add Extract Lung Tool (experimental)

diff --git a/vv/qt_ui/vvToolExtractLung.ui b/vv/qt_ui/vvToolExtractLung.ui
new file mode 100644 (file)
index 0000000..8d02831
--- /dev/null
+++ b/vv/qt_ui/vvToolExtractLung.ui
@@ -0,0 +1,351 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>vvToolExtractLung</class>
+ <widget class="QWidget" name="vvToolExtractLung">
+  <property name="geometry">
+   <rect>
+    <x>0</x>
+    <y>0</y>
+    <width>412</width>
+    <height>384</height>
+   </rect>
+  </property>
+  <property name="windowTitle">
+   <string>Form</string>
+  </property>
+  <layout class="QVBoxLayout" name="verticalLayout">
+   <item>
+    <widget class="QLabel" name="mLabelInput">
+     <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="mMaskLoaderBox">
+     <property name="title">
+      <string>GroupBox</string>
+     </property>
+     <layout class="QGridLayout" name="gridLayout">
+      <item row="1" column="0">
+       <widget class="vvLabelImageLoaderWidget" name="mPatientMaskInputWidget" native="true">
+        <zorder>mOptionsBox</zorder>
+        <zorder>mOptionsBox</zorder>
+       </widget>
+      </item>
+     </layout>
+    </widget>
+   </item>
+   <item>
+    <widget class="QGroupBox" name="mOptionsBox">
+     <property name="title">
+      <string>GroupBox</string>
+     </property>
+     <layout class="QVBoxLayout" name="verticalLayout_2">
+      <item>
+       <layout class="QHBoxLayout" name="horizontalLayout_5">
+        <item>
+         <widget class="QCheckBox" name="mFullConnectivityCheckBox_2">
+          <property name="text">
+           <string>Resample before (faster)</string>
+          </property>
+          <property name="checked">
+           <bool>false</bool>
+          </property>
+          <property name="tristate">
+           <bool>false</bool>
+          </property>
+         </widget>
+        </item>
+        <item>
+         <widget class="QDoubleSpinBox" name="mSamplingSpinBox">
+          <property name="enabled">
+           <bool>false</bool>
+          </property>
+         </widget>
+        </item>
+        <item>
+         <widget class="QLabel" name="dimensionStaticLabel_6">
+          <property name="enabled">
+           <bool>false</bool>
+          </property>
+          <property name="sizePolicy">
+           <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
+            <horstretch>0</horstretch>
+            <verstretch>0</verstretch>
+           </sizepolicy>
+          </property>
+          <property name="text">
+           <string>mm</string>
+          </property>
+         </widget>
+        </item>
+        <item>
+         <spacer name="horizontalSpacer_5">
+          <property name="orientation">
+           <enum>Qt::Horizontal</enum>
+          </property>
+          <property name="sizeHint" stdset="0">
+           <size>
+            <width>40</width>
+            <height>20</height>
+           </size>
+          </property>
+         </spacer>
+        </item>
+       </layout>
+      </item>
+      <item>
+       <layout class="QGridLayout" name="gridLayout_2">
+        <item row="2" column="2">
+         <widget class="vvIntensityValueSlider" name="mThresholdSlider2" native="true">
+          <property name="enabled">
+           <bool>false</bool>
+          </property>
+          <zorder>mPatientMaskInputWidget</zorder>
+         </widget>
+        </item>
+        <item row="1" column="1">
+         <widget class="QLabel" name="label_2">
+          <property name="text">
+           <string>Initial upper threshold for air</string>
+          </property>
+         </widget>
+        </item>
+        <item row="1" column="2">
+         <widget class="vvIntensityValueSlider" name="mThresholdSlider1" native="true"/>
+        </item>
+        <item row="2" column="1">
+         <widget class="QRadioButton" name="mRadioButtonLowerThan">
+          <property name="text">
+           <string>lower threshold for air</string>
+          </property>
+          <property name="autoExclusive">
+           <bool>false</bool>
+          </property>
+         </widget>
+        </item>
+       </layout>
+      </item>
+      <item>
+       <layout class="QHBoxLayout" name="horizontalLayout_4">
+        <item>
+         <widget class="QLabel" name="dimensionStaticLabel_2">
+          <property name="sizePolicy">
+           <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
+            <horstretch>0</horstretch>
+            <verstretch>0</verstretch>
+           </sizepolicy>
+          </property>
+          <property name="text">
+           <string>Min size</string>
+          </property>
+         </widget>
+        </item>
+        <item>
+         <widget class="QSpinBox" name="mMinSizeSpinBox">
+          <property name="maximum">
+           <number>999999</number>
+          </property>
+          <property name="value">
+           <number>100</number>
+          </property>
+         </widget>
+        </item>
+        <item>
+         <spacer name="horizontalSpacer">
+          <property name="orientation">
+           <enum>Qt::Horizontal</enum>
+          </property>
+          <property name="sizeHint" stdset="0">
+           <size>
+            <width>40</width>
+            <height>20</height>
+           </size>
+          </property>
+         </spacer>
+        </item>
+       </layout>
+      </item>
+      <item>
+       <widget class="QCheckBox" name="mFullConnectivityCheckBox">
+        <property name="text">
+         <string>Full connectivity</string>
+        </property>
+        <property name="checked">
+         <bool>true</bool>
+        </property>
+        <property name="tristate">
+         <bool>true</bool>
+        </property>
+       </widget>
+      </item>
+      <item>
+       <layout class="QHBoxLayout" name="horizontalLayout_2">
+        <item>
+         <widget class="QLabel" name="dimensionStaticLabel_3">
+          <property name="sizePolicy">
+           <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
+            <horstretch>0</horstretch>
+            <verstretch>0</verstretch>
+           </sizepolicy>
+          </property>
+          <property name="text">
+           <string>Remove</string>
+          </property>
+         </widget>
+        </item>
+        <item>
+         <widget class="QSpinBox" name="mBackgroundValueSpinBox"/>
+        </item>
+        <item>
+         <spacer name="horizontalSpacer_4">
+          <property name="orientation">
+           <enum>Qt::Horizontal</enum>
+          </property>
+          <property name="sizeHint" stdset="0">
+           <size>
+            <width>40</width>
+            <height>20</height>
+           </size>
+          </property>
+         </spacer>
+        </item>
+       </layout>
+      </item>
+      <item>
+       <layout class="QHBoxLayout" name="horizontalLayout_3">
+        <item>
+         <widget class="QLabel" name="dimensionStaticLabel_4">
+          <property name="sizePolicy">
+           <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
+            <horstretch>0</horstretch>
+            <verstretch>0</verstretch>
+           </sizepolicy>
+          </property>
+          <property name="text">
+           <string>First Keep</string>
+          </property>
+         </widget>
+        </item>
+        <item>
+         <widget class="QSpinBox" name="mBackgroundValueSpinBox_2"/>
+        </item>
+        <item>
+         <spacer name="horizontalSpacer_3">
+          <property name="orientation">
+           <enum>Qt::Horizontal</enum>
+          </property>
+          <property name="sizeHint" stdset="0">
+           <size>
+            <width>40</width>
+            <height>20</height>
+           </size>
+          </property>
+         </spacer>
+        </item>
+       </layout>
+      </item>
+      <item>
+       <layout class="QHBoxLayout" name="horizontalLayout">
+        <item>
+         <widget class="QLabel" name="dimensionStaticLabel_5">
+          <property name="sizePolicy">
+           <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
+            <horstretch>0</horstretch>
+            <verstretch>0</verstretch>
+           </sizepolicy>
+          </property>
+          <property name="text">
+           <string>Last Keep</string>
+          </property>
+         </widget>
+        </item>
+        <item>
+         <widget class="QSpinBox" name="mBackgroundValueSpinBox_3"/>
+        </item>
+        <item>
+         <spacer name="horizontalSpacer_2">
+          <property name="orientation">
+           <enum>Qt::Horizontal</enum>
+          </property>
+          <property name="sizeHint" stdset="0">
+           <size>
+            <width>40</width>
+            <height>20</height>
+           </size>
+          </property>
+         </spacer>
+        </item>
+       </layout>
+      </item>
+     </layout>
+    </widget>
+   </item>
+  </layout>
+ </widget>
+ <customwidgets>
+  <customwidget>
+   <class>vvIntensityValueSlider</class>
+   <extends>QWidget</extends>
+   <header>vvIntensityValueSlider.h</header>
+   <container>1</container>
+  </customwidget>
+  <customwidget>
+   <class>vvLabelImageLoaderWidget</class>
+   <extends>QWidget</extends>
+   <header>vvLabelImageLoaderWidget.h</header>
+   <container>1</container>
+  </customwidget>
+ </customwidgets>
+ <resources>
+  <include location="../vvIcons.qrc"/>
+ </resources>
+ <connections>
+  <connection>
+   <sender>mFullConnectivityCheckBox_2</sender>
+   <signal>toggled(bool)</signal>
+   <receiver>mSamplingSpinBox</receiver>
+   <slot>setEnabled(bool)</slot>
+   <hints>
+    <hint type="sourcelabel">
+     <x>151</x>
+     <y>141</y>
+    </hint>
+    <hint type="destinationlabel">
+     <x>233</x>
+     <y>134</y>
+    </hint>
+   </hints>
+  </connection>
+  <connection>
+   <sender>mFullConnectivityCheckBox_2</sender>
+   <signal>toggled(bool)</signal>
+   <receiver>dimensionStaticLabel_6</receiver>
+   <slot>setEnabled(bool)</slot>
+   <hints>
+    <hint type="sourcelabel">
+     <x>73</x>
+     <y>141</y>
+    </hint>
+    <hint type="destinationlabel">
+     <x>287</x>
+     <y>143</y>
+    </hint>
+   </hints>
+  </connection>
+ </connections>
+</ui>

diff --git a/vv/vvToolExtractLung.cxx b/vv/vvToolExtractLung.cxx
new file mode 100644 (file)
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 <QMessageBox>
+
+//------------------------------------------------------------------------------
+// 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<vvToolExtractLung>(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<vvImage::Pointer> 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 (file)
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 <QtDesigner/QDesignerExportWidget>
+
+//------------------------------------------------------------------------------
+class vvToolExtractLung:
+  public vvToolWidgetBase,
+  public vvToolBase<vvToolExtractLung>, 
+  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<ArgsInfoType> FilterType;
+  FilterType::Pointer mFilter;
+  vvImage::Pointer mPatient;
+  double mPatientBackgroundValue;
+
+}; // end class vvToolExtractLung
+//------------------------------------------------------------------------------
+
+#endif
+