( maskingNode->GetData() );
//TODO Get 3D Surface of current time step
if(surface.IsNull())
{
MITK_ERROR << "Selection does not contain a surface";
QMessageBox::information( this, "Image and Surface Masking", "Selection does not contain a surface", QMessageBox::Ok );
this->EnableButtons();
return;
}
mitk::Image::Pointer maskImage = this->ConvertSurfaceToImage( referenceImage, surface );
//2. mask reference image with mask image
if(maskImage.IsNotNull() &&
referenceImage->GetLargestPossibleRegion().GetSize() == maskImage->GetLargestPossibleRegion().GetSize() )
{
resultImage = this->MaskImage( referenceImage, maskImage );
}
}
mitk::ProgressBar::GetInstance()->Progress();
if( resultImage.IsNull() )
{
MITK_ERROR << "Masking failed";
QMessageBox::information( this, "Image and Surface Masking", "Masking failed. For more information please see logging window.", QMessageBox::Ok );
this->EnableButtons();
mitk::ProgressBar::GetInstance()->Progress(4);
return;
}
//Add result to data storage
this->AddToDataStorage(
dataSelectionWidget->GetDataStorage(),
resultImage,
dataSelectionWidget->GetSelection(0)->GetName() + "_" + dataSelectionWidget->GetSelection(1)->GetName(),
dataSelectionWidget->GetSelection(0));
this->EnableButtons();
mitk::ProgressBar::GetInstance()->Progress();
}
mitk::Image::Pointer QmitkImageMaskingWidget::MaskImage(mitk::Image::Pointer referenceImage, mitk::Image::Pointer maskImage )
{
- mitk::Image::Pointer resultImage(nullptr);
+ mitk::ScalarType backgroundValue = 0.0;
+
+ if (m_Controls.rbnMinimum->isChecked())
+ {
+ backgroundValue = referenceImage->GetStatistics()->GetScalarValueMin();
+ }
+ else if (m_Controls.rbnCustom->isChecked())
+ {
+ auto warningTitle = QStringLiteral("Invalid custom pixel value");
+
+ bool ok = false;
+ auto originalBackgroundValue = m_Controls.txtCustom->text().toDouble(&ok);
- mitk::MaskImageFilter::Pointer maskFilter = mitk::MaskImageFilter::New();
- maskFilter->SetInput( referenceImage );
- maskFilter->SetMask( maskImage );
+ if (!ok)
+ {
+ // Input is not even a number
+ QMessageBox::warning(nullptr, warningTitle, "Please enter a valid number as custom pixel value.");
+ return nullptr;
+ }
+ else
+ {
+ // Clamp to the numerical limits of the pixel/component type
+ double bottom, top;
+ AccessByItk_n(referenceImage, GetRange, (bottom, top));
+ backgroundValue = std::max(bottom, std::min(originalBackgroundValue, top));
+
+ // Get rid of decimals for integral numbers
+ auto type = referenceImage->GetPixelType().GetComponentType();
+ if (type != itk::ImageIOBase::FLOAT && type != itk::ImageIOBase::DOUBLE)
+ backgroundValue = std::round(backgroundValue);
+ }
+
+ // Ask the user for permission before correcting their input
+ if (std::abs(originalBackgroundValue - backgroundValue) > 1e-4)
+ {
+ auto warningText = QString(
+ "The custom pixel value %1 lies not within the range of valid pixel values for the selected image.
"
+ "Apply the closest valid pixel value %2 instead?
").arg(originalBackgroundValue).arg(backgroundValue);
+
+ auto ret = QMessageBox::warning(
+ nullptr,
+ warningTitle,
+ warningText,
+ QMessageBox::StandardButton::Apply | QMessageBox::StandardButton::Cancel,
+ QMessageBox::StandardButton::Apply);
+
+ if (QMessageBox::StandardButton::Apply != ret)
+ return nullptr;
+
+ m_Controls.txtCustom->setText(QString("%1").arg(backgroundValue));
+ }
+ }
+
+ auto maskFilter = mitk::MaskImageFilter::New();
+ maskFilter->SetInput(referenceImage);
+ maskFilter->SetMask(maskImage);
maskFilter->OverrideOutsideValueOn();
- maskFilter->SetOutsideValue( referenceImage->GetStatistics()->GetScalarValueMin() );
+ maskFilter->SetOutsideValue(backgroundValue);
+
try
{
maskFilter->Update();
}
- catch(itk::ExceptionObject& excpt)
+ catch(const itk::ExceptionObject& e)
{
- MITK_ERROR << excpt.GetDescription();
+ MITK_ERROR << e.GetDescription();
return nullptr;
}
- resultImage = maskFilter->GetOutput();
-
- return resultImage;
+ return maskFilter->GetOutput();
}
mitk::Image::Pointer QmitkImageMaskingWidget::ConvertSurfaceToImage( mitk::Image::Pointer image, mitk::Surface::Pointer surface )
{
mitk::ProgressBar::GetInstance()->AddStepsToDo(2);
mitk::ProgressBar::GetInstance()->Progress();
mitk::SurfaceToImageFilter::Pointer surfaceToImageFilter = mitk::SurfaceToImageFilter::New();
surfaceToImageFilter->MakeOutputBinaryOn();
surfaceToImageFilter->SetInput(surface);
surfaceToImageFilter->SetImage(image);
try
{
surfaceToImageFilter->Update();
}
catch(itk::ExceptionObject& excpt)
{
MITK_ERROR << excpt.GetDescription();
return nullptr;
}
mitk::ProgressBar::GetInstance()->Progress();
mitk::Image::Pointer resultImage = mitk::Image::New();
resultImage = surfaceToImageFilter->GetOutput();
return resultImage;
}
void QmitkImageMaskingWidget::AddToDataStorage(mitk::DataStorage::Pointer dataStorage, mitk::Image::Pointer segmentation, const std::string& name, mitk::DataNode::Pointer parent )
{
auto dataNode = mitk::DataNode::New();
dataNode->SetName(name);
dataNode->SetData(segmentation);
if (parent.IsNotNull())
{
mitk::LevelWindow levelWindow;
parent->GetLevelWindow(levelWindow);
dataNode->SetLevelWindow(levelWindow);
}
dataStorage->Add(dataNode, parent);
}
diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.h b/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.h
index 37a5711983..7a24096fb5 100644
--- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.h
+++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidget.h
@@ -1,74 +1,77 @@
/*============================================================================
The Medical Imaging Interaction Toolkit (MITK)
Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.
Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.
============================================================================*/
#ifndef QmitkImageMaskingWidget_h
#define QmitkImageMaskingWidget_h
#include "../QmitkSegmentationUtilityWidget.h"
#include
#include
namespace mitk {
class Image;
}
/*!
\brief QmitkImageMaskingWidget
Tool masks an image with a binary image or a surface. The Method requires
an image and a binary image mask or a surface. The input image and the binary
image mask must be of the same size. Masking with a surface creates first a
binary image of the surface and then use this for the masking of the input image.
*/
class QmitkImageMaskingWidget : public QmitkSegmentationUtilityWidget
{
Q_OBJECT
public:
/** @brief Default constructor, including creation of GUI elements and signals/slots connections. */
explicit QmitkImageMaskingWidget(mitk::SliceNavigationController* timeNavigationController, QWidget* parent = nullptr);
/** @brief Defaul destructor. */
~QmitkImageMaskingWidget() override;
private slots:
/** @brief This slot is called if the selection in the workbench is changed. */
void OnSelectionChanged(unsigned int index, const mitk::DataNode* selection);
/** @brief This slot is called if user activates the button to mask an image. */
void OnMaskImagePressed();
+ /** @brief This slot is called if the user toggles the "Custom" radio button. */
+ void OnCustomValueButtonToggled(bool checked);
+
private:
/** @brief Check if selections is valid. */
void SelectionControl( unsigned int index, const mitk::DataNode* selection);
/** @brief Enable buttons if data selction is valid. */
void EnableButtons(bool enable = true);
/** @brief Mask an image with a given binary mask. Note that the input image and the mask image must be of the same size. */
itk::SmartPointer MaskImage(itk::SmartPointer referenceImage, itk::SmartPointer maskImage );
/** @brief Convert a surface into an binary image. */
itk::SmartPointer ConvertSurfaceToImage( itk::SmartPointer image, mitk::Surface::Pointer surface );
/** @brief Adds a new data object to the DataStorage.*/
void AddToDataStorage(mitk::DataStorage::Pointer dataStorage, itk::SmartPointer segmentation,
const std::string& name, mitk::DataNode::Pointer parent = nullptr);
Ui::QmitkImageMaskingWidgetControls m_Controls;
};
#endif
diff --git a/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidgetControls.ui b/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidgetControls.ui
index 7ff3b3184c..ff45a758c6 100644
--- a/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidgetControls.ui
+++ b/Plugins/org.mitk.gui.qt.segmentation/src/internal/SegmentationUtilities/ImageMasking/QmitkImageMaskingWidgetControls.ui
@@ -1,56 +1,109 @@
QmitkImageMaskingWidgetControls
0
0
- 147
- 155
+ 238
+ 329
-
0
0
+ -
+
+
+ Background value
+
+
+
-
+
+
+ Zero
+
+
+ true
+
+
+
+ -
+
+
+ Minimum
+
+
+
+ -
+
+
-
+
+
+
+ 0
+ 0
+
+
+
+ Custom:
+
+
+
+ -
+
+
+ false
+
+
+ 0
+
+
+
+
+
+
+
+
-
Mask
-
Qt::Vertical
20
40
QmitkDataSelectionWidget
QWidget
internal/Common/QmitkDataSelectionWidget.h
1