020);
+ gdcm::SQItem* k=roi_info->GetFirstSQItem();
+ for(gdcm::SQItem* i=rois->GetFirstSQItem(); i!=0; i=rois->GetNextSQItem()) { //loop over ROIS
+ assert(k!=0);
+ vtkSmartPointer<vtkAppendPolyData> append=vtkSmartPointer<vtkAppendPolyData>::New();
+ std::istringstream ss(i->GetEntryValue(0x3006,0x0084));
+ int roi_number;
+ ss >> roi_number;
+ if (std::find(selected_contours.begin(),selected_contours.end(),roi_number) != selected_contours.end()) { //Only read selected ROIs
+ vvMesh::Pointer current_roi=vvMesh::New();
+ std::vector<double> rgb=clitk::parse_string<double>(i->GetEntryValue(0x3006,0x002a),'\\');
+ assert(rgb.size()==3);
+ current_roi->r=rgb[0]/255;
+ current_roi->g=rgb[1]/255;
+ current_roi->b=rgb[2]/255;
+ current_roi->structure_name=k->GetEntryValue(0x3006,0x0026);
+ gdcm::SeqEntry * contours=i->GetSeqEntry(0x3006,0x0040);
+ double z0=-1; //Used to determine spacing between slices, assumed to be constant
+ for(gdcm::SQItem* j=contours->GetFirstSQItem(); j!=0; j=contours->GetNextSQItem()) { //loop over 2D contours
+ std::string contour_type=j->GetEntryValue(0x3006,0x0042);
+ if (contour_type=="CLOSED_PLANAR ") {
+ int point_number=clitk::parse_value<int>(j->GetEntryValue(0x3006,0x0046));
+ std::vector<float> points=clitk::parse_string<float>(j->GetEntryValue(0x3006,0x0050),'\\');
+ assert(points.size() == static_cast<unsigned int>(point_number)*3);
+ if (z0 == -1) //First contour
+ z0=points[2];
+ //2nd contour, spacing not yet set. Need to be sure we are on a different slice,
+ //sometimes there is more than one closed contour per slice
+ else if (current_roi->GetSpacing()==-1 && points[2] != z0 )
+ current_roi->SetSpacing(points[2]-z0);
+ vtkPolyData * contour=vtkPolyData::New();
+ contour->Allocate(); //for cell structures
+ contour->SetPoints(vtkPoints::New());
+ vtkIdType ids[2];
+ for (unsigned int idx=0; idx<points.size(); idx+=3) {
+ contour->GetPoints()->InsertNextPoint(points[idx],points[idx+1],points[idx+2]);
+ ids[0]=idx/3;
+ ids[1]=(ids[0]+1)%point_number; //0-1,1-2,...,n-1-0
+ contour->GetLines()->InsertNextCell(2,ids);
+ }
+ append->AddInput(contour);
+ } else if (contour_type == "POINT ")
+ ; // silently ignore POINT type since we don't need them at the moment
else
- {
- //std::cerr << "Warning: ignoring ROI #" << roi_number << std::endl;
- }
- k=roi_info->GetNextSQItem(); //increment the second loop variable
+ std::cerr << "Warning: contour type " << contour_type << " not handled!" << std::endl;
+ }
+ append->Update();
+ current_roi->AddMesh(append->GetOutput());
+ result.push_back(current_roi);
+ } else {
+ //std::cerr << "Warning: ignoring ROI #" << roi_number << std::endl;
}
- return result;
+ k=roi_info->GetNextSQItem(); //increment the second loop variable
+ }
+#endif
+ return result;
}
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff