From: dsarrut Date: Wed, 7 Jul 2010 07:09:35 +0000 (+0000) Subject: add Extract Lung Tool (experimental) X-Git-Tag: v1.2.0~552 X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=commitdiff_plain;h=3e8098373d82c788bd7ca72fe270a6374728e074;p=clitk.git add Extract Lung Tool (experimental) --- diff --git a/vv/qt_ui/vvToolExtractLung.ui b/vv/qt_ui/vvToolExtractLung.ui new file mode 100644 index 0000000..8d02831 --- /dev/null +++ b/vv/qt_ui/vvToolExtractLung.ui @@ -0,0 +1,351 @@ + + + vvToolExtractLung + + + + 0 + 0 + 412 + 384 + + + + Form + + + + + + + 11 + 75 + true + + + + QFrame::NoFrame + + + No selected image + + + Qt::AlignCenter + + + + + + + GroupBox + + + + + mOptionsBox + mOptionsBox + + + + + + + + + GroupBox + + + + + + + + Resample before (faster) + + + false + + + false + + + + + + + false + + + + + + + false + + + + 0 + 0 + + + + mm + + + + + + + Qt::Horizontal + + + + 40 + 20 + + + + + + + + + + + + false + + mPatientMaskInputWidget + + + + + + Initial upper threshold for air + + + + + + + + + + lower threshold for air + + + false + + + + + + + + + + + + 0 + 0 + + + + Min size + + + + + + + 999999 + + + 100 + + + + + + + Qt::Horizontal + + + + 40 + 20 + + + + + + + + + + Full connectivity + + + true + + + true + + + + + + + + + + 0 + 0 + + + + Remove + + + + + + + + + + Qt::Horizontal + + + + 40 + 20 + + + + + + + + + + + + + 0 + 0 + + + + First Keep + + + + + + + + + + Qt::Horizontal + + + + 40 + 20 + + + + + + + + + + + + + 0 + 0 + + + + Last Keep + + + + + + + + + + Qt::Horizontal + + + + 40 + 20 + + + + + + + + + + + + + + vvIntensityValueSlider + QWidget +
vvIntensityValueSlider.h
+ 1 + + + vvLabelImageLoaderWidget + QWidget +
vvLabelImageLoaderWidget.h
+ 1 + + + + + + + + mFullConnectivityCheckBox_2 + toggled(bool) + mSamplingSpinBox + setEnabled(bool) + + + 151 + 141 + + + 233 + 134 + + + + + mFullConnectivityCheckBox_2 + toggled(bool) + dimensionStaticLabel_6 + setEnabled(bool) + + + 73 + 141 + + + 287 + 143 + + + + + diff --git a/vv/vvToolExtractLung.cxx b/vv/vvToolExtractLung.cxx new file mode 100644 index 0000000..7c78a0a --- /dev/null +++ b/vv/vvToolExtractLung.cxx @@ -0,0 +1,193 @@ +/*========================================================================= + 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://oncora1.lyon.fnclcc.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 "vvProgressDialog.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); + connect(mPatientMaskInputWidget, SIGNAL(accepted()), this, SLOT(PatientMaskInputIsSelected())); + + // Default values + cmdline_parser_clitkExtractLung_init(&mArgsInfo); + + // Create a new ExtractLung filter + mFilter = FilterType::New(); + + // Add input selector + AddInputSelector("Select 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); +} +//------------------------------------------------------------------------------ + + +//------------------------------------------------------------------------------ +void vvToolExtractLung::InputIsSelected(vvSlicerManager *m) +{ + DD("InputIsSelected"); + // Hide selector + HideInputSelector(); // splitter + mToolInputSelectionWidget->hide(); + mCurrentSlicerManager = m; + mCurrentImage = m->GetImage(); + mMaskLoaderBox->setEnabled(true); + mLabelInput->setText(m->GetFileName().c_str()); +} +//------------------------------------------------------------------------------ + + +//------------------------------------------------------------------------------ +void vvToolExtractLung::PatientMaskInputIsSelected() +{ + DD("PatientMaskInputIsSelected"); + mMaskLoaderBox->setEnabled(false); + mOptionsBox->setEnabled(true); + + // Get Patient mask and BG value + mPatient = mPatientMaskInputWidget->GetImage(); + mPatientBackgroundValue = mPatientMaskInputWidget->GetBackgroundValue(); +} +//------------------------------------------------------------------------------ + + +//------------------------------------------------------------------------------ +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; +} +//------------------------------------------------------------------------------ + + +//------------------------------------------------------------------------------ +void vvToolExtractLung::apply() +{ + DD("apply"); + QApplication::setOverrideCursor(QCursor(Qt::WaitCursor)); + + GetArgsInfoFromGUI(); + + 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(); + return; + } + + // Get output + std::vector output = mFilter->GetOutputVVImages(); + DD(output.size()); + + // Set Lung into VV + DD("lung"); + 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) { + DD("trachea"); + 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(); +} +//------------------------------------------------------------------------------ + + diff --git a/vv/vvToolExtractLung.h b/vv/vvToolExtractLung.h new file mode 100644 index 0000000..b45c75e --- /dev/null +++ b/vv/vvToolExtractLung.h @@ -0,0 +1,70 @@ +/*========================================================================= + 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://oncora1.lyon.fnclcc.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 +======================================================================-====*/ + +#ifndef VVTOOLEXTRACTLUNG_H +#define VVTOOLEXTRACTLUNG_H + +// clitk +#include "clitkExtractLungGenericFilter.h" +#include "../segmentation/clitkExtractLung_ggo.h" + +// vv +#include "ui_vvToolExtractLung.h" +#include "vvToolBase.h" +#include "vvToolWidgetBase.h" +#include "vvROIActor.h" + +// qt +#include + +//------------------------------------------------------------------------------ +class vvToolExtractLung: + public vvToolWidgetBase, + public vvToolBase, + private Ui::vvToolExtractLung +{ + Q_OBJECT + public: + vvToolExtractLung(vvMainWindowBase* parent=0, Qt::WindowFlags f=0); + ~vvToolExtractLung(); + + //----------------------------------------------------- + static void Initialize(); + virtual void InputIsSelected(vvSlicerManager *m); + void GetArgsInfoFromGUI(); + + //----------------------------------------------------- +public slots: + virtual void apply(); + virtual bool close(); + void PatientMaskInputIsSelected(); + + //----------------------------------------------------- +protected: + typedef args_info_clitkExtractLung ArgsInfoType; + ArgsInfoType mArgsInfo; + typedef clitk::ExtractLungGenericFilter FilterType; + FilterType::Pointer mFilter; + vvImage::Pointer mPatient; + double mPatientBackgroundValue; + +}; // end class vvToolExtractLung +//------------------------------------------------------------------------------ + +#endif +