diff --git a/Plugins/org.mitk.gui.qt.regiongrowing/src/internal/QmitkRegionGrowingView.cpp b/Plugins/org.mitk.gui.qt.regiongrowing/src/internal/QmitkRegionGrowingView.cpp index 23b993e067..fa3a4cbf97 100644 --- a/Plugins/org.mitk.gui.qt.regiongrowing/src/internal/QmitkRegionGrowingView.cpp +++ b/Plugins/org.mitk.gui.qt.regiongrowing/src/internal/QmitkRegionGrowingView.cpp @@ -1,294 +1,355 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ // Blueberry #include #include // Qmitk #include "QmitkRegionGrowingView.h" //! [cpp-includes] // Qmitk #include "QmitkPointListWidget.h" #include "QmitkRenderWindow.h" // MITK #include "mitkColorProperty.h" #include "mitkITKImageImport.h" #include "mitkImageAccessByItk.h" #include "mitkImageCast.h" #include "mitkProperties.h" // ITK #include //! [cpp-includes] // Qt #include +#include "MitkRegionIterator.h" + const std::string QmitkRegionGrowingView::VIEW_ID = "org.mitk.views.example.regiongrowing"; -QmitkRegionGrowingView::QmitkRegionGrowingView() : m_PointListWidget(NULL) +QmitkRegionGrowingView::QmitkRegionGrowingView() : m_PointListWidget(NULL), m_ThresholdMethod(ThresholdMethod::easy) { } void QmitkRegionGrowingView::SetFocus() { m_Controls.buttonPerformImageProcessing->setFocus(); } void QmitkRegionGrowingView::CreateQtPartControl(QWidget *parent) { // create GUI widgets from the Qt Designer's .ui file m_Controls.setupUi(parent); + + //add different methods for threshold determination + m_Controls.comboBoxThresholdMethod->addItem("easy"); + m_Controls.comboBoxThresholdMethod->addItem("mean"); + m_Controls.comboBoxThresholdMethod->addItem("stddiv"); + connect(m_Controls.buttonPerformImageProcessing, SIGNAL(clicked()), this, SLOT(DoImageProcessing())); connect(m_Controls.checkBoxCustomRange, SIGNAL(clicked(bool)), this, SLOT(UseCustomRange(bool))); connect(m_Controls.pushButtonClearPointList, SIGNAL(clicked()), this, SLOT(ClearPointSet())); - + connect(m_Controls.comboBoxThresholdMethod, SIGNAL(currentIndexChanged(int)), this, SLOT(SetThresholdMethod(int))); + //! [cpp-createqtpartcontrol] // create a QmitkPointListWidget and add it to the widget created from .ui file m_PointListWidget = new QmitkPointListWidget(); m_Controls.verticalLayout->addWidget(m_PointListWidget, 1); // retrieve a possibly existing IRenderWindowPart if (mitk::IRenderWindowPart *renderWindowPart = GetRenderWindowPart()) { // let the point set widget know about the render window part (crosshair updates) RenderWindowPartActivated(renderWindowPart); } mitk::DataNode::Pointer pointSetNode = this->GetDataStorage()->GetNamedNode("seed points for region growing"); + m_PointSet = mitk::PointSet::New(); if (pointSetNode == nullptr) { // create a new DataNode containing a PointSet with some interaction - m_PointSet = mitk::PointSet::New(); pointSetNode = mitk::DataNode::New(); pointSetNode->SetData(m_PointSet); pointSetNode->SetName("seed points for region growing"); pointSetNode->SetProperty("helper object", mitk::BoolProperty::New(true)); pointSetNode->SetProperty("layer", mitk::IntProperty::New(1024)); + pointSetNode->SetProperty("globalObject_RWM", mitk::BoolProperty::New(true)); // add the pointset to the data storage (for rendering and access by other modules) GetDataStorage()->Add(pointSetNode); } // tell the GUI widget about the point set m_PointListWidget->SetPointSetNode(pointSetNode); //! [cpp-createqtpartcontrol] - + UpdatePointSet(); connect(m_PointListWidget, SIGNAL(PointListChanged()), this, SLOT(UpdatePointSet())); } void QmitkRegionGrowingView::OnSelectionChanged(berry::IWorkbenchPart::Pointer /*source*/, const QList &nodes) { // iterate all selected objects, adjust warning visibility foreach (mitk::DataNode::Pointer node, nodes) { if (node.IsNotNull() && dynamic_cast(node->GetData())) { m_Controls.labelWarning->setVisible(false); m_Controls.buttonPerformImageProcessing->setEnabled(true); return; } } m_Controls.labelWarning->setVisible(true); m_Controls.buttonPerformImageProcessing->setEnabled(false); } void QmitkRegionGrowingView::RenderWindowPartActivated(mitk::IRenderWindowPart *renderWindowPart) { // let the point set widget know about the slice navigation controllers // in the active render window part (crosshair updates) foreach (QmitkRenderWindow *renderWindow, renderWindowPart->GetQmitkRenderWindows().values()) { m_PointListWidget->AddSliceNavigationController(renderWindow->GetSliceNavigationController()); } } void QmitkRegionGrowingView::RenderWindowPartDeactivated(mitk::IRenderWindowPart *renderWindowPart) { foreach (QmitkRenderWindow *renderWindow, renderWindowPart->GetQmitkRenderWindows().values()) { m_PointListWidget->RemoveSliceNavigationController(renderWindow->GetSliceNavigationController()); } } void QmitkRegionGrowingView::DoImageProcessing() { QList nodes = this->GetDataManagerSelection(); if (nodes.empty()) return; mitk::DataNode *node = nodes.front(); if (!node) { // Nothing selected. Inform the user and return QMessageBox::information(NULL, "Template", "Please load and select an image before starting image processing."); return; } // here we have a valid mitk::DataNode // a node itself is not very useful, we need its data item (the image) mitk::BaseData *data = node->GetData(); if (data) { // test if this data item is an image or not (could also be a surface or something totally different) mitk::Image *image = dynamic_cast(data); if (image) { //! [cpp-doimageprocessing] // So we have an image. Let's see if the user has set some seed points already if (m_PointSet->GetSize() == 0) { // no points there. Not good for region growing QMessageBox::information(NULL, "Region growing functionality", "Please set some seed points inside the image first.\n" "(hold Shift key and click left mouse button inside the image.)"); return; } // actually perform region growing. Here we have both an image and some seed points AccessByItk_1( image, ItkImageProcessing, image->GetGeometry()) // some magic to call the correctly templated function //! [cpp-doimageprocessing] } } } void QmitkRegionGrowingView::UseCustomRange(bool useCustomRange) { m_Controls.spinBoxMax->setEnabled(useCustomRange); m_Controls.spinBoxMin->setEnabled(useCustomRange); } void QmitkRegionGrowingView::UpdatePointSet() { m_PointSet = m_PointListWidget->GetPointSet(); } void QmitkRegionGrowingView::ClearPointSet() { QMessageBox::StandardButton reply; reply = QMessageBox::question(nullptr, "Test", "Are you sure?", QMessageBox::Yes | QMessageBox::No, QMessageBox::No); if (reply == QMessageBox::Yes) { m_PointSet->Clear(); } else { //Clearing point set canceled } } //! [cpp-itkimageaccess] template void QmitkRegionGrowingView::ItkImageProcessing(itk::Image *itkImage, mitk::BaseGeometry *imageGeometry) { typedef itk::Image InputImageType; typedef typename InputImageType::IndexType IndexType; // instantiate an ITK region growing filter, set its parameters typedef itk::ConnectedThresholdImageFilter RegionGrowingFilterType; typename RegionGrowingFilterType::Pointer regionGrower = RegionGrowingFilterType::New(); regionGrower->SetInput(itkImage); // don't forget this // determine a thresholding interval IndexType seedIndex; mitk::PointSet::PointsContainer *points = m_PointSet->GetPointSet()->GetPoints(); for (mitk::PointSet::PointsConstIterator pointsIterator = points->Begin(); pointsIterator != points->End(); ++pointsIterator) { // first test if this point is inside the image at all if (!imageGeometry->IsInside(pointsIterator.Value())) { continue; } TPixel min(std::numeric_limits::max()); TPixel max(std::numeric_limits::min()); if (m_Controls.checkBoxCustomRange->isChecked()) { max = m_Controls.spinBoxMax->value(); min = m_Controls.spinBoxMin->value(); } // convert world coordinates to image indices imageGeometry->WorldToIndex(pointsIterator.Value(), seedIndex); - // get the pixel value at this point - TPixel currentPixelValue = itkImage->GetPixel(seedIndex); + //================================================= - if (!m_Controls.checkBoxCustomRange->isChecked()) - { - // adjust minimum and maximum values - if (currentPixelValue > max) - max = currentPixelValue; + MitkRegionIterator mitkRegionIterator(itkImage, 1); + int thresholdRange = 0; + + //================================================= - if (currentPixelValue < min) - min = currentPixelValue; - } + // get the pixel value at this point + TPixel currentPixelValue = itkImage->GetPixel(seedIndex); regionGrower->AddSeed(seedIndex); MITK_INFO << "Values between " << min << " and " << max; if (!m_Controls.checkBoxCustomRange->isChecked()) { - min -= 130; - max += 130; + switch (m_ThresholdMethod) + { + case 0: + // adjust minimum and maximum values + if (currentPixelValue > max) + max = currentPixelValue; + + if (currentPixelValue < min) + min = currentPixelValue; + thresholdRange = 130; + break; + + case 1: + // adjust minimum and maximum values + max = mitkRegionIterator.GetMeanPixelValueForRegion(seedIndex); + min = mitkRegionIterator.GetMeanPixelValueForRegion(seedIndex); + + thresholdRange = mitkRegionIterator.GetThresholdByMeanMethod(seedIndex); + break; + + case 2: + // adjust minimum and maximum values + max = mitkRegionIterator.GetMeanPixelValueForRegion(seedIndex); + min = mitkRegionIterator.GetMeanPixelValueForRegion(seedIndex); + + mitkRegionIterator.SetRadius(3); + thresholdRange = mitkRegionIterator.GetThresholdByStdDivMethod(seedIndex); + break; + } + min -= thresholdRange; + max += thresholdRange; } m_Controls.spinBoxMin->setValue(min); m_Controls.spinBoxMax->setValue(max); // set thresholds and execute filter regionGrower->SetLower(min); regionGrower->SetUpper(max); regionGrower->Update(); mitk::Image::Pointer resultImage; mitk::CastToMitkImage(regionGrower->GetOutput(), resultImage); mitk::DataNode::Pointer newNode = mitk::DataNode::New(); newNode->SetData(resultImage); // set some properties newNode->SetProperty("binary", mitk::BoolProperty::New(true)); newNode->SetProperty("name", mitk::StringProperty::New("dumb segmentation")); newNode->SetProperty("color", mitk::ColorProperty::New(1.0, 0.0, 0.0)); newNode->SetProperty("volumerendering", mitk::BoolProperty::New(true)); newNode->SetProperty("layer", mitk::IntProperty::New(1)); newNode->SetProperty("opacity", mitk::FloatProperty::New(0.5)); + newNode->SetProperty("globalObject_RWM", mitk::BoolProperty::New(true)); // add result to data tree this->GetDataStorage()->Add(newNode); mitk::RenderingManager::GetInstance()->RequestUpdateAll(); regionGrower->ClearSeeds(); } } //! [cpp-itkimageaccess] +void QmitkRegionGrowingView::SetThresholdMethod(int index) +{ + int currentIndex = m_Controls.comboBoxThresholdMethod->currentIndex(); + + switch (currentIndex) + { + case 0: + m_ThresholdMethod = ThresholdMethod::easy; + break; + + case 1: + m_ThresholdMethod = ThresholdMethod::mean; + break; + + case 2: + m_ThresholdMethod = ThresholdMethod::stddiv; + break; + + default: + m_ThresholdMethod = ThresholdMethod::easy; + break; + } +} + diff --git a/Plugins/org.mitk.gui.qt.regiongrowing/src/internal/QmitkRegionGrowingView.h b/Plugins/org.mitk.gui.qt.regiongrowing/src/internal/QmitkRegionGrowingView.h index 33200c3ae0..0faa41b5b5 100644 --- a/Plugins/org.mitk.gui.qt.regiongrowing/src/internal/QmitkRegionGrowingView.h +++ b/Plugins/org.mitk.gui.qt.regiongrowing/src/internal/QmitkRegionGrowingView.h @@ -1,99 +1,106 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef QmitkRegionGrowingView_h #define QmitkRegionGrowingView_h #include #include #include "ui_QmitkRegionGrowingViewControls.h" //! [includes] #include "mitkIRenderWindowPartListener.h" #include "mitkPointSet.h" #include class QmitkPointListWidget; //! [includes] /** \brief QmitkRegionGrowingView \warning This class is not yet documented. Use "git blame" and ask the author to provide basic documentation. \sa QmitkAbstractView \ingroup ${plugin_target}_internal */ class QmitkRegionGrowingView : public QmitkAbstractView, public mitk::IRenderWindowPartListener { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: static const std::string VIEW_ID; QmitkRegionGrowingView(); protected slots: /// \brief Called when the user clicks the GUI button void DoImageProcessing(); void UseCustomRange(bool useCustomRange); void UpdatePointSet(); void ClearPointSet(); + void SetThresholdMethod(int index); + protected: virtual void CreateQtPartControl(QWidget *parent) override; virtual void SetFocus() override; virtual void OnSelectionChanged(berry::IWorkbenchPart::Pointer source, const QList &nodes) override; //! [render-window-part-listener] void RenderWindowPartActivated(mitk::IRenderWindowPart *renderWindowPart) override; void RenderWindowPartDeactivated(mitk::IRenderWindowPart *renderWindowPart) override; //! [render-window-part-listener] Ui::QmitkRegionGrowingViewControls m_Controls; private: //! [itkimageprocessing] /** \brief ITK image processing function This function is templated like an ITK image. The MITK-Macro AccessByItk determines the actual pixel type and dimensionality of a given MITK image and calls this function for further processing (in our case region growing) */ template void ItkImageProcessing(itk::Image *itkImage, mitk::BaseGeometry *imageGeometry); //! [itkimageprocessing] + //template + //void iterateOverNeighborhood(itk::Image *itkImage, IndexType seedIndex, int radius); + //! [members] /// \brief This is the actual seed point data object mitk::PointSet::Pointer m_PointSet; QmitkPointListWidget *m_PointListWidget; //! [members] + + enum ThresholdMethod { easy, mean, stddiv } m_ThresholdMethod; }; #endif // QmitkRegionGrowingView_h diff --git a/Plugins/org.mitk.gui.qt.regiongrowing/src/internal/QmitkRegionGrowingViewControls.ui b/Plugins/org.mitk.gui.qt.regiongrowing/src/internal/QmitkRegionGrowingViewControls.ui index 10ef6a421a..b345d6c345 100644 --- a/Plugins/org.mitk.gui.qt.regiongrowing/src/internal/QmitkRegionGrowingViewControls.ui +++ b/Plugins/org.mitk.gui.qt.regiongrowing/src/internal/QmitkRegionGrowingViewControls.ui @@ -1,108 +1,111 @@ QmitkRegionGrowingViewControls 0 0 222 161 0 0 QmitkTemplate QLabel { color: rgb(255, 0, 0) } Please select an image! Customize Range ClearPoint List + + + Min false 99999 Max false 99999 Do image processing Start Region Growing!