ADd first version of interactive segmentation (erode/dilate)

diff --git a/vv/qt_ui/vvToolSegmentation.ui b/vv/qt_ui/vvToolSegmentation.ui
new file mode 100644 (file)
index 0000000..4931841
--- /dev/null
+++ b/vv/qt_ui/vvToolSegmentation.ui
@@ -0,0 +1,32 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<ui version="4.0">
+ <class>vvToolSegmentation</class>
+ <widget class="QWidget" name="vvToolSegmentation">
+  <property name="geometry">
+   <rect>
+    <x>0</x>
+    <y>0</y>
+    <width>408</width>
+    <height>285</height>
+   </rect>
+  </property>
+  <property name="windowTitle">
+   <string>Binarize image</string>
+  </property>
+  <widget class="QPushButton" name="pushButton">
+   <property name="geometry">
+    <rect>
+     <x>140</x>
+     <y>120</y>
+     <width>86</width>
+     <height>27</height>
+    </rect>
+   </property>
+   <property name="text">
+    <string>PushButton</string>
+   </property>
+  </widget>
+ </widget>
+ <resources/>
+ <connections/>
+</ui>

diff --git a/vv/vvToolSegmentation.cxx b/vv/vvToolSegmentation.cxx
new file mode 100644 (file)
index 0000000..dea3513
--- /dev/null
+++ b/vv/vvToolSegmentation.cxx
@@ -0,0 +1,254 @@
+/*=========================================================================
+  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 "vvToolSegmentation.h"
+#include "vvSlicerManager.h"
+#include "vvSlicer.h"
+#include "vvToolInputSelectorWidget.h"
+#include "vvImageWriter.h"
+
+// Qt
+#include <QFileDialog>
+#include <QMessageBox>
+
+// vtk
+#include "vtkImageContinuousErode3D.h"
+#include "vtkImageContinuousDilate3D.h"
+ 
+//------------------------------------------------------------------------------
+// Create the tool and automagically (I like this word) insert it in
+// the main window menu.
+ADD_TOOL(vvToolSegmentation);
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolSegmentation::Initialize()
+{
+  SetToolName("Segmentation");
+  SetToolMenuName("Interactive Segmentation");
+  SetToolIconFilename(":/common/icons/ducky.ico");
+  SetToolTip("Image interactive segmentation (trial).");
+  SetToolExperimental(true);
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+vvToolSegmentation::vvToolSegmentation(vvMainWindowBase * parent, Qt::WindowFlags f)
+  :vvToolWidgetBase(parent,f),
+   vvToolBase<vvToolSegmentation>(parent),
+   Ui::vvToolSegmentation()
+{
+  // GUI Initialization
+  Ui_vvToolSegmentation::setupUi(mToolWidget);
+  setAttribute(Qt::WA_DeleteOnClose);
+
+  // Set how many inputs are needed for this tool
+  AddInputSelector("Select one image");
+  
+  // Init
+  mKernelValue = 3; // FIXME must be odd. If even -> not symmetrical
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+vvToolSegmentation::~vvToolSegmentation()
+{
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+bool vvToolSegmentation::close()
+{
+  mRefMaskActor->RemoveActors();
+  QWidget::close();  
+  mCurrentSlicerManager->Render();
+  return true;
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolSegmentation::InputIsSelected(vvSlicerManager * m)
+{
+  DD("InputIsSelected");
+  mCurrentSlicerManager = m;
+  mCurrentImage = mCurrentSlicerManager->GetImage();
+
+  // Refuse if non 3D image
+  if (mCurrentImage->GetNumberOfDimensions() != 3) {
+    QMessageBox::information(this,tr("Sorry only 3D yet"), tr("Sorry only 3D yet"));
+    close();
+    return;
+  }
+
+  // Change gui
+  //mLabelInputInfo->setText(QString("%1").arg(m->GetFileName().c_str()));
+
+  // Open mask
+  OpenBinaryImage();
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolSegmentation::apply()
+{
+  DD("apply");
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolSegmentation::OpenBinaryImage()
+{
+  DD("OpenBinaryImage");
+
+  // Load browser and select image
+  QString Extensions = "Images files ( *.mha *.mhd *.hdr *.his)";
+  Extensions += ";;All Files (*)";
+  QString filename =
+    QFileDialog::getOpenFileName(this,tr("Open binary image"),
+                                 mMainWindowBase->GetInputPathName(),Extensions);
+  DD(filename.toStdString());
+  if (filename.size() == 0) return;
+  
+  // Open Image
+  QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
+  vvImageReader::Pointer reader = vvImageReader::New();
+  std::vector<std::string> filenames;
+  filenames.push_back(filename.toStdString());
+  reader->SetInputFilenames(filenames);
+  reader->Update(vvImageReader::IMAGE);
+  QApplication::restoreOverrideCursor();
+  
+  if (reader->GetLastError().size() != 0) {
+    std::cerr << "Error while reading " << filename.toStdString() << std::endl;
+    QString error = "Cannot open file \n";
+    error += reader->GetLastError().c_str();
+    QMessageBox::information(this,tr("Reading problem"),error);
+    return;
+  }
+
+  mMaskImage = reader->GetOutput();
+  int dim = mMaskImage->GetNumberOfDimensions();
+  if (dim != 3 ) {
+    QMessageBox::information(this,tr("Sorry only 3D yet"), tr("Sorry only 3D yet"));
+    close();
+    return;
+  }
+
+  // Add a new roi actor
+  mRefMaskActor = QSharedPointer<vvROIActor>(new vvROIActor);
+  std::vector<double> color;
+  color.push_back(1);
+  color.push_back(0);
+  color.push_back(0);
+  clitk::DicomRT_ROI::Pointer roi = clitk::DicomRT_ROI::New();
+  roi->SetFromBinaryImage(mMaskImage, 1, std::string("toto"), color, filename.toStdString());
+  mRefMaskActor->SetBGMode(true);
+  mRefMaskActor->SetROI(roi);
+  mRefMaskActor->SetSlicerManager(mCurrentSlicerManager);
+  mRefMaskActor->Initialize(10, true);
+  mRefMaskActor->Update();
+
+  // Prepare widget to get keyboard event
+  grabKeyboard();
+  //connect(this, SIGNAL(keyPressEvent(QKeyEvent*)), this, SLOT(keyPressed(QKeyEvent*)));
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolSegmentation::keyPressEvent(QKeyEvent * event)
+{
+  vvToolWidgetBase::keyPressEvent(event);
+  //DD("key");
+  
+  if (event->text() == "e") {
+    Erode();
+  }
+  if (event->text() == "d") {
+    Dilate(); // FIXME -> extend image BB !!
+  }
+  if (event->text() == "s") {
+    vvImageWriter::Pointer writer = vvImageWriter::New();
+    writer->SetOutputFileName("a.mha");
+    writer->SetInput(mMaskImage);
+    writer->Update();
+  }
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolSegmentation::Erode()
+{
+  QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
+  vtkImageContinuousErode3D* erode = vtkImageContinuousErode3D::New();
+  erode->SetKernelSize(mKernelValue,mKernelValue,mKernelValue);
+  vtkImageData* image = mMaskImage->GetVTKImages()[0];
+  erode->SetInput(image);
+  erode->Update();
+  image->DeepCopy(erode->GetOutput());
+  image->Update();
+  UpdateAndRender();
+  erode->Delete();
+  QApplication::restoreOverrideCursor();
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolSegmentation::Dilate()
+{
+  QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));
+  vtkImageContinuousDilate3D* dilate = vtkImageContinuousDilate3D::New();
+  dilate->SetKernelSize(mKernelValue,mKernelValue,mKernelValue);
+  vtkImageData* image = mMaskImage->GetVTKImages()[0];
+  dilate->SetInput(image);
+  dilate->Update();
+  image->DeepCopy(dilate->GetOutput());
+  image->Update();
+  UpdateAndRender();
+  dilate->Delete();
+  QApplication::restoreOverrideCursor();
+}
+//------------------------------------------------------------------------------
+
+
+//------------------------------------------------------------------------------
+void vvToolSegmentation::UpdateAndRender()
+{
+  bool visible = mRefMaskActor->IsVisible();
+  bool cvisible = mRefMaskActor->IsContourVisible();
+  mRefMaskActor->SetVisible(false);
+  mRefMaskActor->SetContourVisible(false);
+  mCurrentSlicerManager->Render();
+
+  //mRefMaskActor->RemoveActors();
+  mRefMaskActor->UpdateImage();
+  mRefMaskActor->SetVisible(visible);
+  mRefMaskActor->SetContourVisible(cvisible);
+  mCurrentSlicerManager->Render();
+}
+//------------------------------------------------------------------------------

diff --git a/vv/vvToolSegmentation.h b/vv/vvToolSegmentation.h
new file mode 100644 (file)
index 0000000..7b8bb8c
--- /dev/null
+++ b/vv/vvToolSegmentation.h
@@ -0,0 +1,64 @@
+/*=========================================================================
+  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
+===========================================================================**/
+#ifndef VVTOOLSEGMENTATION_H
+#define VVTOOLSEGMENTATION_H
+
+#include <QtDesigner/QDesignerExportWidget>
+
+#include "vvToolBase.h"
+#include "vvToolWidgetBase.h"
+#include "vvROIActor.h"
+#include "ui_vvToolSegmentation.h"
+
+//------------------------------------------------------------------------------
+class vvToolSegmentation:
+  public vvToolWidgetBase,
+  public vvToolBase<vvToolSegmentation>, 
+  private Ui::vvToolSegmentation 
+{
+  Q_OBJECT
+    public:
+  vvToolSegmentation(vvMainWindowBase * parent=0, Qt::WindowFlags f=0);
+  ~vvToolSegmentation();
+
+  //-----------------------------------------------------
+  static void Initialize();
+  virtual void InputIsSelected(vvSlicerManager * m);
+  void OpenBinaryImage();
+  void Erode();
+  void Dilate();
+  void UpdateAndRender();
+
+  //-----------------------------------------------------
+  public slots:
+  virtual void apply();
+  virtual void keyPressEvent(QKeyEvent * event);
+  virtual bool close();
+  // virtual void reject();
+
+ protected:
+  // virtual void closeEvent(QCloseEvent *event);
+  Ui::vvToolSegmentation ui;
+  QSharedPointer<vvROIActor> mRefMaskActor;
+  vvImage::Pointer mMaskImage;
+  int mKernelValue;
+
+}; // end class vvToolSegmentation
+//------------------------------------------------------------------------------
+
+#endif