X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=vv%2FvvToolExtractLung.cxx;h=59b41331472a7798dea91d9bb3e80c1e0aaa54ed;hb=6612a70a1a2056589f70f57bf6b81269be1c645f;hp=7c78a0aecba73e5d352460843cf13fc01f1dad36;hpb=3e8098373d82c788bd7ca72fe270a6374728e074;p=clitk.git

diff --git a/vv/vvToolExtractLung.cxx b/vv/vvToolExtractLung.cxx
index 7c78a0a..59b4133 100644
--- a/vv/vvToolExtractLung.cxx
+++ b/vv/vvToolExtractLung.cxx
@@ -3,7 +3,7 @@
 
   Authors belong to:
   - University of LYON              http://www.universite-lyon.fr/
-  - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.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
@@ -14,7 +14,7 @@
 
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-  ======================================================================-====*/
+  ===========================================================================**/
 
 // vv
 #include "vvToolExtractLung.h"
@@ -23,7 +23,7 @@
 #include "vvImageReader.h"
 #include "vvImageWriter.h"
 #include "vvLabelImageLoaderWidget.h"
-#include "vvProgressDialog.h"
+#include "vvThreadedFilter.h"
 
 // Qt
 #include <QMessageBox>
@@ -45,16 +45,20 @@ vvToolExtractLung::vvToolExtractLung(vvMainWindowBase * parent, Qt::WindowFlags
   Ui_vvToolExtractLung::setupUi(mToolWidget);
   mMaskLoaderBox->setEnabled(false);
   mOptionsBox->setEnabled(false);
+  mPatientMaskInputWidget->SetText("Patient mask");
   connect(mPatientMaskInputWidget, SIGNAL(accepted()), this, SLOT(PatientMaskInputIsSelected()));
 
   // Default values
-  cmdline_parser_clitkExtractLung_init(&mArgsInfo);
+  mArgsInfo = new ArgsInfoType;
+  cmdline_parser_clitkExtractLung_init(mArgsInfo);
+  SetGUIFromArgsInfo();
+  m_IsThreadInterrupted = false;
 
   // Create a new ExtractLung filter
-  mFilter = FilterType::New();  
+  mFilter = new FilterType;  // used in AddInputSelector
 
   // Add input selector
-  AddInputSelector("Select image", mFilter);
+  AddInputSelector("Select CT thorax image", mFilter);
 }
 //------------------------------------------------------------------------------
 
@@ -73,6 +77,7 @@ void vvToolExtractLung::Initialize() {
   SetToolIconFilename(":/common/icons/lung-overlay.png");
   SetToolTip("Extract lung mask from thorax CT.");
   SetToolExperimental(true);
+  //  SetToolInMenu("Segmentation");
 }
 //------------------------------------------------------------------------------
 
@@ -80,7 +85,6 @@ void vvToolExtractLung::Initialize() {
 //------------------------------------------------------------------------------
 void vvToolExtractLung::InputIsSelected(vvSlicerManager *m)
 {
-  DD("InputIsSelected");
   // Hide selector
   HideInputSelector(); // splitter
   mToolInputSelectionWidget->hide();
@@ -95,13 +99,36 @@ void vvToolExtractLung::InputIsSelected(vvSlicerManager *m)
 //------------------------------------------------------------------------------
 void vvToolExtractLung::PatientMaskInputIsSelected()
 {
-  DD("PatientMaskInputIsSelected");
-  mMaskLoaderBox->setEnabled(false);
-  mOptionsBox->setEnabled(true);
-
   // Get Patient mask and BG value
   mPatient = mPatientMaskInputWidget->GetImage();  
   mPatientBackgroundValue = mPatientMaskInputWidget->GetBackgroundValue();
+  
+  // Check patient dimension
+  if (mPatient->GetNumberOfDimensions() != 3) {
+    QMessageBox::information(this,tr("*Error*"), "Mask image must be 3D");
+    return;
+  }
+   
+  mMaskLoaderBox->setEnabled(false);
+  mOptionsBox->setEnabled(true);
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolExtractLung::SetGUIFromArgsInfo() 
+{
+  mAirUpperThresholdSlider->SetText("Upper threshold for air");
+  mAirUpperThresholdSlider->SetMinimum(-1200);
+  mAirUpperThresholdSlider->SetMaximum(2000);
+  DD(mArgsInfo->upper_arg);
+  mAirUpperThresholdSlider->SetValue(mArgsInfo->upper_arg);
+
+  mAirLowerThresholdSlider->SetText("Lower threshold for air");
+  mAirLowerThresholdSlider->SetMinimum(-1200);
+  mAirLowerThresholdSlider->SetMaximum(2000);
+  mAirLowerThresholdSlider->SetValue(mArgsInfo->lower_arg);
+
 }
 //------------------------------------------------------------------------------
 
@@ -109,16 +136,19 @@ void vvToolExtractLung::PatientMaskInputIsSelected()
 //------------------------------------------------------------------------------
 void vvToolExtractLung::GetArgsInfoFromGUI() 
 {
-  DD("GetArgsInfoFromGUI");
-  mArgsInfo.patientBG_arg = 0; //mPatientBackgroundValueSpinBox->value();
-  mArgsInfo.verboseOption_flag = true;
-  mArgsInfo.verboseStep_flag = true;
-  mArgsInfo.writeStep_flag = false;
-  mArgsInfo.input_given = 0;
-  mArgsInfo.patient_given = 0;
-  mArgsInfo.output_given = 0;
-  mArgsInfo.outputTrachea_given = 0;
-  mArgsInfo.remove1_given = 0;
+  // mArgsInfo->patientBG_arg = mPatientMaskInputWidget->GetBackgroundValue();
+  mArgsInfo->verboseOption_flag = true; // DEBUG. TO CHANGE
+  mArgsInfo->verboseStep_flag = true; // DEBUG. TO CHANGE
+  mArgsInfo->writeStep_flag = false;
+  mArgsInfo->input_given = 0;
+  // mArgsInfo->patient_given = 0;
+  mArgsInfo->output_given = 0;
+  mArgsInfo->outputTrachea_given = 0;
+  //  mArgsInfo->remove1_given = 0;
+  
+  mArgsInfo->upper_arg = mAirUpperThresholdSlider->GetValue();
+  mArgsInfo->lower_arg = mAirLowerThresholdSlider->GetValue();
+  if (mRadioButtonLowerThan->isChecked()) mArgsInfo->lower_given = 1;
 }
 //------------------------------------------------------------------------------
 
@@ -126,37 +156,67 @@ void vvToolExtractLung::GetArgsInfoFromGUI()
 //------------------------------------------------------------------------------
 void vvToolExtractLung::apply() 
 {
-  DD("apply");
+  // Change cursor to wait
   QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
   
+  // Read options from GUI and put it in the ArgsInfo struct
   GetArgsInfoFromGUI();
+  
+  // Check options
+  if (mArgsInfo->lower_given) {
+    if (mArgsInfo->lower_arg > mArgsInfo->upper_arg) {    
+      QApplication::restoreOverrideCursor(); 
+      QMessageBox::information(this,tr("Error"), "Lower threshold cannot be greater than upper threshold.");
+      return;
+    }
+  }
 
-  mFilter->SetIOVerbose(true);  
+  // Create new filter
+  if (mFilter) delete mFilter;
+  mFilter = new FilterType;  // needed when thread cancel the filter
+  // mFilter->StopOnErrorOff();
+  //  mFilter->SetIOVerbose(true);
   mFilter->AddInputVVImage(mCurrentImage); // CT
   mFilter->AddInputVVImage(mPatient); // patient mask
-  mFilter->SetArgsInfo(mArgsInfo);
-
-  DD("mfilter->Update");
-  // vvThreadedFilter a;
-  // a->SetFilter(mFilter)
-  // connect(a, SIGNAL(rejected()), this, SLOT(FilterHasBeenCanceled()));
-  // a->Update();
-  // if (a->HasError()) { DD(a->GetError()); return; }
-  mFilter->Update();
-
-  // Check error
-  if (mFilter->HasError()) {
-    QMessageBox::information(this,tr("*Error* while finding lung"), mFilter->GetLastError().c_str());
-    reject();
+  mFilter->SetArgsInfo(*mArgsInfo);
+
+  // Created threaded execution
+  vvThreadedFilter thread;
+  connect(&thread, SIGNAL(ThreadInterrupted()), this, SLOT(ThreadInterrupted()));
+  thread.SetFilter(mFilter);
+
+  try {
+    thread.Update();
+  }
+  catch(std::runtime_error e) {
+    DD("Error exception handling");
+    DD(m_IsThreadInterrupted);
+  // Check if the thread has been canceled. In this case, return
+  if (m_IsThreadInterrupted) {
+    m_IsThreadInterrupted = false;
+    QApplication::restoreOverrideCursor(); 
     return;
   }
+  disconnect(&thread, SIGNAL(ThreadInterrupted()), this, SLOT(ThreadInterrupted()));
+    
+  // Check error during filter
+  // if (mFilter->HasError()) {
+    QApplication::restoreOverrideCursor();
+    QMessageBox::information(this,tr("Error"), e.what());//mFilter->GetLastError().c_str());
+    return;
+  // }
+  } // end exception
   
   // Get output
   std::vector<vvImage::Pointer> output = mFilter->GetOutputVVImages();
-  DD(output.size());
+  if (output.size() == 0) {
+    std::cerr << "Error : no output ?" << std::endl;
+    QApplication::restoreOverrideCursor();
+    close();
+    return;
+  }
   
   // Set Lung into VV
-  DD("lung");
   vvImage::Pointer lung = output[0];
   std::ostringstream osstream;
   osstream << "Lung_" << mCurrentSlicerManager->GetSlicer(0)->GetFileName() << ".mhd";
@@ -167,7 +227,6 @@ void vvToolExtractLung::apply()
 
   // Set trachea into VV
   if (output.size() == 2) {
-    DD("trachea");
     vvImage::Pointer trachea = output[1];
     std::ostringstream osstream;
     osstream << "Trachea_" << mCurrentSlicerManager->GetSlicer(0)->GetFileName() << ".mhd";
@@ -191,3 +250,10 @@ bool vvToolExtractLung::close()
 //------------------------------------------------------------------------------
 
 
+//------------------------------------------------------------------------------
+void vvToolExtractLung::ThreadInterrupted() 
+{ 
+  m_IsThreadInterrupted = true; 
+}
+//------------------------------------------------------------------------------
+