/*========================================================================= 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 ===========================================================================**/ // vv #include "vvToolExtractLung.h" #include "vvToolStructureSetManager.h" #include "vvSlicer.h" #include "vvImageReader.h" #include "vvImageWriter.h" #include "vvLabelImageLoaderWidget.h" #include "vvThreadedFilter.h" // Qt #include //------------------------------------------------------------------------------ // Create the tool and automagically (I like this word) insert it in // the main window menu. ADD_TOOL(vvToolExtractLung); //------------------------------------------------------------------------------ //------------------------------------------------------------------------------ vvToolExtractLung::vvToolExtractLung(vvMainWindowBase * parent, Qt::WindowFlags f): vvToolWidgetBase(parent,f), vvToolBase(parent), Ui::vvToolExtractLung() { // GUI Ui_vvToolExtractLung::setupUi(mToolWidget); mMaskLoaderBox->setEnabled(false); mOptionsBox->setEnabled(false); mPatientMaskInputWidget->SetText("Patient mask"); connect(mPatientMaskInputWidget, SIGNAL(accepted()), this, SLOT(PatientMaskInputIsSelected())); // Default values mArgsInfo = new ArgsInfoType; cmdline_parser_clitkExtractLung_init(mArgsInfo); SetGUIFromArgsInfo(); m_IsThreadInterrupted = false; // Create a new ExtractLung filter mFilter = new FilterType; // used in AddInputSelector // Add input selector AddInputSelector("Select CT thorax image", mFilter); } //------------------------------------------------------------------------------ //------------------------------------------------------------------------------ vvToolExtractLung::~vvToolExtractLung() { } //------------------------------------------------------------------------------ //------------------------------------------------------------------------------ void vvToolExtractLung::Initialize() { SetToolName("ExtractLung"); SetToolMenuName("Extract lungs"); SetToolIconFilename(":/common/icons/lung-overlay.png"); SetToolTip("Extract lung mask from thorax CT."); SetToolExperimental(true); // SetToolInMenu("Segmentation"); } //------------------------------------------------------------------------------ //------------------------------------------------------------------------------ void vvToolExtractLung::InputIsSelected(vvSlicerManager *m) { // Hide selector HideInputSelector(); // splitter mToolInputSelectionWidget->hide(); mCurrentSlicerManager = m; mCurrentImage = m->GetImage(); mMaskLoaderBox->setEnabled(true); mLabelInput->setText(m->GetFileName().c_str()); } //------------------------------------------------------------------------------ //------------------------------------------------------------------------------ void vvToolExtractLung::PatientMaskInputIsSelected() { // 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); } //------------------------------------------------------------------------------ //------------------------------------------------------------------------------ void vvToolExtractLung::GetArgsInfoFromGUI() { // 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; } //------------------------------------------------------------------------------ //------------------------------------------------------------------------------ void vvToolExtractLung::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; } } // 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); // 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 output = mFilter->GetOutputVVImages(); if (output.size() == 0) { std::cerr << "Error : no output ?" << std::endl; QApplication::restoreOverrideCursor(); close(); return; } // Set Lung into VV vvImage::Pointer lung = output[0]; std::ostringstream osstream; osstream << "Lung_" << mCurrentSlicerManager->GetSlicer(0)->GetFileName() << ".mhd"; vvSlicerManager * v = AddImage(lung,osstream.str()); v->SetPreset(5); vvToolStructureSetManager::AddImage(mCurrentSlicerManager, "Right lung", lung, 1, false); // Right is greater than Left vvToolStructureSetManager::AddImage(mCurrentSlicerManager, "Left lung", lung, 2, false); // Set trachea into VV if (output.size() == 2) { vvImage::Pointer trachea = output[1]; std::ostringstream osstream; osstream << "Trachea_" << mCurrentSlicerManager->GetSlicer(0)->GetFileName() << ".mhd"; vvSlicerManager * v = AddImage(trachea,osstream.str()); v->SetPreset(5); vvToolStructureSetManager::AddImage(mCurrentSlicerManager, "Trachea", trachea, 0); } // End QApplication::restoreOverrideCursor(); close(); } //------------------------------------------------------------------------------ //------------------------------------------------------------------------------ bool vvToolExtractLung::close() { return vvToolWidgetBase::close(); } //------------------------------------------------------------------------------ //------------------------------------------------------------------------------ void vvToolExtractLung::ThreadInterrupted() { m_IsThreadInterrupted = true; } //------------------------------------------------------------------------------