diff --git a/Modules/Segmentation/Interactions/mitkOtsuTool3D.cpp b/Modules/Segmentation/Interactions/mitkOtsuTool3D.cpp
index 917451a48c..a04cb3e085 100644
--- a/Modules/Segmentation/Interactions/mitkOtsuTool3D.cpp
+++ b/Modules/Segmentation/Interactions/mitkOtsuTool3D.cpp
@@ -1,277 +1,253 @@
/*============================================================================
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.
============================================================================*/
// MITK
#include "mitkOtsuTool3D.h"
#include "mitkImageAccessByItk.h"
#include "mitkLabelSetImage.h"
#include "mitkOtsuSegmentationFilter.h"
#include "mitkRenderingManager.h"
#include "mitkToolManager.h"
#include <mitkITKImageImport.h>
#include <mitkImageCast.h>
#include <mitkLevelWindowProperty.h>
#include <mitkLookupTableProperty.h>
#include <mitkRenderingModeProperty.h>
#include <mitkSliceNavigationController.h>
// ITK
#include <itkBinaryThresholdImageFilter.h>
#include <itkOrImageFilter.h>
#include <itkOtsuMultipleThresholdsImageFilter.h>
// us
#include <usGetModuleContext.h>
#include <usModule.h>
#include <usModuleContext.h>
#include <usModuleResource.h>
#include <mitkImageStatisticsHolder.h>
namespace mitk
{
MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, OtsuTool3D, "Otsu Segmentation");
}
-mitk::OtsuTool3D::OtsuTool3D()
+mitk::OtsuTool3D::OtsuTool3D() : AutoSegmentationWithPreviewTool(true)
{
}
mitk::OtsuTool3D::~OtsuTool3D()
{
}
+void mitk::OtsuTool3D::SetSelectedRegions(const SelectedRegionVectorType& regions)
+{
+ if (this->m_SelectedRegions != regions)
+ {
+ this->m_SelectedRegions = regions;
+ //Note: we do not call this->Modified() on puprose. Reason: changing the
+ //selected regions should not force to run otsu filter in DoUpdatePreview due to changed MTime.
+ }
+}
+
+mitk::OtsuTool3D::SelectedRegionVectorType mitk::OtsuTool3D::GetSelectedRegions() const
+{
+ return this->m_SelectedRegions;
+}
+
void mitk::OtsuTool3D::Activated()
{
Superclass::Activated();
- if (m_ToolManager)
- {
- m_OriginalImage = dynamic_cast<mitk::Image *>(m_ToolManager->GetReferenceData(0)->GetData());
-
- m_BinaryPreviewNode = mitk::DataNode::New();
- m_BinaryPreviewNode->SetName("Binary_Preview");
- m_BinaryPreviewNode->SetProperty("color", ColorProperty::New(0.0, 1.0, 0.0));
- m_BinaryPreviewNode->SetProperty("opacity", FloatProperty::New(0.3));
- // m_BinaryPreviewNode->SetBoolProperty("helper object", true);
- // m_BinaryPreviewNode->SetProperty("binary", mitk::BoolProperty::New(true));
- m_ToolManager->GetDataStorage()->Add(this->m_BinaryPreviewNode);
-
- m_MultiLabelResultNode = mitk::DataNode::New();
- m_MultiLabelResultNode->SetName("Otsu_Preview");
- // m_MultiLabelResultNode->SetBoolProperty("helper object", true);
- m_MultiLabelResultNode->SetVisibility(true);
-
- m_MaskedImagePreviewNode = mitk::DataNode::New();
- m_MaskedImagePreviewNode->SetName("Volume_Preview");
- // m_MultiLabelResultNode->SetBoolProperty("helper object", true);
- m_MaskedImagePreviewNode->SetVisibility(false);
-
- m_ToolManager->GetDataStorage()->Add(this->m_MultiLabelResultNode);
- }
+ m_SelectedRegions = {};
+ m_NumberOfBins = 128;
+ m_NumberOfRegions = 2;
+ m_UseValley = false;
+
+ m_OtsuResultNode = mitk::DataNode::New();
+ m_OtsuResultNode->SetName("Otsu_Preview");
+ // m_MultiLabelResultNode->SetBoolProperty("helper object", true);
+ m_OtsuResultNode->SetVisibility(true);
+ m_OtsuResultNode->SetOpacity(1.0);
+
+ m_ToolManager->GetDataStorage()->Add(this->m_OtsuResultNode);
}
void mitk::OtsuTool3D::Deactivated()
{
- m_ToolManager->GetDataStorage()->Remove(this->m_MultiLabelResultNode);
- m_MultiLabelResultNode = nullptr;
- m_ToolManager->GetDataStorage()->Remove(this->m_BinaryPreviewNode);
- m_BinaryPreviewNode = nullptr;
- m_ToolManager->GetDataStorage()->Remove(this->m_MaskedImagePreviewNode);
- m_MaskedImagePreviewNode = nullptr;
+ m_ToolManager->GetDataStorage()->Remove(this->m_OtsuResultNode);
+ m_OtsuResultNode = nullptr;
Superclass::Deactivated();
}
const char **mitk::OtsuTool3D::GetXPM() const
{
return nullptr;
}
us::ModuleResource mitk::OtsuTool3D::GetIconResource() const
{
us::Module *module = us::GetModuleContext()->GetModule();
us::ModuleResource resource = module->GetResource("Otsu_48x48.png");
return resource;
}
-void mitk::OtsuTool3D::RunSegmentation(int regions, bool useValley, int numberOfBins)
+const char* mitk::OtsuTool3D::GetName() const
{
- int numberOfThresholds = regions - 1;
+ return "Otsu";
+}
+void mitk::OtsuTool3D::UpdateCleanUp()
+{
+ if (m_OtsuResultNode.IsNotNull())
+ m_OtsuResultNode->SetVisibility(m_SelectedRegions.empty());
- const auto timePoint = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint();
- auto image3D = Get3DImageByTimePoint(m_OriginalImage, timePoint);
+ if (nullptr != this->GetPreviewSegmentationNode())
+ this->GetPreviewSegmentationNode()->SetVisibility(!m_SelectedRegions.empty());
- if (nullptr == image3D)
+ if (m_SelectedRegions.empty())
{
- MITK_WARN << "Cannot run segementation. Currently selected timepoint is not in the time bounds of the selected reference image. Time point: " << timePoint;
- return;
+ this->ResetPreviewNode();
}
+}
- mitk::OtsuSegmentationFilter::Pointer otsuFilter = mitk::OtsuSegmentationFilter::New();
- otsuFilter->SetNumberOfThresholds(numberOfThresholds);
- otsuFilter->SetValleyEmphasis(useValley);
- otsuFilter->SetNumberOfBins(numberOfBins);
- otsuFilter->SetInput(image3D);
+void mitk::OtsuTool3D::DoUpdatePreview(const Image* inputAtTimeStep, Image* previewImage, TimeStepType timeStep)
+{
+ int numberOfThresholds = m_NumberOfRegions - 1;
- try
+ const auto timePoint = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetSelectedTimePoint();
+ mitk::LabelSetImage::Pointer otsuResultImage = dynamic_cast<LabelSetImage*>(this->m_OtsuResultNode->GetData());
+
+ if (nullptr == m_OtsuResultNode->GetData()
+ || this->GetMTime() > m_OtsuResultNode->GetData()->GetMTime()
+ || this->m_LastOtsuTimeStep != timeStep //this covers the case where dynamic
+ //segmentations have to compute a preview
+ //for all time steps on confirmation
+ || this->GetLastTimePointOfUpdate() != timePoint //this ensures that static seg
+ //previews work with dynamic images
+ //with avoiding unnecessary other otsu computations
+ )
{
- otsuFilter->Update();
+ if (nullptr == inputAtTimeStep)
+ {
+ MITK_WARN << "Cannot run segementation. Currently selected input image is not set.";
+ return;
+ }
+
+ this->m_LastOtsuTimeStep = timeStep;
+
+ mitk::OtsuSegmentationFilter::Pointer otsuFilter = mitk::OtsuSegmentationFilter::New();
+ otsuFilter->SetNumberOfThresholds(numberOfThresholds);
+ otsuFilter->SetValleyEmphasis(m_UseValley);
+ otsuFilter->SetNumberOfBins(m_NumberOfBins);
+ otsuFilter->SetInput(inputAtTimeStep);
+ otsuFilter->AddObserver(itk::ProgressEvent(), m_ProgressCommand);
+
+ try
+ {
+ otsuFilter->Update();
+ }
+ catch (...)
+ {
+ mitkThrow() << "itkOtsuFilter error (image dimension must be in {2, 3} and image must not be RGB)";
+ }
+
+ otsuResultImage = mitk::LabelSetImage::New();
+ otsuResultImage->InitializeByLabeledImage(otsuFilter->GetOutput());
+ this->m_OtsuResultNode->SetData(otsuResultImage);
+ this->m_OtsuResultNode->SetProperty("binary", mitk::BoolProperty::New(false));
+ mitk::RenderingModeProperty::Pointer renderingMode = mitk::RenderingModeProperty::New();
+ renderingMode->SetValue(mitk::RenderingModeProperty::LOOKUPTABLE_LEVELWINDOW_COLOR);
+ this->m_OtsuResultNode->SetProperty("Image Rendering.Mode", renderingMode);
+ mitk::LookupTable::Pointer lut = mitk::LookupTable::New();
+ mitk::LookupTableProperty::Pointer prop = mitk::LookupTableProperty::New(lut);
+ vtkSmartPointer<vtkLookupTable> lookupTable = vtkSmartPointer<vtkLookupTable>::New();
+ lookupTable->SetHueRange(1.0, 0.0);
+ lookupTable->SetSaturationRange(1.0, 1.0);
+ lookupTable->SetValueRange(1.0, 1.0);
+ lookupTable->SetTableRange(-1.0, 1.0);
+ lookupTable->Build();
+ lut->SetVtkLookupTable(lookupTable);
+ prop->SetLookupTable(lut);
+ this->m_OtsuResultNode->SetProperty("LookupTable", prop);
+ mitk::LevelWindowProperty::Pointer levWinProp = mitk::LevelWindowProperty::New();
+ mitk::LevelWindow levelwindow;
+ levelwindow.SetRangeMinMax(0, numberOfThresholds + 1);
+ levWinProp->SetLevelWindow(levelwindow);
+ this->m_OtsuResultNode->SetProperty("levelwindow", levWinProp);
}
- catch (...)
+
+ if (!m_SelectedRegions.empty())
{
- mitkThrow() << "itkOtsuFilter error (image dimension must be in {2, 3} and image must not be RGB)";
+ AccessByItk_n(otsuResultImage, CalculatePreview, (previewImage, timeStep));
}
-
- m_ToolManager->GetDataStorage()->Remove(this->m_MultiLabelResultNode);
- m_MultiLabelResultNode = nullptr;
- m_MultiLabelResultNode = mitk::DataNode::New();
- m_MultiLabelResultNode->SetName("Otsu_Preview");
- m_MultiLabelResultNode->SetVisibility(true);
- m_ToolManager->GetDataStorage()->Add(this->m_MultiLabelResultNode);
- m_MultiLabelResultNode->SetOpacity(1.0);
-
- mitk::LabelSetImage::Pointer resultImage = mitk::LabelSetImage::New();
- resultImage->InitializeByLabeledImage(otsuFilter->GetOutput());
- this->m_MultiLabelResultNode->SetData(resultImage);
- m_MultiLabelResultNode->SetProperty("binary", mitk::BoolProperty::New(false));
- mitk::RenderingModeProperty::Pointer renderingMode = mitk::RenderingModeProperty::New();
- renderingMode->SetValue(mitk::RenderingModeProperty::LOOKUPTABLE_LEVELWINDOW_COLOR);
- m_MultiLabelResultNode->SetProperty("Image Rendering.Mode", renderingMode);
- mitk::LookupTable::Pointer lut = mitk::LookupTable::New();
- mitk::LookupTableProperty::Pointer prop = mitk::LookupTableProperty::New(lut);
- vtkSmartPointer<vtkLookupTable> lookupTable = vtkSmartPointer<vtkLookupTable>::New();
- lookupTable->SetHueRange(1.0, 0.0);
- lookupTable->SetSaturationRange(1.0, 1.0);
- lookupTable->SetValueRange(1.0, 1.0);
- lookupTable->SetTableRange(-1.0, 1.0);
- lookupTable->Build();
- lut->SetVtkLookupTable(lookupTable);
- prop->SetLookupTable(lut);
- m_MultiLabelResultNode->SetProperty("LookupTable", prop);
- mitk::LevelWindowProperty::Pointer levWinProp = mitk::LevelWindowProperty::New();
- mitk::LevelWindow levelwindow;
- levelwindow.SetRangeMinMax(0, numberOfThresholds + 1);
- levWinProp->SetLevelWindow(levelwindow);
- m_MultiLabelResultNode->SetProperty("levelwindow", levWinProp);
-
- // m_BinaryPreviewNode->SetVisibility(false);
- // m_MultiLabelResultNode->SetVisibility(true);
- // this->m_OtsuSegmentationDialog->setCursor(Qt::ArrowCursor);
- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
-}
-
-void mitk::OtsuTool3D::ConfirmSegmentation()
-{
- mitk::LabelSetImage::Pointer resultImage = mitk::LabelSetImage::New();
- resultImage->InitializeByLabeledImage(dynamic_cast<mitk::Image *>(m_BinaryPreviewNode->GetData()));
- GetTargetSegmentationNode()->SetData(resultImage);
-
- m_ToolManager->ActivateTool(-1);
-}
-
-void mitk::OtsuTool3D::UpdateBinaryPreview(std::vector<int> regionIDs)
-{
- m_MultiLabelResultNode->SetVisibility(false);
- mitk::Image::Pointer multiLabelSegmentation = dynamic_cast<mitk::Image *>(m_MultiLabelResultNode->GetData());
- AccessByItk_1(multiLabelSegmentation, CalculatePreview, regionIDs);
}
template <typename TPixel, unsigned int VImageDimension>
-void mitk::OtsuTool3D::CalculatePreview(itk::Image<TPixel, VImageDimension> *itkImage, std::vector<int> regionIDs)
+void mitk::OtsuTool3D::CalculatePreview(itk::Image<TPixel, VImageDimension> *itkImage, mitk::Image* segmentation, unsigned int timeStep)
{
typedef itk::Image<TPixel, VImageDimension> InputImageType;
typedef itk::Image<mitk::Tool::DefaultSegmentationDataType, VImageDimension> OutputImageType;
typedef itk::BinaryThresholdImageFilter<InputImageType, OutputImageType> FilterType;
typename FilterType::Pointer filter = FilterType::New();
// InputImageType::Pointer itkImage;
- typename OutputImageType::Pointer itkBinaryTempImage1;
- typename OutputImageType::Pointer itkBinaryTempImage2;
typename OutputImageType::Pointer itkBinaryResultImage;
- // mitk::Image::Pointer multiLabelSegmentation = dynamic_cast<mitk::Image*>(m_MultiLabelResultNode->GetData());
- // mitk::CastToItkImage(multiLabelSegmentation, itkImage);
-
filter->SetInput(itkImage);
- filter->SetLowerThreshold(regionIDs[0]);
- filter->SetUpperThreshold(regionIDs[0]);
+ filter->SetLowerThreshold(m_SelectedRegions[0]);
+ filter->SetUpperThreshold(m_SelectedRegions[0]);
filter->SetInsideValue(1);
filter->SetOutsideValue(0);
+ filter->AddObserver(itk::ProgressEvent(), m_ProgressCommand);
filter->Update();
- itkBinaryTempImage2 = filter->GetOutput();
-
- typename itk::OrImageFilter<OutputImageType, OutputImageType>::Pointer orFilter =
- itk::OrImageFilter<OutputImageType, OutputImageType>::New();
+ itkBinaryResultImage = filter->GetOutput();
+ itkBinaryResultImage->DisconnectPipeline();
// if more than one region id is used compute the union of all given binary regions
- for (auto it = regionIDs.begin(); it != regionIDs.end(); ++it)
+ for (const auto regionID : m_SelectedRegions)
{
- filter->SetLowerThreshold(*it);
- filter->SetUpperThreshold(*it);
- filter->SetInsideValue(1);
- filter->SetOutsideValue(0);
- filter->Update();
- itkBinaryTempImage1 = filter->GetOutput();
-
- orFilter->SetInput1(itkBinaryTempImage1);
- orFilter->SetInput2(itkBinaryTempImage2);
-
- orFilter->UpdateLargestPossibleRegion();
- itkBinaryResultImage = orFilter->GetOutput();
- itkBinaryTempImage2 = itkBinaryResultImage;
+ if (regionID != m_SelectedRegions[0])
+ {
+ filter->SetLowerThreshold(regionID);
+ filter->SetUpperThreshold(regionID);
+ filter->SetInsideValue(1);
+ filter->SetOutsideValue(0);
+ filter->Update();
+
+ typename OutputImageType::Pointer tempImage = filter->GetOutput();
+
+ typename itk::OrImageFilter<OutputImageType, OutputImageType>::Pointer orFilter =
+ itk::OrImageFilter<OutputImageType, OutputImageType>::New();
+ orFilter->SetInput1(tempImage);
+ orFilter->SetInput2(itkBinaryResultImage);
+ orFilter->AddObserver(itk::ProgressEvent(), m_ProgressCommand);
+
+ orFilter->UpdateLargestPossibleRegion();
+ itkBinaryResultImage = orFilter->GetOutput();
+ }
}
//----------------------------------------------------------------------------------------------------
- mitk::Image::Pointer binarySegmentation;
- mitk::CastToMitkImage(itkBinaryResultImage, binarySegmentation);
- m_BinaryPreviewNode->SetData(binarySegmentation);
- m_BinaryPreviewNode->SetVisibility(true);
- m_BinaryPreviewNode->SetProperty("outline binary", mitk::BoolProperty::New(false));
-
- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
-}
-
-const char *mitk::OtsuTool3D::GetName() const
-{
- return "Otsu";
-}
-void mitk::OtsuTool3D::UpdateVolumePreview(bool volumeRendering)
-{
- if (volumeRendering)
- {
- m_MaskedImagePreviewNode->SetBoolProperty("volumerendering", true);
- m_MaskedImagePreviewNode->SetBoolProperty("volumerendering.uselod", true);
- }
- else
- {
- m_MaskedImagePreviewNode->SetBoolProperty("volumerendering", false);
- }
- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
-}
-
-void mitk::OtsuTool3D::ShowMultiLabelResultNode(bool show)
-{
- m_MultiLabelResultNode->SetVisibility(show);
- m_BinaryPreviewNode->SetVisibility(!show);
- mitk::RenderingManager::GetInstance()->RequestUpdateAll();
+ segmentation->SetVolume((void*)(itkBinaryResultImage->GetPixelContainer()->GetBufferPointer()), timeStep);
}
-int mitk::OtsuTool3D::GetNumberOfBins()
+unsigned int mitk::OtsuTool3D::GetMaxNumberOfBins() const
{
- ScalarType min = m_OriginalImage.GetPointer()->GetStatistics()->GetScalarValueMin();
- ScalarType max = m_OriginalImage.GetPointer()->GetStatistics()->GetScalarValueMaxNoRecompute();
- return static_cast<int>(max - min) + 1;
+ const auto min = this->GetReferenceData()->GetStatistics()->GetScalarValueMin();
+ const auto max = this->GetReferenceData()->GetStatistics()->GetScalarValueMaxNoRecompute();
+ return static_cast<unsigned int>(max - min) + 1;
}
diff --git a/Modules/Segmentation/Interactions/mitkOtsuTool3D.h b/Modules/Segmentation/Interactions/mitkOtsuTool3D.h
index f4e22cab62..7761ec60dd 100644
--- a/Modules/Segmentation/Interactions/mitkOtsuTool3D.h
+++ b/Modules/Segmentation/Interactions/mitkOtsuTool3D.h
@@ -1,68 +1,80 @@
/*============================================================================
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 MITKOTSUTOOL3D_H
#define MITKOTSUTOOL3D_H
#include "itkImage.h"
-#include "mitkAutoSegmentationTool.h"
+#include "mitkAutoSegmentationWithPreviewTool.h"
+#include "mitkDataNode.h"
#include <MitkSegmentationExports.h>
namespace us
{
class ModuleResource;
}
namespace mitk
{
class Image;
- class MITKSEGMENTATION_EXPORT OtsuTool3D : public AutoSegmentationTool
+ class MITKSEGMENTATION_EXPORT OtsuTool3D : public AutoSegmentationWithPreviewTool
{
public:
- mitkClassMacro(OtsuTool3D, AutoSegmentationTool);
+ mitkClassMacro(OtsuTool3D, AutoSegmentationWithPreviewTool);
itkFactorylessNewMacro(Self);
itkCloneMacro(Self);
- const char *GetName() const override;
+ const char *GetName() const override;
const char **GetXPM() const override;
us::ModuleResource GetIconResource() const override;
void Activated() override;
void Deactivated() override;
- void RunSegmentation(int regions, bool useValley, int numberOfBins);
- void ConfirmSegmentation();
- // void UpdateBinaryPreview(int regionID);
- void UpdateBinaryPreview(std::vector<int> regionIDs);
- void UpdateVolumePreview(bool volumeRendering);
- void ShowMultiLabelResultNode(bool);
+ itkSetMacro(NumberOfBins, unsigned int);
+ itkGetConstMacro(NumberOfBins, unsigned int);
- int GetNumberOfBins();
+ itkSetMacro(NumberOfRegions, unsigned int);
+ itkGetConstMacro(NumberOfRegions, unsigned int);
+
+ itkSetMacro(UseValley, bool);
+ itkGetConstMacro(UseValley, bool);
+ itkBooleanMacro(UseValley);
+
+ using SelectedRegionVectorType = std::vector<int>;
+ void SetSelectedRegions(const SelectedRegionVectorType& regions);
+ SelectedRegionVectorType GetSelectedRegions() const;
+
+ /**Returns the number of max bins based on the current input image.*/
+ unsigned int GetMaxNumberOfBins() const;
protected:
OtsuTool3D();
~OtsuTool3D() override;
+ void UpdateCleanUp() override;
+ void DoUpdatePreview(const Image* inputAtTimeStep, Image* previewImage, TimeStepType timeStep) override;
+
template <typename TPixel, unsigned int VImageDimension>
- void CalculatePreview(itk::Image<TPixel, VImageDimension> *itkImage, std::vector<int> regionIDs);
+ void CalculatePreview(itk::Image<TPixel, VImageDimension> *itkImage, mitk::Image* segmentation, unsigned int timeStep);
- itk::SmartPointer<Image> m_OriginalImage;
- // holds the user selected binary segmentation
- mitk::DataNode::Pointer m_BinaryPreviewNode;
- // holds the multilabel result as a preview image
- mitk::DataNode::Pointer m_MultiLabelResultNode;
- // holds the user selected binary segmentation masked original image
- mitk::DataNode::Pointer m_MaskedImagePreviewNode;
+ unsigned int m_NumberOfBins = 128;
+ unsigned int m_NumberOfRegions = 2;
+ bool m_UseValley = false;
+ SelectedRegionVectorType m_SelectedRegions = {};
+ // holds the multilabel result as a preview image
+ mitk::DataNode::Pointer m_OtsuResultNode;
+ TimeStepType m_LastOtsuTimeStep = 0;
}; // class
} // namespace
#endif
diff --git a/Modules/SegmentationUI/Qmitk/QmitkOtsuTool3DGUI.cpp b/Modules/SegmentationUI/Qmitk/QmitkOtsuTool3DGUI.cpp
index 2d9b8f8032..031b353dab 100644
--- a/Modules/SegmentationUI/Qmitk/QmitkOtsuTool3DGUI.cpp
+++ b/Modules/SegmentationUI/Qmitk/QmitkOtsuTool3DGUI.cpp
@@ -1,184 +1,214 @@
/*============================================================================
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.
============================================================================*/
#include "QmitkOtsuTool3DGUI.h"
#include "QmitkConfirmSegmentationDialog.h"
#include <QMessageBox>
#include <qlabel.h>
#include <qlayout.h>
#include <qlistwidget.h>
#include <qpushbutton.h>
#include <qspinbox.h>
MITK_TOOL_GUI_MACRO(MITKSEGMENTATIONUI_EXPORT, QmitkOtsuTool3DGUI, "")
QmitkOtsuTool3DGUI::QmitkOtsuTool3DGUI() : QmitkToolGUI(), m_NumberOfRegions(0)
{
m_Controls.setupUi(this);
connect(m_Controls.previewButton, SIGNAL(clicked()), this, SLOT(OnSpinboxValueAccept()));
connect(m_Controls.m_selectionListWidget, SIGNAL(itemSelectionChanged()), this, SLOT(OnRegionSelectionChanged()));
connect(m_Controls.m_Spinbox, SIGNAL(valueChanged(int)), this, SLOT(OnRegionSpinboxChanged(int)));
connect(m_Controls.m_ConfSegButton, SIGNAL(clicked()), this, SLOT(OnSegmentationRegionAccept()));
connect(this, SIGNAL(NewToolAssociated(mitk::Tool *)), this, SLOT(OnNewToolAssociated(mitk::Tool *)));
connect(m_Controls.advancedSettingsButton, SIGNAL(toggled(bool)), this, SLOT(OnAdvancedSettingsButtonToggled(bool)));
this->OnAdvancedSettingsButtonToggled(false);
}
QmitkOtsuTool3DGUI::~QmitkOtsuTool3DGUI()
{
+ if (m_OtsuTool3DTool.IsNotNull())
+ {
+ m_OtsuTool3DTool->CurrentlyBusy -=
+ mitk::MessageDelegate1<QmitkOtsuTool3DGUI, bool>(this, &QmitkOtsuTool3DGUI::BusyStateChanged);
+ }
}
void QmitkOtsuTool3DGUI::OnRegionSpinboxChanged(int numberOfRegions)
{
// we have to change to minimum number of histogram bins accordingly
int curBinValue = m_Controls.m_BinsSpinBox->value();
if (curBinValue < numberOfRegions)
m_Controls.m_BinsSpinBox->setValue(numberOfRegions);
}
void QmitkOtsuTool3DGUI::OnRegionSelectionChanged()
{
m_SelectedItems = m_Controls.m_selectionListWidget->selectedItems();
- if (m_SelectedItems.size() == 0)
- {
- m_Controls.m_ConfSegButton->setEnabled(false);
- m_OtsuTool3DTool->ShowMultiLabelResultNode(true);
- return;
- }
-
if (m_OtsuTool3DTool.IsNotNull())
{
// update preview of region
QList<QListWidgetItem *>::Iterator it;
std::vector<int> regionIDs;
for (it = m_SelectedItems.begin(); it != m_SelectedItems.end(); ++it)
regionIDs.push_back((*it)->text().toInt());
- m_OtsuTool3DTool->UpdateBinaryPreview(regionIDs);
- m_Controls.m_ConfSegButton->setEnabled(true);
+
+ m_OtsuTool3DTool->SetSelectedRegions(regionIDs);
+ m_OtsuTool3DTool->UpdatePreview();
+
+ m_Controls.m_ConfSegButton->setEnabled(!regionIDs.empty());
}
}
void QmitkOtsuTool3DGUI::OnAdvancedSettingsButtonToggled(bool toggled)
{
m_Controls.m_ValleyCheckbox->setVisible(toggled);
m_Controls.binLabel->setVisible(toggled);
m_Controls.m_BinsSpinBox->setVisible(toggled);
if (toggled)
{
- int max = m_OtsuTool3DTool->GetNumberOfBins();
+ int max = m_OtsuTool3DTool->GetMaxNumberOfBins();
if (max >= m_Controls.m_BinsSpinBox->minimum())
{
m_Controls.m_BinsSpinBox->setMaximum(max);
}
}
}
void QmitkOtsuTool3DGUI::OnNewToolAssociated(mitk::Tool *tool)
{
+ if (m_OtsuTool3DTool.IsNotNull())
+ {
+ m_OtsuTool3DTool->CurrentlyBusy -=
+ mitk::MessageDelegate1<QmitkOtsuTool3DGUI, bool>(this, &QmitkOtsuTool3DGUI::BusyStateChanged);
+ }
+
m_OtsuTool3DTool = dynamic_cast<mitk::OtsuTool3D *>(tool);
+
+ if (m_OtsuTool3DTool.IsNotNull())
+ {
+ m_OtsuTool3DTool->CurrentlyBusy +=
+ mitk::MessageDelegate1<QmitkOtsuTool3DGUI, bool>(this, &QmitkOtsuTool3DGUI::BusyStateChanged);
+
+ m_OtsuTool3DTool->SetOverwriteExistingSegmentation(true);
+ m_OtsuTool3DTool->IsTimePointChangeAwareOff();
+ m_Controls.m_CheckProcessAll->setVisible(m_OtsuTool3DTool->GetTargetSegmentationNode()->GetData()->GetTimeSteps() > 1);
+ }
}
void QmitkOtsuTool3DGUI::OnSegmentationRegionAccept()
{
QmitkConfirmSegmentationDialog dialog;
QString segName = QString::fromStdString(m_OtsuTool3DTool->GetCurrentSegmentationName());
- dialog.SetSegmentationName(segName);
- int result = dialog.exec();
-
- switch (result)
+ if (m_OtsuTool3DTool.IsNotNull())
{
- case QmitkConfirmSegmentationDialog::CREATE_NEW_SEGMENTATION:
+ if (this->m_Controls.m_CheckCreateNew->isChecked())
+ {
m_OtsuTool3DTool->SetOverwriteExistingSegmentation(false);
- break;
- case QmitkConfirmSegmentationDialog::OVERWRITE_SEGMENTATION:
+ }
+ else
+ {
m_OtsuTool3DTool->SetOverwriteExistingSegmentation(true);
- break;
- case QmitkConfirmSegmentationDialog::CANCEL_SEGMENTATION:
- return;
- }
+ }
- if (m_OtsuTool3DTool.IsNotNull() && m_Controls.m_selectionListWidget->currentItem() != nullptr)
- {
+ m_OtsuTool3DTool->SetCreateAllTimeSteps(this->m_Controls.m_CheckProcessAll->isChecked());
+
+ this->m_Controls.m_ConfSegButton->setEnabled(false);
m_OtsuTool3DTool->ConfirmSegmentation();
}
}
void QmitkOtsuTool3DGUI::OnSpinboxValueAccept()
{
if (m_NumberOfRegions == m_Controls.m_Spinbox->value() &&
m_UseValleyEmphasis == m_Controls.m_ValleyCheckbox->isChecked() &&
m_NumberOfBins == m_Controls.m_BinsSpinBox->value())
return;
if (m_OtsuTool3DTool.IsNotNull())
{
try
{
int proceed;
QMessageBox *messageBox = new QMessageBox(QMessageBox::Question,
nullptr,
"The otsu segmentation computation may take several minutes depending "
"on the number of Regions you selected. Proceed anyway?",
QMessageBox::Ok | QMessageBox::Cancel);
if (m_Controls.m_Spinbox->value() >= 5)
{
proceed = messageBox->exec();
if (proceed != QMessageBox::Ok)
return;
}
m_NumberOfRegions = m_Controls.m_Spinbox->value();
m_UseValleyEmphasis = m_Controls.m_ValleyCheckbox->isChecked();
m_NumberOfBins = m_Controls.m_BinsSpinBox->value();
+ m_OtsuTool3DTool->SetNumberOfRegions(m_NumberOfRegions);
+ m_OtsuTool3DTool->SetUseValley(m_UseValleyEmphasis);
+ m_OtsuTool3DTool->SetNumberOfBins(m_NumberOfBins);
- this->setCursor(Qt::WaitCursor);
- m_OtsuTool3DTool->RunSegmentation(m_NumberOfRegions, m_UseValleyEmphasis, m_NumberOfBins);
- this->setCursor(Qt::ArrowCursor);
+ m_OtsuTool3DTool->UpdatePreview();
}
catch (...)
{
this->setCursor(Qt::ArrowCursor);
QMessageBox *messageBox =
new QMessageBox(QMessageBox::Critical,
nullptr,
"itkOtsuFilter error: image dimension must be in {2, 3} and no RGB images can be handled.");
messageBox->exec();
delete messageBox;
return;
}
+
// insert regions into widget
QString itemName;
QListWidgetItem *item;
m_Controls.m_selectionListWidget->clear();
for (int i = 0; i < m_Controls.m_Spinbox->value(); ++i)
{
itemName = QString::number(i);
item = new QListWidgetItem(itemName);
m_Controls.m_selectionListWidget->addItem(item);
}
// deactivate 'confirm segmentation'-button
m_Controls.m_ConfSegButton->setEnabled(false);
+ m_OtsuTool3DTool->IsTimePointChangeAwareOn();
}
}
-void QmitkOtsuTool3DGUI::OnVolumePreviewChecked(int state)
+void QmitkOtsuTool3DGUI::BusyStateChanged(bool value)
{
- if (state == 1)
+ if (value)
+ {
+ QApplication::setOverrideCursor(QCursor(Qt::BusyCursor));
+ }
+ else
{
+ QApplication::restoreOverrideCursor();
}
+
+ m_Controls.m_ValleyCheckbox->setEnabled(!value);
+ m_Controls.binLabel->setEnabled(!value);
+ m_Controls.m_BinsSpinBox->setEnabled(!value);
+ m_Controls.m_ConfSegButton->setEnabled(!m_OtsuTool3DTool->GetSelectedRegions().empty() && !value);
+ m_Controls.m_CheckProcessAll->setEnabled(!value);
+ m_Controls.m_CheckCreateNew->setEnabled(!value);
+ m_Controls.previewButton->setEnabled(!value);
}
diff --git a/Modules/SegmentationUI/Qmitk/QmitkOtsuTool3DGUI.h b/Modules/SegmentationUI/Qmitk/QmitkOtsuTool3DGUI.h
index f562f73560..ce2ad862fe 100644
--- a/Modules/SegmentationUI/Qmitk/QmitkOtsuTool3DGUI.h
+++ b/Modules/SegmentationUI/Qmitk/QmitkOtsuTool3DGUI.h
@@ -1,83 +1,83 @@
/*============================================================================
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 QmitkOtsuTool3DGUI_h_Included
#define QmitkOtsuTool3DGUI_h_Included
#include "QmitkToolGUI.h"
#include "mitkOtsuTool3D.h"
#include "ui_QmitkOtsuToolWidgetControls.h"
#include <MitkSegmentationUIExports.h>
#include <QListWidget>
#include <QPushButton>
class QSpinBox;
class QLabel;
/**
\ingroup org_mitk_gui_qt_interactivesegmentation_internal
\brief GUI for mitk::.
\sa mitk::
This GUI shows ...
Last contributor: $Author$
*/
class MITKSEGMENTATIONUI_EXPORT QmitkOtsuTool3DGUI : public QmitkToolGUI
{
Q_OBJECT
public:
mitkClassMacro(QmitkOtsuTool3DGUI, QmitkToolGUI);
itkFactorylessNewMacro(Self);
itkCloneMacro(Self);
signals :
public slots :
protected slots :
void OnNewToolAssociated(mitk::Tool *);
void OnSpinboxValueAccept();
void OnSegmentationRegionAccept();
void OnRegionSelectionChanged();
void OnRegionSpinboxChanged(int);
- void OnVolumePreviewChecked(int);
-
private slots:
void OnAdvancedSettingsButtonToggled(bool toggled);
protected:
QmitkOtsuTool3DGUI();
~QmitkOtsuTool3DGUI() override;
+ void BusyStateChanged(bool value) override;
+
mitk::OtsuTool3D::Pointer m_OtsuTool3DTool;
Ui_QmitkOtsuToolWidgetControls m_Controls;
int m_NumberOfRegions;
bool m_UseValleyEmphasis;
int m_NumberOfBins;
QList<QListWidgetItem *> m_SelectedItems;
};
#endif
diff --git a/Modules/SegmentationUI/Qmitk/QmitkOtsuToolWidgetControls.ui b/Modules/SegmentationUI/Qmitk/QmitkOtsuToolWidgetControls.ui
index e5484bf97b..d0f8af9c9e 100644
--- a/Modules/SegmentationUI/Qmitk/QmitkOtsuToolWidgetControls.ui
+++ b/Modules/SegmentationUI/Qmitk/QmitkOtsuToolWidgetControls.ui
@@ -1,214 +1,234 @@
<?xml version="1.0" encoding="UTF-8"?>
<ui version="4.0">
<class>QmitkOtsuToolWidgetControls</class>
<widget class="QWidget" name="QmitkOtsuToolWidgetControls">
<property name="geometry">
<rect>
<x>0</x>
<y>0</y>
<width>192</width>
- <height>293</height>
+ <height>300</height>
</rect>
</property>
<property name="sizePolicy">
<sizepolicy hsizetype="Ignored" vsizetype="Minimum">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="minimumSize">
<size>
<width>100</width>
<height>0</height>
</size>
</property>
<property name="maximumSize">
<size>
<width>100000</width>
<height>100000</height>
</size>
</property>
<property name="windowTitle">
<string>QmitkOtsuToolWidget</string>
</property>
<property name="toolTip">
<string>Move to adjust the segmentation</string>
</property>
<layout class="QVBoxLayout" name="verticalLayout">
<item>
<layout class="QHBoxLayout" name="horizontalLayout">
<property name="sizeConstraint">
<enum>QLayout::SetNoConstraint</enum>
</property>
<item>
<widget class="QLabel" name="numberOfRegionsLabel">
<property name="sizePolicy">
<sizepolicy hsizetype="Ignored" vsizetype="Minimum">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="text">
<string>Number of Regions:</string>
</property>
</widget>
</item>
<item>
<widget class="QSpinBox" name="m_Spinbox">
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Minimum">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="maximumSize">
<size>
<width>40</width>
<height>16777215</height>
</size>
</property>
<property name="minimum">
<number>2</number>
</property>
<property name="maximum">
<number>32</number>
</property>
</widget>
</item>
</layout>
</item>
<item>
<widget class="ctkExpandButton" name="advancedSettingsButton">
<property name="sizePolicy">
<sizepolicy hsizetype="Expanding" vsizetype="Fixed">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="minimumSize">
<size>
<width>0</width>
<height>32</height>
</size>
</property>
<property name="text">
<string>Advanced settings</string>
</property>
<property name="toolButtonStyle">
<enum>Qt::ToolButtonTextBesideIcon</enum>
</property>
<property name="mirrorOnExpand" stdset="0">
<bool>true</bool>
</property>
</widget>
</item>
<item>
<layout class="QGridLayout" name="advancedSettingsLayout">
<item row="0" column="0">
<widget class="QCheckBox" name="m_ValleyCheckbox">
<property name="text">
<string>Use Valley Emphasis</string>
</property>
</widget>
</item>
<item row="1" column="0">
<widget class="QLabel" name="binLabel">
<property name="text">
<string>Number of Histogram Bins:</string>
</property>
</widget>
</item>
<item row="1" column="1">
<widget class="QSpinBox" name="m_BinsSpinBox">
<property name="minimum">
<number>2</number>
</property>
<property name="maximum">
<number>4096</number>
</property>
<property name="value">
<number>128</number>
</property>
</widget>
</item>
</layout>
</item>
<item>
<widget class="QListWidget" name="m_selectionListWidget">
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Minimum">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="maximumSize">
<size>
<width>10000000</width>
<height>100</height>
</size>
</property>
<property name="autoScrollMargin">
<number>0</number>
</property>
<property name="selectionMode">
<enum>QAbstractItemView::MultiSelection</enum>
</property>
<property name="resizeMode">
<enum>QListView::Adjust</enum>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="previewButton">
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Minimum">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="maximumSize">
<size>
<width>100000</width>
<height>16777215</height>
</size>
</property>
<property name="text">
<string>Preview</string>
</property>
</widget>
</item>
<item>
<widget class="QPushButton" name="m_ConfSegButton">
<property name="enabled">
<bool>false</bool>
</property>
<property name="sizePolicy">
<sizepolicy hsizetype="Minimum" vsizetype="Minimum">
<horstretch>0</horstretch>
<verstretch>0</verstretch>
</sizepolicy>
</property>
<property name="maximumSize">
<size>
<width>100000</width>
<height>16777215</height>
</size>
</property>
<property name="text">
<string>Confirm Segmentation</string>
</property>
</widget>
</item>
+ <item>
+ <widget class="QCheckBox" name="m_CheckProcessAll">
+ <property name="toolTip">
+ <string>"Add the confirmed segmentation as a new segmentation instead of overwriting the currently selected."</string>
+ </property>
+ <property name="text">
+ <string>Process all time steps</string>
+ </property>
+ </widget>
+ </item>
+ <item>
+ <widget class="QCheckBox" name="m_CheckCreateNew">
+ <property name="toolTip">
+ <string>Add the confirmed segmentation as a new segmentation instead of overwriting the currently selected.</string>
+ </property>
+ <property name="text">
+ <string>Create as new segmentation</string>
+ </property>
+ </widget>
+ </item>
</layout>
</widget>
<layoutdefault spacing="6" margin="11"/>
<customwidgets>
<customwidget>
<class>ctkExpandButton</class>
<extends>QToolButton</extends>
<header>ctkExpandButton.h</header>
</customwidget>
</customwidgets>
<resources/>
<connections/>
</ui>