X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=vv%2FvvDeformableRegistration.cxx;h=12a2959aa33679b8ab5f6bde9349e0d859eeba5c;hb=82b7d4913d5fbd074f7ab4cc641513546d9f39a4;hp=e5f861c49d08ba290b6ed5646f4068da26a11a30;hpb=931a42358442f4ee4f314613c991c838d4b4e3b7;p=clitk.git

diff --git a/vv/vvDeformableRegistration.cxx b/vv/vvDeformableRegistration.cxx
index e5f861c..12a2959 100644
--- a/vv/vvDeformableRegistration.cxx
+++ b/vv/vvDeformableRegistration.cxx
@@ -1,3 +1,20 @@
+/*=========================================================================
+  Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
+
+  Authors belong 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        See included LICENSE.txt file
+  - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
 #include <sstream>
 #include <cstdlib>
 #include <string>
@@ -10,6 +27,7 @@
 
 #include "vtkVOXImageWriter.h"
 #include <vtkImageData.h>
+#include <vtkVersion.h>
 
 #include "clitkCommon.h"
 #include "vvSlicerManager.h"
@@ -19,162 +37,158 @@
 #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 << "/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;
-    std::system(("rm -r " + filename.str()).c_str());
+    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";
+#if VTK_MAJOR_VERSION <= 5
+    vox->SetInput(images[i]);
+#else
+    vox->SetInputData(images[i]);
+#endif
+    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::Pointer reader = vvImageReader::New();
+  reader->SetInputFilename(output_filename);
+  reader->Update(vvImageReader::VECTORFIELD);
+  finish=clock();
+  DD((finish - start)/static_cast<double>(CLOCKS_PER_SEC));
+  mOutput = reader->GetOutput();
 }