--- /dev/null
+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>vvToolExtractPatient</class>
+ <widget class="QWidget" name="vvToolExtractPatient">
+ <property name="geometry">
+ <rect>
+ <x>0</x>
+ <y>0</y>
+ <width>249</width>
+ <height>199</height>
+ </rect>
+ </property>
+ <property name="windowTitle">
+ <string>Form</string>
+ </property>
+ <layout class="QVBoxLayout" name="verticalLayout">
+ <item>
+ <widget class="QLabel" name="mLabelInput">
+ <property name="sizePolicy">
+ <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+ <horstretch>0</horstretch>
+ <verstretch>0</verstretch>
+ </sizepolicy>
+ </property>
+ <property name="font">
+ <font>
+ <pointsize>11</pointsize>
+ <weight>75</weight>
+ <bold>true</bold>
+ </font>
+ </property>
+ <property name="frameShape">
+ <enum>QFrame::NoFrame</enum>
+ </property>
+ <property name="text">
+ <string>No selected image</string>
+ </property>
+ <property name="alignment">
+ <set>Qt::AlignCenter</set>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QGroupBox" name="mOptionsBox">
+ <property name="title">
+ <string>Extract Patient Options</string>
+ </property>
+ <layout class="QVBoxLayout" name="verticalLayout_3">
+ <item>
+ <layout class="QVBoxLayout" name="verticalLayout_2">
+ <item>
+ <widget class="vvIntensityValueSlider" name="mAirUpperThresholdSlider" native="true"/>
+ </item>
+ <item>
+ <widget class="QRadioButton" name="mRadioButtonLowerThan">
+ <property name="text">
+ <string>use lower</string>
+ </property>
+ <property name="autoExclusive">
+ <bool>false</bool>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="vvIntensityValueSlider" name="mAirLowerThresholdSlider" native="true">
+ <property name="enabled">
+ <bool>false</bool>
+ </property>
+ </widget>
+ </item>
+ </layout>
+ </item>
+ </layout>
+ </widget>
+ </item>
+ </layout>
+ </widget>
+ <customwidgets>
+ <customwidget>
+ <class>vvIntensityValueSlider</class>
+ <extends>QWidget</extends>
+ <header>vvIntensityValueSlider.h</header>
+ <container>1</container>
+ </customwidget>
+ </customwidgets>
+ <resources>
+ <include location="../vvIcons.qrc"/>
+ </resources>
+ <connections>
+ <connection>
+ <sender>mRadioButtonLowerThan</sender>
+ <signal>toggled(bool)</signal>
+ <receiver>mAirLowerThresholdSlider</receiver>
+ <slot>setEnabled(bool)</slot>
+ <hints>
+ <hint type="sourcelabel">
+ <x>64</x>
+ <y>275</y>
+ </hint>
+ <hint type="destinationlabel">
+ <x>79</x>
+ <y>299</y>
+ </hint>
+ </hints>
+ </connection>
+ </connections>
+</ui>
--- /dev/null
+/*=========================================================================
+ 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 "vvToolExtractPatient.h"
+#include "vvToolStructureSetManager.h"
+#include "vvSlicer.h"
+#include "vvImageReader.h"
+#include "vvImageWriter.h"
+#include "vvLabelImageLoaderWidget.h"
+#include "vvThreadedFilter.h"
+
+// Qt
+#include <QMessageBox>
+
+//------------------------------------------------------------------------------
+// Create the tool and automagically (I like this word) insert it in
+// the main window menu.
+ADD_TOOL(vvToolExtractPatient);
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+vvToolExtractPatient::vvToolExtractPatient(vvMainWindowBase * parent, Qt::WindowFlags f):
+ vvToolWidgetBase(parent,f),
+ vvToolBase<vvToolExtractPatient>(parent),
+ Ui::vvToolExtractPatient()
+{
+ // GUI
+ Ui_vvToolExtractPatient::setupUi(mToolWidget);
+ mOptionsBox->setEnabled(true);
+ //connect(mPatientMaskInputWidget, SIGNAL(accepted()), this, SLOT(PatientMaskInputIsSelected()));
+
+ // Default values
+ mArgsInfo = new ArgsInfoType;
+ cmdline_parser_clitkExtractPatient_init(mArgsInfo);
+ SetGUIFromArgsInfo();
+ m_IsThreadInterrupted = false;
+
+ // Create a new ExtractPatient filter
+ mFilter = new FilterType; // used in AddInputSelector
+
+ // Add input selector
+ AddInputSelector("Select CT thorax image", mFilter);
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+vvToolExtractPatient::~vvToolExtractPatient()
+{
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolExtractPatient::Initialize() {
+ SetToolName("ExtractPatient");
+ SetToolMenuName("Extract Patient");
+ SetToolIconFilename(":/common/icons/Patient-overlay.png");
+ SetToolTip("Extract Patient mask from thorax CT.");
+ // SetToolExperimental(true);
+ // SetToolInMenu("Segmentation");
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolExtractPatient::InputIsSelected(vvSlicerManager *m)
+{
+ // Hide selector
+ HideInputSelector(); // splitter
+ mToolInputSelectionWidget->hide();
+ mCurrentSlicerManager = m;
+ mCurrentImage = m->GetImage();
+ mLabelInput->setText(m->GetFileName().c_str());
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+// void vvToolExtractPatient::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 vvToolExtractPatient::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 vvToolExtractPatient::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 vvToolExtractPatient::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;
+ DD("new filter");
+ 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
+ DD("thread");
+ vvThreadedFilter thread;
+ connect(&thread, SIGNAL(ThreadInterrupted()), this, SLOT(ThreadInterrupted()));
+ thread.SetFilter(mFilter);
+ thread.Update();
+
+ // 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"), mFilter->GetLastError().c_str());
+ return;
+ }
+
+ // Get output
+ std::vector<vvImage::Pointer> output = mFilter->GetOutputVVImages();
+ if (output.size() == 0) {
+ std::cerr << "Error : no output ?" << std::endl;
+ QApplication::restoreOverrideCursor();
+ close();
+ return;
+ }
+
+ // Set Patient into VV
+ vvImage::Pointer Patient = output[0];
+ std::ostringstream osstream;
+ osstream << "Patient_" << mCurrentSlicerManager->GetSlicer(0)->GetFileName() << ".mhd";
+ vvSlicerManager * v = AddImage(Patient,osstream.str());
+ v->SetPreset(5);
+ vvToolStructureSetManager::AddImage(mCurrentSlicerManager, "Right Patient", Patient, 1, false); // Right is greater than Left
+// vvToolStructureSetManager::AddImage(mCurrentSlicerManager, "Left Patient", Patient, 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 vvToolExtractPatient::close()
+{
+ return vvToolWidgetBase::close();
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolExtractPatient::ThreadInterrupted()
+{
+ m_IsThreadInterrupted = true;
+}
+//------------------------------------------------------------------------------
+
--- /dev/null
+/*=========================================================================
+ 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 VVTOOLEXTRACTPATIENT_H
+#define VVTOOLEXTRACTPATIENT_H
+
+// clitk
+#include "clitkExtractPatientGenericFilter.h"
+#include "../segmentation/clitkExtractPatient_ggo.h"
+
+// vv
+#include "ui_vvToolExtractPatient.h"
+#include "vvToolBase.h"
+#include "vvToolWidgetBase.h"
+#include "vvROIActor.h"
+
+// qt
+#include <QtDesigner/QDesignerExportWidget>
+
+//------------------------------------------------------------------------------
+class vvToolExtractPatient:
+ public vvToolWidgetBase,
+ public vvToolBase<vvToolExtractPatient>,
+ private Ui::vvToolExtractPatient
+{
+ Q_OBJECT
+ public:
+ vvToolExtractPatient(vvMainWindowBase* parent=0, Qt::WindowFlags f=0);
+ ~vvToolExtractPatient();
+
+ //-----------------------------------------------------
+ static void Initialize();
+ virtual void InputIsSelected(vvSlicerManager *m);
+ void GetArgsInfoFromGUI();
+ void SetGUIFromArgsInfo();
+
+ //-----------------------------------------------------
+public slots:
+ virtual void apply();
+ virtual bool close();
+ // void PatientMaskInputIsSelected();
+ void ThreadInterrupted();
+
+ //-----------------------------------------------------
+protected:
+ typedef args_info_clitkExtractPatient ArgsInfoType;
+ ArgsInfoType * mArgsInfo;
+ typedef clitk::ExtractPatientGenericFilter<ArgsInfoType> FilterType;
+ FilterType * mFilter;
+ vvImage::Pointer mPatient;
+ double mPatientBackgroundValue;
+ bool m_IsThreadInterrupted;
+
+}; // end class vvToolExtractPatient
+//------------------------------------------------------------------------------
+
+#endif
+
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff