/*=========================================================================
Program: vv http://www.creatis.insa-lyon.fr/rio/vv
- Authors belong to:
+ 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
#include "vvImageReader.h"
vvDeformableRegistration::vvDeformableRegistration(vvImage::Pointer image,unsigned int ref,\
- unsigned int iter, unsigned int nthread,double a, double s,std::string output_f,unsigned int stop) :
- mImage(image),
- refimage(ref),
- nb_iter(iter),
- n_thread(nthread),
- progress(0),
- stop(stop),
- alpha(a),
- sigma(s),
- output_filename(output_f),
- aborted(false)
+ unsigned int iter, unsigned int nthread,double a, double s,std::string output_f,unsigned int stop) :
+ mImage(image),
+ refimage(ref),
+ nb_iter(iter),
+ n_thread(nthread),
+ progress(0),
+ stop(stop),
+ alpha(a),
+ sigma(s),
+ output_filename(output_f),
+ aborted(false)
{
}
void vvDeformableRegistration::abort()
{
- aborted=true;
- std::system("killall deformableregistration");
- std::system("killall clitkVFMerge");
+ aborted=true;
+ std::system("killall deformableregistration");
+ std::system("killall clitkVFMerge");
}
unsigned int vvDeformableRegistration::getProgress()
{
- QMutexLocker locker(&progress_mutex);
- unsigned int retval=progress;
- return retval;
+ QMutexLocker locker(&progress_mutex);
+ unsigned int retval=progress;
+ return retval;
}
void vvDeformableRegistration::cleanup(int frame_number) //remove temporary files
{
- std::string temp_dir=mTempPath.toStdString();
- for (int i=0;i<frame_number;i++)
- {
- std::stringstream filename;
- filename << temp_dir << "/deformation_" << i << ".vf";
- std::system((std::string("rm ") + filename.str()).c_str());
- }
- for (int i=0;i<frame_number;i++)
- {
- std::stringstream filename;
- filename << temp_dir << "/temp_" << i << ".vox";
- std::system(("rm " + filename.str()).c_str());
- }
+ std::string temp_dir=mTempPath.toStdString();
+ for (int i=0; i<frame_number; i++) {
std::stringstream filename;
- filename << temp_dir;
- std::system(("rm -r " + filename.str()).c_str());
+ filename << temp_dir << "/deformation_" << i << ".vf";
+ std::system((std::string("rm ") + filename.str()).c_str());
+ }
+ for (int i=0; i<frame_number; i++) {
+ std::stringstream filename;
+ filename << temp_dir << "/temp_" << i << ".vox";
+ std::system(("rm " + filename.str()).c_str());
+ }
+ std::stringstream filename;
+ filename << temp_dir;
+ std::system(("rm -r " + filename.str()).c_str());
}
void vvDeformableRegistration::partial_run(int low_index,int high_index,int refimage,std::string ref_file)
{
- std::string temp_dir=mTempPath.toStdString();
- DD(ref_file);
- DD(low_index);
- DD(high_index);
- for (int i=low_index;i<high_index;i++)
- {
- if (aborted)
- break;
- if (i==refimage)
- continue;
- std::stringstream filename;
- std::stringstream registration_command;
- filename << temp_dir << "/temp_" << i << ".vox";
- std::stringstream output_vf;
- output_vf << temp_dir << "/deformation_" << i << ".vf";
- registration_command << "deformableregistration -r " << ref_file
- << " -d " << filename.str() << " -o " << output_vf.str()
- << " --alpha=" << alpha
- << " --sigma=" << sigma
- << " --stop=" << stop
- << " --iter=" << nb_iter;
- if (i>low_index && i-1 != refimage) //if possible, use the previous computations to speed up the process
- {
- std::stringstream old_vf;
- old_vf << temp_dir << "/deformation_" << i-1 << ".vf";
- registration_command << " --vf=" << old_vf.str();
- }
- DD(registration_command.str());
- std::system(registration_command.str().c_str());
- progress_mutex.lock();
- progress++;
- progress_mutex.unlock();
+ std::string temp_dir=mTempPath.toStdString();
+ DD(ref_file);
+ DD(low_index);
+ DD(high_index);
+ for (int i=low_index; i<high_index; i++) {
+ if (aborted)
+ break;
+ if (i==refimage)
+ continue;
+ std::stringstream filename;
+ std::stringstream registration_command;
+ filename << temp_dir << "/temp_" << i << ".vox";
+ std::stringstream output_vf;
+ output_vf << temp_dir << "/deformation_" << i << ".vf";
+ registration_command << "deformableregistration -r " << ref_file
+ << " -d " << filename.str() << " -o " << output_vf.str()
+ << " --alpha=" << alpha
+ << " --sigma=" << sigma
+ << " --stop=" << stop
+ << " --iter=" << nb_iter;
+ if (i>low_index && i-1 != refimage) { //if possible, use the previous computations to speed up the process
+ std::stringstream old_vf;
+ old_vf << temp_dir << "/deformation_" << i-1 << ".vf";
+ registration_command << " --vf=" << old_vf.str();
}
+ DD(registration_command.str());
+ std::system(registration_command.str().c_str());
+ progress_mutex.lock();
+ progress++;
+ progress_mutex.unlock();
+ }
}
void vvDeformableRegistration::run()
{
- clock_t start,finish;
- start=clock();
- vtkVOXImageWriter * vox = vtkVOXImageWriter::New();
- std::stringstream command;
- std::string ref_file;
- mTempPath=QDir::tempPath()+QString("/vv-")+QString::number(qApp->applicationPid());
- QDir temp_qt_dir;
- DD(temp_qt_dir.mkpath(mTempPath));
- std::string temp_dir=mTempPath.toStdString();
- DD(temp_dir);
- std::vector<vtkImageData*> images=mImage->GetVTKImages();
- for (unsigned int i=0;i<images.size();i++)
- {
- std::stringstream filename;
- filename << temp_dir << "/temp_" << i << ".vox";
- vox->SetInput(images[i]);
- vox->SetFileName(filename.str().c_str());
- if (i==refimage)
- ref_file=filename.str();
- vox->Write();
- }
- vox->Delete();
- progress++;
- int reg_per_thread=static_cast<int>(images.size()-1)/n_thread;
- int remainder=static_cast<int>(images.size()-1) - reg_per_thread*n_thread;
+ clock_t start,finish;
+ start=clock();
+ vtkVOXImageWriter * vox = vtkVOXImageWriter::New();
+ std::stringstream command;
+ std::string ref_file;
+ mTempPath=QDir::tempPath()+QString("/vv-")+QString::number(qApp->applicationPid());
+ QDir temp_qt_dir;
+ DD(temp_qt_dir.mkpath(mTempPath));
+ std::string temp_dir=mTempPath.toStdString();
+ DD(temp_dir);
+ std::vector<vtkImageData*> images=mImage->GetVTKImages();
+ for (unsigned int i=0; i<images.size(); i++) {
+ std::stringstream filename;
+ filename << temp_dir << "/temp_" << i << ".vox";
+ vox->SetInput(images[i]);
+ vox->SetFileName(filename.str().c_str());
+ if (i==refimage)
+ ref_file=filename.str();
+ vox->Write();
+ }
+ vox->Delete();
+ progress++;
+ int reg_per_thread=static_cast<int>(images.size()-1)/n_thread;
+ int remainder=static_cast<int>(images.size()-1) - reg_per_thread*n_thread;
#pragma omp parallel for num_threads(n_thread) schedule(static)
- for (int i=0;i<static_cast<int>(n_thread);i++)
- {
- ///Static scheduling
- int remainder_shift=((i<remainder)?i:remainder);
- unsigned int start_image=i*reg_per_thread+remainder_shift;
- unsigned int end_image=((i+1)*reg_per_thread+remainder_shift+((i<remainder)?1:0));
- if (end_image<=refimage)
- partial_run(start_image,end_image,refimage,ref_file);
- else if (start_image<=refimage)
- partial_run(start_image,end_image+1,refimage,ref_file);
- else
- partial_run(start_image+1,end_image+1,refimage,ref_file);
- }
- if (aborted)
- {
- cleanup(images.size());
- return;
- }
- command.str("");
- int computed_vf=(refimage==0)?1:0; //index of an image that isn't the reference image
- command << "clitkZeroVF -i " << temp_dir << "/deformation_" << computed_vf << ".vf -o " << temp_dir <<
- "/deformation_" << refimage << ".vf";
- DD(command.str()); //create zero VF for the ref image
- std::system(command.str().c_str());
- command.str("");
- command << "clitkVFMerge ";
- for (unsigned int i=0;i<images.size();i++) command << temp_dir << "/deformation_" << i << ".vf ";
- command << " --xorigin " << images[0]->GetOrigin()[0];
- command << " --yorigin " << images[0]->GetOrigin()[1];
- command << " --zorigin " << images[0]->GetOrigin()[2];
- command << " -o " << output_filename << std::endl;
- DD(command.str());
- std::system(command.str().c_str());
+ for (int i=0; i<static_cast<int>(n_thread); i++) {
+ ///Static scheduling
+ int remainder_shift=((i<remainder)?i:remainder);
+ unsigned int start_image=i*reg_per_thread+remainder_shift;
+ unsigned int end_image=((i+1)*reg_per_thread+remainder_shift+((i<remainder)?1:0));
+ if (end_image<=refimage)
+ partial_run(start_image,end_image,refimage,ref_file);
+ else if (start_image<=refimage)
+ partial_run(start_image,end_image+1,refimage,ref_file);
+ else
+ partial_run(start_image+1,end_image+1,refimage,ref_file);
+ }
+ if (aborted) {
cleanup(images.size());
- if (aborted)
- {
- std::system(("rm " + output_filename).c_str());
- return;
- }
- vvImageReader reader;
- reader.SetInputFilename(output_filename);
- reader.Update(VECTORFIELD);
- finish=clock();
- DD((finish - start)/static_cast<double>(CLOCKS_PER_SEC));
- mOutput=reader.GetOutput();
+ return;
+ }
+ command.str("");
+ int computed_vf=(refimage==0)?1:0; //index of an image that isn't the reference image
+ command << "clitkZeroVF -i " << temp_dir << "/deformation_" << computed_vf << ".vf -o " << temp_dir <<
+ "/deformation_" << refimage << ".vf";
+ DD(command.str()); //create zero VF for the ref image
+ std::system(command.str().c_str());
+ command.str("");
+ command << "clitkVFMerge ";
+ for (unsigned int i=0; i<images.size(); i++) command << temp_dir << "/deformation_" << i << ".vf ";
+ command << " --xorigin " << images[0]->GetOrigin()[0];
+ command << " --yorigin " << images[0]->GetOrigin()[1];
+ command << " --zorigin " << images[0]->GetOrigin()[2];
+ command << " -o " << output_filename << std::endl;
+ DD(command.str());
+ std::system(command.str().c_str());
+ cleanup(images.size());
+ if (aborted) {
+ std::system(("rm " + output_filename).c_str());
+ return;
+ }
+ vvImageReader reader;
+ reader.SetInputFilename(output_filename);
+ reader.Update(VECTORFIELD);
+ finish=clock();
+ DD((finish - start)/static_cast<double>(CLOCKS_PER_SEC));
+ mOutput=reader.GetOutput();
}
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff