diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/CMakeLists.txt b/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/CMakeLists.txt
index 6ce35d9cd8..c9b5b2d86b 100644
--- a/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/CMakeLists.txt
+++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/CMakeLists.txt
@@ -1,8 +1,8 @@
project(org_mitk_gui_qt_pharmacokinetics_curvedescriptor)
mitk_create_plugin(
EXPORT_DIRECTIVE CURVEDESCRIPTORS_EXPORT
EXPORTED_INCLUDE_SUFFIXES src
MODULE_DEPENDS
- PRIVATE MitkQtWidgetsExt MitkPharmacokinetics MitkModelFitUI MitkPharmacokineticsUI
+ PRIVATE MitkQtWidgetsExt MitkPharmacokinetics MitkModelFitUI MitkPharmacokineticsUI MitkSegmentationUI
)
diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/src/internal/PerfusionCurveDescriptionParameterView.cpp b/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/src/internal/PerfusionCurveDescriptionParameterView.cpp
index bed7e751c9..912d0ae893 100644
--- a/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/src/internal/PerfusionCurveDescriptionParameterView.cpp
+++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/src/internal/PerfusionCurveDescriptionParameterView.cpp
@@ -1,243 +1,235 @@
/*============================================================================
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 <QMessageBox>
#include <QThreadPool>
#include "mitkWorkbenchUtil.h"
#include "PerfusionCurveDescriptionParameterView.h"
#include "QmitkDescriptionParameterBackgroundJob.h"
#include "mitkAreaUnderTheCurveDescriptionParameter.h"
#include "mitkAreaUnderFirstMomentDescriptionParameter.h"
#include "mitkMeanResidenceTimeDescriptionParameter.h"
#include "mitkTimeToPeakCurveDescriptionParameter.h"
#include "mitkMaximumCurveDescriptionParameter.h"
#include "mitkPixelBasedDescriptionParameterImageGenerator.h"
#include "mitkCurveParameterFunctor.h"
#include "mitkExtractTimeGrid.h"
#include <mitkNodePredicateAnd.h>
#include <mitkNodePredicateOr.h>
#include <mitkNodePredicateNot.h>
#include <mitkNodePredicateProperty.h>
#include <mitkNodePredicateDataType.h>
#include <mitkNodePredicateDimension.h>
#include "mitkNodePredicateFunction.h"
+#include <mitkMultiLabelPredicateHelper.h>
#include <iostream>
const std::string PerfusionCurveDescriptionParameterView::VIEW_ID =
"org.mitk.views.pharmacokinetics.curvedescriptor";
void PerfusionCurveDescriptionParameterView::SetFocus()
{
m_Controls.btnCalculateParameters->setFocus();
}
void PerfusionCurveDescriptionParameterView::CreateQtPartControl(QWidget* parent)
{
m_Controls.setupUi(parent);
m_Controls.btnCalculateParameters->setEnabled(false);
m_Controls.timeSeriesNodeSelector->SetNodePredicate(this->m_isValidTimeSeriesImagePredicate);
m_Controls.timeSeriesNodeSelector->SetDataStorage(this->GetDataStorage());
m_Controls.timeSeriesNodeSelector->SetSelectionIsOptional(false);
m_Controls.timeSeriesNodeSelector->SetInvalidInfo("Please select time series.");
m_Controls.timeSeriesNodeSelector->SetAutoSelectNewNodes(true);
connect(m_Controls.timeSeriesNodeSelector,
&QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged,
this,
&PerfusionCurveDescriptionParameterView::OnNodeSelectionChanged);
connect(m_Controls.btnCalculateParameters, SIGNAL(clicked()), this,
SLOT(OnCalculateParametersButtonClicked()));
InitParameterList();
}
void PerfusionCurveDescriptionParameterView::OnNodeSelectionChanged( const QList<mitk::DataNode::Pointer>& /*nodes*/)
{
m_Controls.btnCalculateParameters->setEnabled(false);
if (m_Controls.timeSeriesNodeSelector->GetSelectedNode().IsNotNull())
{
this->m_selectedNode = m_Controls.timeSeriesNodeSelector->GetSelectedNode();
m_selectedImage = dynamic_cast<mitk::Image*>(m_selectedNode->GetData());
}
else
{
this->m_selectedNode = nullptr;
this->m_selectedImage = nullptr;
}
if (m_selectedImage.IsNotNull())
{
m_Controls.btnCalculateParameters->setEnabled(true);
}
else if (m_selectedNode.IsNotNull())
{
this->OnJobStatusChanged("Cannot compute parameters. Selected node is not an image.");
}
else
{
this->OnJobStatusChanged("Cannot compute parameters. No node selected.");
}
}
PerfusionCurveDescriptionParameterView::PerfusionCurveDescriptionParameterView()
{
m_selectedNode = nullptr;
m_selectedImage = nullptr;
- mitk::NodePredicateDataType::Pointer isLabelSet = mitk::NodePredicateDataType::New("LabelSetImage");
mitk::NodePredicateDataType::Pointer isImage = mitk::NodePredicateDataType::New("Image");
- mitk::NodePredicateProperty::Pointer isBinary = mitk::NodePredicateProperty::New("binary", mitk::BoolProperty::New(true));
- mitk::NodePredicateAnd::Pointer isLegacyMask = mitk::NodePredicateAnd::New(isImage, isBinary);
- mitk::NodePredicateDimension::Pointer is3D = mitk::NodePredicateDimension::New(3);
- mitk::NodePredicateOr::Pointer isMask = mitk::NodePredicateOr::New(isLegacyMask, isLabelSet);
- mitk::NodePredicateAnd::Pointer isNoMask = mitk::NodePredicateAnd::New(isImage, mitk::NodePredicateNot::New(isMask));
- mitk::NodePredicateAnd::Pointer is3DImage = mitk::NodePredicateAnd::New(isImage, is3D, isNoMask);
- this->m_IsMaskPredicate = mitk::NodePredicateAnd::New(isMask, mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object"))).GetPointer();
-
- this->m_IsNoMaskImagePredicate = mitk::NodePredicateAnd::New(isNoMask, mitk::NodePredicateNot::New(mitk::NodePredicateProperty::New("helper object"))).GetPointer();
+ auto isNoMask = mitk::NodePredicateNot::New(mitk::GetMultiLabelSegmentationPredicate());
auto isDynamicData = mitk::NodePredicateFunction::New([](const mitk::DataNode* node)
{
return (node && node->GetData() && node->GetData()->GetTimeSteps() > 1);
});
this->m_isValidTimeSeriesImagePredicate = mitk::NodePredicateAnd::New(isDynamicData, isImage, isNoMask);
}
void PerfusionCurveDescriptionParameterView::InitParameterList()
{
m_ParameterMap.clear();
mitk::CurveDescriptionParameterBase::Pointer parameterFunction =
mitk::AreaUnderTheCurveDescriptionParameter::New().GetPointer();
m_ParameterMap.insert(std::make_pair(ParameterNameType("AUC"), parameterFunction));
parameterFunction = mitk::AreaUnderFirstMomentDescriptionParameter::New().GetPointer();
m_ParameterMap.insert(std::make_pair(ParameterNameType("AUMC"), parameterFunction));
parameterFunction = mitk::MeanResidenceTimeDescriptionParameter::New().GetPointer();
m_ParameterMap.insert(std::make_pair(ParameterNameType("MRT"), parameterFunction));
parameterFunction = mitk::MaximumCurveDescriptionParameter::New().GetPointer();
m_ParameterMap.insert(std::make_pair(ParameterNameType("Maximum"), parameterFunction));
parameterFunction = mitk::TimeToPeakCurveDescriptionParameter::New().GetPointer();
m_ParameterMap.insert(std::make_pair(ParameterNameType("TimeToPeak"), parameterFunction));
for (ParameterMapType::const_iterator pos = m_ParameterMap.begin(); pos != m_ParameterMap.end();
++pos)
{
QListWidgetItem* item = new QListWidgetItem(QString::fromStdString(pos->first),
this->m_Controls.parameterlist);
item->setFlags(item->flags() | Qt::ItemIsUserCheckable);
item->setCheckState(Qt::Unchecked);
}
};
void PerfusionCurveDescriptionParameterView::ConfigureFunctor(mitk::CurveParameterFunctor* functor)
const
{
functor->SetGrid(mitk::ExtractTimeGrid(m_selectedImage));
for (int pos = 0; pos < this->m_Controls.parameterlist->count(); ++pos)
{
QListWidgetItem* item = this->m_Controls.parameterlist->item(pos);
mitk::CurveDescriptionParameterBase::Pointer parameterFunction = m_ParameterMap.at(
item->text().toStdString());
if (item->checkState() == Qt::Checked)
{
functor->RegisterDescriptionParameter(item->text().toStdString(), parameterFunction);
}
}
}
void PerfusionCurveDescriptionParameterView::OnCalculateParametersButtonClicked()
{
mitk::PixelBasedDescriptionParameterImageGenerator::Pointer generator =
mitk::PixelBasedDescriptionParameterImageGenerator::New();
mitk::CurveParameterFunctor::Pointer functor = mitk::CurveParameterFunctor::New();
this->ConfigureFunctor(functor);
generator->SetFunctor(functor);
generator->SetDynamicImage(m_selectedImage);
/////////////////////////
//create job and put it into the thread pool
DescriptionParameterBackgroundJob* pJob = new DescriptionParameterBackgroundJob(generator,
this->m_selectedNode);
pJob->setAutoDelete(true);
connect(pJob, SIGNAL(Error(QString)), this, SLOT(OnJobError(QString)));
connect(pJob, SIGNAL(Finished()), this, SLOT(OnJobFinished()));
connect(pJob, SIGNAL(ResultsAreAvailable(mitk::modelFit::ModelFitResultNodeVectorType,
const DescriptionParameterBackgroundJob*)), this,
SLOT(OnJobResultsAreAvailable(mitk::modelFit::ModelFitResultNodeVectorType,
const DescriptionParameterBackgroundJob*)), Qt::BlockingQueuedConnection);
connect(pJob, SIGNAL(JobProgress(double)), this, SLOT(OnJobProgress(double)));
connect(pJob, SIGNAL(JobStatusChanged(QString)), this, SLOT(OnJobStatusChanged(QString)));
QThreadPool* threadPool = QThreadPool::globalInstance();
threadPool->start(pJob);
}
void PerfusionCurveDescriptionParameterView::OnJobFinished()
{
this->m_Controls.infoBox->append(QString("Fitting finished"));
};
void PerfusionCurveDescriptionParameterView::OnJobError(QString err)
{
MITK_ERROR << err.toStdString().c_str();
m_Controls.infoBox->append(QString("<font color='red'><b>") + err + QString("</b></font>"));
};
void PerfusionCurveDescriptionParameterView::OnJobResultsAreAvailable(
mitk::modelFit::ModelFitResultNodeVectorType results, const DescriptionParameterBackgroundJob* pJob)
{
for (auto image : results)
{
this->GetDataStorage()->Add(image, pJob->GetParentNode());
}
};
void PerfusionCurveDescriptionParameterView::OnJobProgress(double progress)
{
this->m_Controls.progressBar->setValue(100 * progress);
QString report = QString("Progress. ") + QString::number(progress);
this->m_Controls.infoBox->append(report);
};
void PerfusionCurveDescriptionParameterView::OnJobStatusChanged(QString info)
{
this->m_Controls.infoBox->append(info);
MITK_INFO << info.toStdString().c_str();
}
diff --git a/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/src/internal/PerfusionCurveDescriptionParameterView.h b/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/src/internal/PerfusionCurveDescriptionParameterView.h
index 0b92d70387..6520d88989 100644
--- a/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/src/internal/PerfusionCurveDescriptionParameterView.h
+++ b/Plugins/org.mitk.gui.qt.pharmacokinetics.curvedescriptor/src/internal/PerfusionCurveDescriptionParameterView.h
@@ -1,107 +1,105 @@
/*============================================================================
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 PerfusionCurveDescriptionParameterView_h
#define PerfusionCurveDescriptionParameterView_h
#include <QString>
#include <QmitkAbstractView.h>
#include "ui_PerfusionCurveDescriptionParameterViewControls.h"
#include "mitkCurveDescriptionParameterBase.h"
#include <QmitkDescriptionParameterBackgroundJob.h>
#include <mitkImage.h>
namespace mitk
{
class CurveParameterFunctor;
}
/*!
* @brief Test Plugin for SUV calculations of PET images
*/
class PerfusionCurveDescriptionParameterView : public QmitkAbstractView
{
Q_OBJECT
public:
typedef mitk::CurveDescriptionParameterBase::CurveDescriptionParameterNameType ParameterNameType;
/*! @brief The view's unique ID - required by MITK */
static const std::string VIEW_ID;
PerfusionCurveDescriptionParameterView();
protected slots:
void InitParameterList();
void OnJobFinished();
void OnJobError(QString err);
void OnJobResultsAreAvailable(mitk::modelFit::ModelFitResultNodeVectorType results,
const DescriptionParameterBackgroundJob* pJob);
void OnJobProgress(double progress);
void OnJobStatusChanged(QString info);
/*!
* @brief Is triggered of the update button is clicked and the selected node should get the (new) iso level set.
*/
void OnCalculateParametersButtonClicked();
protected:
// Overridden base class functions
/*!
* @brief Sets up the UI controls and connects the slots and signals. Gets
* called by the framework to create the GUI at the right time.
* @param[in,out] parent The parent QWidget, as this class itself is not a QWidget
* subclass.
*/
void CreateQtPartControl(QWidget* parent) override;
/*!
* @brief Sets the focus to the plot curve button. Gets called by the framework to set the
* focus on the right widget.
*/
void SetFocus() override;
/** Configures the passed functor according to the selected image and parameters*/
void ConfigureFunctor(mitk::CurveParameterFunctor* functor) const;
void OnNodeSelectionChanged(const QList<mitk::DataNode::Pointer>& nodes);
// Variables
/*! @brief The view's UI controls */
Ui::PerfusionCurveDescriptionParameterViewControls m_Controls;
mitk::DataNode::Pointer m_selectedNode;
private:
typedef std::map<ParameterNameType, mitk::CurveDescriptionParameterBase::Pointer > ParameterMapType;
ParameterMapType m_ParameterMap;
mitk::Image::Pointer m_selectedImage;
- mitk::NodePredicateBase::Pointer m_IsNoMaskImagePredicate;
- mitk::NodePredicateBase::Pointer m_IsMaskPredicate;
mitk::NodePredicateBase::Pointer m_isValidTimeSeriesImagePredicate;
};
#endif