diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp
index 73ffe142f3..116ba033bd 100644
--- a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp
+++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp
@@ -1,1356 +1,1334 @@
/*===================================================================
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.
===================================================================*/
#include "QmitkImageStatisticsView.h"
// Qt includes
#include <QClipboard>
#include <QScrollBar>
#include <QVector>
// berry includes
#include <berryIWorkbenchPage.h>
// mitk includes
#include "mitkNodePredicateDataType.h"
#include "mitkNodePredicateOr.h"
#include "mitkPlanarFigureInteractor.h"
#include "mitkImageTimeSelector.h"
#include <QmitkRenderWindow.h>
// itk includes
#include "itksys/SystemTools.hxx"
#include <mitkImageCast.h>
#include "itkImageRegionConstIteratorWithIndex.h"
#include <limits>
//blueberry includes
#include <berryWorkbenchPlugin.h>
#include <berryQtPreferences.h>
const std::string QmitkImageStatisticsView::VIEW_ID = "org.mitk.views.imagestatistics";
const int QmitkImageStatisticsView::STAT_TABLE_BASE_HEIGHT = 180;
QmitkImageStatisticsView::QmitkImageStatisticsView(QObject* /*parent*/, const char* /*name*/)
: m_Controls( nullptr ),
m_TimeStepperAdapter( nullptr ),
m_SelectedImage( nullptr ),
m_SelectedImageMask( nullptr ),
m_SelectedPlanarFigure( nullptr ),
m_ImageObserverTag( -1 ),
m_ImageMaskObserverTag( -1 ),
m_PlanarFigureObserverTag( -1 ),
m_TimeObserverTag( -1 ),
m_CurrentStatisticsValid( false ),
m_StatisticsUpdatePending( false ),
m_DataNodeSelectionChanged ( false ),
m_Visible(false)
{
this->m_CalculationThread = new QmitkImageStatisticsCalculationThread;
}
QmitkImageStatisticsView::~QmitkImageStatisticsView()
{
if ( m_SelectedImage != nullptr )
m_SelectedImage->RemoveObserver( m_ImageObserverTag );
if ( m_SelectedImageMask != nullptr )
m_SelectedImageMask->RemoveObserver( m_ImageMaskObserverTag );
if ( m_SelectedPlanarFigure != nullptr )
m_SelectedPlanarFigure->RemoveObserver( m_PlanarFigureObserverTag );
while(this->m_CalculationThread->isRunning()) // wait until thread has finished
{
itksys::SystemTools::Delay(100);
}
delete this->m_CalculationThread;
}
void QmitkImageStatisticsView::CreateQtPartControl(QWidget *parent)
{
if (m_Controls == nullptr)
{
m_Controls = new Ui::QmitkImageStatisticsViewControls;
m_Controls->setupUi(parent);
CreateConnections();
m_Controls->m_ErrorMessageLabel->hide();
m_Controls->m_StatisticsWidgetStack->setCurrentIndex(0);
m_Controls->m_BinSizeFrame->setEnabled(false);
}
}
void QmitkImageStatisticsView::OnPageSuccessfullyLoaded()
{
berry::IPreferencesService* prefService = berry::WorkbenchPlugin::GetDefault()->GetPreferencesService();
m_StylePref = prefService->GetSystemPreferences()->Node(berry::QtPreferences::QT_STYLES_NODE);
QString styleName = m_StylePref->Get(berry::QtPreferences::QT_STYLE_NAME, "");
/*if (styleName == ":/org.blueberry.ui.qt/darkstyle.qss")
{
this->m_Controls->m_JSHistogram->SendCommand(
"changeTheme('dark')");
}
else
{
this->m_Controls->m_JSHistogram->SendCommand(
"changeTheme(default)");
}*/
}
void QmitkImageStatisticsView::CreateConnections()
{
if ( m_Controls )
{
connect( (QObject*)(this->m_Controls->m_ButtonCopyHistogramToClipboard), SIGNAL(clicked()),(QObject*) this, SLOT(OnClipboardHistogramButtonClicked()) );
connect( (QObject*)(this->m_Controls->m_ButtonCopyStatisticsToClipboard), SIGNAL(clicked()),(QObject*) this, SLOT(OnClipboardStatisticsButtonClicked()) );
connect( (QObject*)(this->m_Controls->m_IgnoreZerosCheckbox), SIGNAL(clicked()),(QObject*) this, SLOT(OnIgnoreZerosCheckboxClicked()) );
connect( (QObject*) this->m_CalculationThread, SIGNAL(finished()),this, SLOT( OnThreadedStatisticsCalculationEnds()),Qt::QueuedConnection);
connect( (QObject*) this, SIGNAL(StatisticsUpdate()),this, SLOT( RequestStatisticsUpdate()), Qt::QueuedConnection);
connect( (QObject*) this->m_Controls->m_StatisticsTable, SIGNAL(cellDoubleClicked(int,int)),this, SLOT( JumpToCoordinates(int,int)) );
connect((QObject*)(this->m_Controls->m_barRadioButton), SIGNAL(clicked()), (QObject*)(this), SLOT(OnBarRadioButtonSelected()));
connect((QObject*)(this->m_Controls->m_lineRadioButton), SIGNAL(clicked()), (QObject*)(this), SLOT(OnLineRadioButtonSelected()));
connect( (QObject*) (this->m_Controls->m_HistogramBinSizeSpinbox), SIGNAL(editingFinished()), this, SLOT(OnHistogramBinSizeBoxValueChanged()));
connect((QObject*)(this->m_Controls->m_UseDefaultBinSizeBox), SIGNAL(clicked()), (QObject*) this, SLOT(OnDefaultBinSizeBoxChanged()));
connect((QObject*)(this->m_Controls->m_ShowSubchartCheckBox), SIGNAL(clicked()), (QObject*) this, SLOT(OnShowSubchartBoxChanged()));
connect((QObject*)(this->m_Controls->m_JSHistogram), SIGNAL(PageSuccessfullyLoaded()), (QObject*) this, SLOT(OnPageSuccessfullyLoaded()));
}
}
void QmitkImageStatisticsView::OnDefaultBinSizeBoxChanged()
{
m_Controls->m_BinSizeFrame->setEnabled(!m_Controls->m_UseDefaultBinSizeBox->isChecked());
if (m_CalculationThread != nullptr){
m_Controls->m_HistogramBinSizeSpinbox->setValue(m_CalculationThread->GetHistogramBinSize());
m_CalculationThread->SetUseDefaultNBins(m_Controls->m_UseDefaultBinSizeBox->isChecked());
}
this->UpdateStatistics();
}
void QmitkImageStatisticsView::OnShowSubchartBoxChanged()
{
bool showSubchart = this->m_Controls->m_ShowSubchartCheckBox->isChecked();
this->m_Controls->m_JSHistogram->Reload(showSubchart);
}
void QmitkImageStatisticsView::OnBarRadioButtonSelected()
{
this->m_Controls->m_JSHistogram->SetChartTypeAndReload(QmitkChartWidget::ChartType::bar);
}
void QmitkImageStatisticsView::OnLineRadioButtonSelected()
{
this->m_Controls->m_JSHistogram->SetChartTypeAndReload(QmitkChartWidget::ChartType::line);
}
void QmitkImageStatisticsView::PartClosed(const berry::IWorkbenchPartReference::Pointer& )
{
}
void QmitkImageStatisticsView::OnTimeChanged(const itk::EventObject& e)
{
if (this->m_SelectedDataNodes.isEmpty() || this->m_SelectedImage == nullptr)
return;
const mitk::SliceNavigationController::GeometryTimeEvent* timeEvent =
dynamic_cast<const mitk::SliceNavigationController::GeometryTimeEvent*>(&e);
assert(timeEvent != nullptr);
int timestep = timeEvent->GetPos();
if (this->m_SelectedImage->GetTimeSteps() > 1)
{
for (int x = 0; x < this->m_Controls->m_StatisticsTable->columnCount(); x++)
{
for (int y = 0; y < this->m_Controls->m_StatisticsTable->rowCount(); y++)
{
QTableWidgetItem* item = this->m_Controls->m_StatisticsTable->item(y, x);
if (item == nullptr)
break;
if (x == timestep)
{
item->setBackgroundColor(Qt::yellow);
}
else
{
if (y % 2 == 0)
item->setBackground(this->m_Controls->m_StatisticsTable->palette().base());
else
item->setBackground(this->m_Controls->m_StatisticsTable->palette().alternateBase());
}
}
}
this->m_Controls->m_StatisticsTable->viewport()->update();
}
if ((this->m_SelectedImage->GetTimeSteps() == 1 && timestep == 0) ||
this->m_SelectedImage->GetTimeSteps() > 1)
{
// display histogram for selected timestep
this->m_Controls->m_JSHistogram->Clear();
QmitkImageStatisticsCalculationThread::HistogramType::ConstPointer histogram =
(QmitkImageStatisticsCalculationThread::HistogramType::ConstPointer)this->m_CalculationThread->GetTimeStepHistogram(timestep);
if (histogram.IsNotNull())
{
bool closedFigure = this->m_CalculationThread->GetStatisticsUpdateSuccessFlag();
if ( closedFigure )
{
this->m_Controls->m_JSHistogram->AddData2D(ConvertHistogramToMap(histogram) );
if (this->m_Controls->m_lineRadioButton->isChecked())
{
this->m_Controls->m_JSHistogram->SetChartType(QmitkChartWidget::ChartType::line);
}
else
{
this->m_Controls->m_JSHistogram->SetChartType(QmitkChartWidget::ChartType::bar);
}
this->m_Controls->m_JSHistogram->SetDataLabels({ m_Controls->m_SelectedFeatureImageLabel->text().toStdString() });
this->m_Controls->m_JSHistogram->SetXAxisLabel("Grey value");
this->m_Controls->m_JSHistogram->SetYAxisLabel("Frequency");
this->m_Controls->m_JSHistogram->Show(this->m_Controls->m_ShowSubchartCheckBox->isChecked());
}
}
}
}
void QmitkImageStatisticsView::JumpToCoordinates(int row ,int col)
{
if(m_SelectedDataNodes.isEmpty())
{
MITK_WARN("QmitkImageStatisticsView") << "No data node selected for statistics calculation." ;
return;
}
mitk::Point3D world;
if (row==5 && !m_WorldMinList.empty())
world = m_WorldMinList[col];
else if (row==4 && !m_WorldMaxList.empty())
world = m_WorldMaxList[col];
else
return;
mitk::IRenderWindowPart* part = this->GetRenderWindowPart();
if (part)
{
part->GetQmitkRenderWindow("axial")->GetSliceNavigationController()->SelectSliceByPoint(world);
part->GetQmitkRenderWindow("sagittal")->GetSliceNavigationController()->SelectSliceByPoint(world);
part->GetQmitkRenderWindow("coronal")->GetSliceNavigationController()->SelectSliceByPoint(world);
mitk::SliceNavigationController::GeometryTimeEvent timeEvent(this->m_SelectedImage->GetTimeGeometry(), col);
part->GetQmitkRenderWindow("axial")->GetSliceNavigationController()->SetGeometryTime(timeEvent);
}
}
void QmitkImageStatisticsView::OnIgnoreZerosCheckboxClicked()
{
emit StatisticsUpdate();
}
void QmitkImageStatisticsView::OnClipboardHistogramButtonClicked()
{
if ( m_CurrentStatisticsValid && !( m_SelectedPlanarFigure != nullptr))
{
const unsigned int t = this->GetRenderWindowPart()->GetTimeNavigationController()->GetTime()->GetPos();
typedef mitk::ImageStatisticsCalculator::HistogramType HistogramType;
const HistogramType *histogram = this->m_CalculationThread->GetTimeStepHistogram(t).GetPointer();
QString clipboard( "Measurement \t Frequency\n" );
for ( HistogramType::ConstIterator it = histogram->Begin();
it != histogram->End();
++it )
{
if( m_Controls->m_HistogramBinSizeSpinbox->value() == 1.0)
{
clipboard = clipboard.append( "%L1 \t %L2\n" )
.arg( it.GetMeasurementVector()[0], 0, 'f', 0 )
.arg( it.GetFrequency() );
}
else
{
clipboard = clipboard.append( "%L1 \t %L2\n" )
.arg( it.GetMeasurementVector()[0], 0, 'f', 2 )
.arg( it.GetFrequency() );
}
}
QApplication::clipboard()->setText(
clipboard, QClipboard::Clipboard );
}
// If a (non-closed) PlanarFigure is selected, display a line profile widget
else if ( m_CurrentStatisticsValid && (m_SelectedPlanarFigure != nullptr ))
{
/*auto intensity = m_Controls->m_JSHistogram->GetFrequency();
auto pixel = m_Controls->m_JSHistogram->GetMeasurement();
QString clipboard( "Pixel \t Intensity\n" );
auto j = pixel.begin();
for (auto i = intensity.begin(); i < intensity.end(); i++)
{
assert(j != pixel.end());
clipboard = clipboard.append( "%L1 \t %L2\n" )
.arg( (*j).toString())
.arg( (*i).toString());
j++;
}
QApplication::clipboard()->setText(
clipboard, QClipboard::Clipboard );
*/
}
else
{
QApplication::clipboard()->clear();
}
}
void QmitkImageStatisticsView::OnClipboardStatisticsButtonClicked()
{
QLocale tempLocal;
QLocale::setDefault(QLocale(QLocale::English, QLocale::UnitedStates));
if ( m_CurrentStatisticsValid && !( m_SelectedPlanarFigure != nullptr))
{
const std::vector<mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer> &statistics =
this->m_CalculationThread->GetStatisticsData();
// Set time borders for for loop ;)
unsigned int startT, endT;
if(this->m_Controls->m_CheckBox4dCompleteTable->checkState()==Qt::CheckState::Unchecked)
{
startT = this->GetRenderWindowPart()->GetTimeNavigationController()->GetTime()->
GetPos();
endT = startT+1;
}
else
{
startT = 0;
endT = statistics.size();
}
QVector< QVector<QString> > statisticsTable;
QStringList headline;
// Create Headline
headline << " "
<< "Mean"
<< "Median"
<< "StdDev"
<< "RMS"
<< "Max"
<< "Min"
<< "NumberOfVoxels"
<< "Skewness"
<< "Kurtosis"
<< "Uniformity"
<< "Entropy"
<< "MPP"
<< "UPP"
<< "V [mm³]";
for(int i=0;i<headline.size();i++)
{
QVector<QString> row;
row.append(headline.at(i));
statisticsTable.append(row);
}
// Fill Table
for(unsigned int t=startT;t<endT;t++)
{
// Copy statistics to clipboard ("%Ln" will use the default locale for
// number formatting)
QStringList value;
value << QString::number(t)
<< QString::number(statistics[t]->GetMean())
<< QString::number(statistics[t]->GetMedian())
<< QString::number(statistics[t]->GetStd())
<< QString::number(statistics[t]->GetRMS())
<< QString::number(statistics[t]->GetMax())
<< QString::number(statistics[t]->GetMin())
<< QString::number(statistics[t]->GetN())
<< QString::number(statistics[t]->GetSkewness())
<< QString::number(statistics[t]->GetKurtosis())
<< QString::number(statistics[t]->GetUniformity())
<< QString::number(statistics[t]->GetEntropy())
<< QString::number(statistics[t]->GetMPP())
<< QString::number(statistics[t]->GetUPP())
<< QString::number(m_Controls->m_StatisticsTable->item(7, 0)->data(Qt::DisplayRole).toDouble());
for(int z=0;z<value.size();z++)
{
statisticsTable[z].append(value.at(z));
}
}
// Create output string
QString clipboard;
for(int i=0;i<statisticsTable.size();i++)
{
for(int t=0;t<statisticsTable.at(i).size();t++)
{
clipboard.append(statisticsTable.at(i).at(t));
clipboard.append("\t");
}
clipboard.append("\n");
}
QApplication::clipboard()->setText(clipboard, QClipboard::Clipboard);
}
else
{
QApplication::clipboard()->clear();
}
QLocale::setDefault(tempLocal);
}
void QmitkImageStatisticsView::OnSelectionChanged( berry::IWorkbenchPart::Pointer /*part*/,
const QList<mitk::DataNode::Pointer> &nodes )
{
if (this->m_Visible)
{
this->SelectionChanged( nodes );
}
else
{
this->m_DataNodeSelectionChanged = true;
}
}
void QmitkImageStatisticsView::SelectionChanged(const QList<mitk::DataNode::Pointer> &selectedNodes)
{
//Clear Histogram if data node is deselected
m_Controls->m_JSHistogram->Clear();
if( this->m_StatisticsUpdatePending )
{
this->m_DataNodeSelectionChanged = true;
return; // not ready for new data now!
}
if (selectedNodes.size() == this->m_SelectedDataNodes.size())
{
int i = 0;
for (; i < selectedNodes.size(); ++i)
{
if (selectedNodes.at(i) != this->m_SelectedDataNodes.at(i))
{
break;
}
}
// node selection did not change
if (i == selectedNodes.size()) return;
}
//reset the feature image and image mask field
m_Controls->m_SelectedFeatureImageLabel->setText("None");
m_Controls->m_SelectedMaskLabel->setText("None");
this->ReinitData();
if (selectedNodes.isEmpty())
{
m_Controls->m_lineRadioButton->setEnabled(true);
m_Controls->m_barRadioButton->setEnabled(true);
m_Controls->m_HistogramBinSizeSpinbox->setEnabled(true);
m_Controls->m_HistogramBinSizeCaptionLabel->setEnabled(true);
+ m_Controls->m_UseDefaultBinSizeBox->setEnabled(true);
m_Controls->m_InfoLabel->setText("");
m_Controls->groupBox->setEnabled(false);
m_Controls->groupBox_3->setEnabled(false);
}
else
{
m_Controls->groupBox->setEnabled(true);
m_Controls->groupBox_3->setEnabled(true);
m_Controls->m_barRadioButton->setChecked(true);
}
if(selectedNodes.size() == 1 || selectedNodes.size() == 2)
{
bool isBinary = false;
selectedNodes.value(0)->GetBoolProperty("binary",isBinary);
mitk::NodePredicateDataType::Pointer isLabelSet = mitk::NodePredicateDataType::New("LabelSetImage");
isBinary |= isLabelSet->CheckNode(selectedNodes.value(0));
if(isBinary)
{
m_Controls->m_lineRadioButton->setEnabled(true);
m_Controls->m_barRadioButton->setEnabled(true);
m_Controls->m_HistogramBinSizeSpinbox->setEnabled(true);
m_Controls->m_HistogramBinSizeCaptionLabel->setEnabled(true);
+ m_Controls->m_UseDefaultBinSizeBox->setEnabled(true);
m_Controls->m_InfoLabel->setText("");
}
for (int i= 0; i< selectedNodes.size(); ++i)
{
this->m_SelectedDataNodes.push_back(selectedNodes.at(i));
}
this->m_DataNodeSelectionChanged = false;
this->m_Controls->m_ErrorMessageLabel->setText( "" );
this->m_Controls->m_ErrorMessageLabel->hide();
emit StatisticsUpdate();
}
else
{
this->m_DataNodeSelectionChanged = false;
}
}
void QmitkImageStatisticsView::ReinitData()
{
while( this->m_CalculationThread->isRunning()) // wait until thread has finished
{
itksys::SystemTools::Delay(100);
}
if(this->m_SelectedImage != nullptr)
{
this->m_SelectedImage->RemoveObserver( this->m_ImageObserverTag);
this->m_SelectedImage = nullptr;
}
if(this->m_SelectedImageMask != nullptr)
{
this->m_SelectedImageMask->RemoveObserver( this->m_ImageMaskObserverTag);
this->m_SelectedImageMask = nullptr;
}
if(this->m_SelectedPlanarFigure != nullptr)
{
this->m_SelectedPlanarFigure->RemoveObserver( this->m_PlanarFigureObserverTag);
this->m_SelectedPlanarFigure = nullptr;
}
this->m_SelectedDataNodes.clear();
this->m_StatisticsUpdatePending = false;
m_Controls->m_ErrorMessageLabel->setText( "" );
m_Controls->m_ErrorMessageLabel->hide();
this->InvalidateStatisticsTableView();
m_Controls->m_StatisticsWidgetStack->setCurrentIndex( 0 );
}
void QmitkImageStatisticsView::OnThreadedStatisticsCalculationEnds()
{
std::stringstream message;
message << "";
m_Controls->m_ErrorMessageLabel->setText( message.str().c_str() );
m_Controls->m_ErrorMessageLabel->hide();
this->WriteStatisticsToGUI();
}
void QmitkImageStatisticsView::UpdateStatistics()
{
mitk::IRenderWindowPart* renderPart = this->GetRenderWindowPart();
if ( renderPart == nullptr )
{
this->m_StatisticsUpdatePending = false;
return;
}
m_WorldMinList.clear();
m_WorldMaxList.clear();
// classify selected nodes
mitk::NodePredicateDataType::Pointer isImage = mitk::NodePredicateDataType::New("Image");
mitk::NodePredicateDataType::Pointer isLabelSet = mitk::NodePredicateDataType::New("LabelSetImage");
mitk::NodePredicateOr::Pointer imagePredicate = mitk::NodePredicateOr::New(isImage, isLabelSet);
std::string maskName;
std::string maskType;
std::string featureImageName;
unsigned int maskDimension = 0;
// reset data from last run
ITKCommandType::Pointer changeListener = ITKCommandType::New();
changeListener->SetCallbackFunction( this, &QmitkImageStatisticsView::SelectedDataModified );
mitk::DataNode::Pointer planarFigureNode;
for( int i= 0 ; i < this->m_SelectedDataNodes.size(); ++i)
{
mitk::PlanarFigure::Pointer planarFig = dynamic_cast<mitk::PlanarFigure*>(this->m_SelectedDataNodes.at(i)->GetData());
if( imagePredicate->CheckNode(this->m_SelectedDataNodes.at(i)) )
{
bool isMask = false;
this->m_SelectedDataNodes.at(i)->GetPropertyValue("binary", isMask);
isMask |= isLabelSet->CheckNode(this->m_SelectedDataNodes.at(i));
if( this->m_SelectedImageMask == nullptr && isMask)
{
this->m_SelectedImageMask = dynamic_cast<mitk::Image*>(this->m_SelectedDataNodes.at(i)->GetData());
this->m_ImageMaskObserverTag = this->m_SelectedImageMask->AddObserver(itk::ModifiedEvent(), changeListener);
maskName = this->m_SelectedDataNodes.at(i)->GetName();
maskType = m_SelectedImageMask->GetNameOfClass();
maskDimension = 3;
}
else if( !isMask )
{
if(this->m_SelectedImage == nullptr)
{
this->m_SelectedImage = static_cast<mitk::Image*>(this->m_SelectedDataNodes.at(i)->GetData());
this->m_ImageObserverTag = this->m_SelectedImage->AddObserver(itk::ModifiedEvent(), changeListener);
}
featureImageName = this->m_SelectedDataNodes.at(i)->GetName();
}
}
else if (planarFig.IsNotNull())
{
if(this->m_SelectedPlanarFigure == nullptr)
{
this->m_SelectedPlanarFigure = planarFig;
this->m_PlanarFigureObserverTag =
this->m_SelectedPlanarFigure->AddObserver(mitk::EndInteractionPlanarFigureEvent(), changeListener);
maskName = this->m_SelectedDataNodes.at(i)->GetName();
maskType = this->m_SelectedPlanarFigure->GetNameOfClass();
maskDimension = 2;
planarFigureNode = m_SelectedDataNodes.at(i);
}
}
else
{
std::stringstream message;
message << "<font color='red'>" << "Invalid data node type!" << "</font>";
m_Controls->m_ErrorMessageLabel->setText( message.str().c_str() );
m_Controls->m_ErrorMessageLabel->show();
}
}
if(maskName == "")
{
maskName = "None";
maskType = "";
maskDimension = 0;
}
if(featureImageName == "")
{
featureImageName = "None";
}
if (m_SelectedPlanarFigure != nullptr && m_SelectedImage == nullptr)
{
mitk::DataStorage::SetOfObjects::ConstPointer parentSet = this->GetDataStorage()->GetSources(planarFigureNode);
for (unsigned int i=0; i<parentSet->Size(); i++)
{
mitk::DataNode::Pointer node = parentSet->ElementAt(i);
if( imagePredicate->CheckNode(node) )
{
bool isMask = false;
node->GetPropertyValue("binary", isMask);
isMask |= isLabelSet->CheckNode(node);
if( !isMask )
{
if(this->m_SelectedImage == nullptr)
{
this->m_SelectedImage = static_cast<mitk::Image*>(node->GetData());
this->m_ImageObserverTag = this->m_SelectedImage->AddObserver(itk::ModifiedEvent(), changeListener);
}
}
}
}
}
unsigned int timeStep = renderPart->GetTimeNavigationController()->GetTime()->GetPos();
if ( m_SelectedImage != nullptr && m_SelectedImage->IsInitialized())
{
// Check if a the selected image is a multi-channel image. If yes, statistics
// cannot be calculated currently.
if ( m_SelectedImage->GetPixelType().GetNumberOfComponents() > 1 )
{
std::stringstream message;
message << "<font color='red'>Multi-component images not supported.</font>";
m_Controls->m_ErrorMessageLabel->setText( message.str().c_str() );
m_Controls->m_ErrorMessageLabel->show();
this->InvalidateStatisticsTableView();
m_Controls->m_StatisticsWidgetStack->setCurrentIndex( 0 );
m_CurrentStatisticsValid = false;
this->m_StatisticsUpdatePending = false;
m_Controls->m_lineRadioButton->setEnabled(true);
m_Controls->m_barRadioButton->setEnabled(true);
m_Controls->m_HistogramBinSizeSpinbox->setEnabled(true);
m_Controls->m_HistogramBinSizeCaptionLabel->setEnabled(true);
+ m_Controls->m_UseDefaultBinSizeBox->setEnabled(true);
m_Controls->m_InfoLabel->setText("");
return;
}
std::stringstream maskLabel;
maskLabel << maskName;
if ( maskDimension > 0 )
{
maskLabel << " [" << maskDimension << "D " << maskType << "]";
}
m_Controls->m_SelectedMaskLabel->setText( maskLabel.str().c_str() );
m_Controls->m_SelectedFeatureImageLabel->setText(featureImageName.c_str());
// check time step validity
if(m_SelectedImage->GetDimension() <= 3 && timeStep > m_SelectedImage->GetDimension(3)-1)
{
timeStep = m_SelectedImage->GetDimension(3)-1;
}
// Add the used mask time step to the mask label so the user knows which mask time step was used
// if the image time step is bigger than the total number of mask time steps (see
// ImageStatisticsCalculator::ExtractImageAndMask)
if (m_SelectedImageMask != nullptr)
{
unsigned int maskTimeStep = timeStep;
if (maskTimeStep >= m_SelectedImageMask->GetTimeSteps())
{
maskTimeStep = m_SelectedImageMask->GetTimeSteps() - 1;
}
m_Controls->m_SelectedMaskLabel->setText(m_Controls->m_SelectedMaskLabel->text() +
QString(" (t=") +
QString::number(maskTimeStep) +
QString(")"));
}
// check if the segmentation mask is empty
if (m_SelectedImageMask != NULL)
{
typedef itk::Image<unsigned char, 3> ItkImageType;
typedef itk::ImageRegionConstIteratorWithIndex< ItkImageType > IteratorType;
ItkImageType::Pointer itkImage;
mitk::CastToItkImage( m_SelectedImageMask, itkImage );
bool empty = true;
IteratorType it( itkImage, itkImage->GetLargestPossibleRegion() );
while ( !it.IsAtEnd() )
{
ItkImageType::ValueType val = it.Get();
if ( val != 0 )
{
empty = false;
break;
}
++it;
}
if ( empty )
{
std::stringstream message;
message << "<font color='red'>Empty segmentation mask selected...</font>";
m_Controls->m_ErrorMessageLabel->setText( message.str().c_str() );
m_Controls->m_ErrorMessageLabel->show();
return;
}
}
//// initialize thread and trigger it
this->m_CalculationThread->SetIgnoreZeroValueVoxel( m_Controls->m_IgnoreZerosCheckbox->isChecked() );
this->m_CalculationThread->Initialize( m_SelectedImage, m_SelectedImageMask, m_SelectedPlanarFigure );
this->m_CalculationThread->SetTimeStep( timeStep );
std::stringstream message;
message << "<font color='red'>Calculating statistics...</font>";
m_Controls->m_ErrorMessageLabel->setText( message.str().c_str() );
m_Controls->m_ErrorMessageLabel->show();
try
{
// Compute statistics
// this->m_CalculationThread->SetUseDefaultBinSize(m_Controls->m_UseDefaultBinSizeBox->isChecked());
this->m_CalculationThread->start();
}
catch ( const mitk::Exception& e)
{
std::stringstream message;
message << "<font color='red'>" << e.GetDescription() << "</font>";
m_Controls->m_ErrorMessageLabel->setText( message.str().c_str() );
m_Controls->m_ErrorMessageLabel->show();
this->m_StatisticsUpdatePending = false;
}
catch ( const std::runtime_error &e )
{
// In case of exception, print error message on GUI
std::stringstream message;
message << "<font color='red'>" << e.what() << "</font>";
m_Controls->m_ErrorMessageLabel->setText( message.str().c_str() );
m_Controls->m_ErrorMessageLabel->show();
this->m_StatisticsUpdatePending = false;
}
catch ( const std::exception &e )
{
MITK_ERROR << "Caught exception: " << e.what();
// In case of exception, print error message on GUI
std::stringstream message;
message << "<font color='red'>Error! Unequal Dimensions of Image and Segmentation. No recompute possible </font>";
m_Controls->m_ErrorMessageLabel->setText( message.str().c_str() );
m_Controls->m_ErrorMessageLabel->show();
this->m_StatisticsUpdatePending = false;
}
}
else
{
this->m_StatisticsUpdatePending = false;
}
}
void QmitkImageStatisticsView::SelectedDataModified()
{
if( !m_StatisticsUpdatePending )
{
emit StatisticsUpdate();
}
}
void QmitkImageStatisticsView::NodeRemoved(const mitk::DataNode *node)
{
while(this->m_CalculationThread->isRunning()) // wait until thread has finished
{
itksys::SystemTools::Delay(100);
}
if (node->GetData() == m_SelectedImage)
{
m_SelectedImage = nullptr;
}
}
void QmitkImageStatisticsView::RequestStatisticsUpdate()
{
if ( !m_StatisticsUpdatePending )
{
if(this->m_DataNodeSelectionChanged)
{
this->SelectionChanged(this->GetCurrentSelection());
}
else
{
this->m_StatisticsUpdatePending = true;
this->UpdateStatistics();
}
}
if (this->GetRenderWindowPart())
this->GetRenderWindowPart()->RequestUpdate();
}
void QmitkImageStatisticsView::OnHistogramBinSizeBoxValueChanged()
{
if (m_Controls->m_HistogramBinSizeSpinbox->value() != m_HistogramBinSize)
{
m_HistogramBinSize = m_Controls->m_HistogramBinSizeSpinbox->value();
this->m_CalculationThread->SetHistogramBinSize(m_Controls->m_HistogramBinSizeSpinbox->value());
this->UpdateStatistics();
}
}
void QmitkImageStatisticsView::WriteStatisticsToGUI()
{
m_Controls->m_JSHistogram->Clear();
//Disconnect OnLineRadioButtonSelected() to prevent reloading chart when radiobutton is checked programmatically
disconnect((QObject*)(this->m_Controls->m_JSHistogram), SIGNAL(PageSuccessfullyLoaded()), 0, 0);
connect((QObject*)(this->m_Controls->m_JSHistogram), SIGNAL(PageSuccessfullyLoaded()), (QObject*) this, SLOT(OnPageSuccessfullyLoaded()));
m_Controls->m_lineRadioButton->setEnabled(true);
m_Controls->m_barRadioButton->setEnabled(true);
m_Controls->m_HistogramBinSizeSpinbox->setEnabled(true);
m_Controls->m_HistogramBinSizeCaptionLabel->setEnabled(true);
m_Controls->m_InfoLabel->setText("");
if(m_DataNodeSelectionChanged)
{
this->m_StatisticsUpdatePending = false;
this->RequestStatisticsUpdate();
return; // stop visualization of results and calculate statistics of new selection
}
if ( this->m_CalculationThread->GetStatisticsUpdateSuccessFlag())
{
if ( this->m_CalculationThread->GetStatisticsChangedFlag() )
{
// Do not show any error messages
m_Controls->m_ErrorMessageLabel->hide();
m_CurrentStatisticsValid = true;
}
- m_Controls->m_StatisticsWidgetStack->setCurrentIndex( 0 );
- m_Controls->m_HistogramBinSizeSpinbox->setValue( this->m_CalculationThread->GetHistogramBinSize() );
- auto histogram = this->m_CalculationThread->GetTimeStepHistogram(this->m_CalculationThread->GetTimeStep()).GetPointer();
-
- m_Controls->m_JSHistogram->AddData2D(ConvertHistogramToMap(histogram));
- m_Controls->m_JSHistogram->SetChartType(QmitkChartWidget::ChartType::bar);
- this->m_Controls->m_JSHistogram->SetDataLabels({ m_Controls->m_SelectedFeatureImageLabel->text().toStdString() });
- this->m_Controls->m_JSHistogram->SetXAxisLabel("Gray value");
- this->m_Controls->m_JSHistogram->SetYAxisLabel("Frequency");
- m_Controls->m_JSHistogram->Show(this->m_Controls->m_ShowSubchartCheckBox->isChecked());
-
- this->FillStatisticsTableView( this->m_CalculationThread->GetStatisticsData(), this->m_CalculationThread->GetStatisticsImage());
- m_CurrentStatisticsValid = true;
- }
- else
- {
- m_Controls->m_SelectedMaskLabel->setText( "None" );
- m_Controls->m_ErrorMessageLabel->setText( m_CalculationThread->GetLastErrorMessage().c_str() );
- m_Controls->m_ErrorMessageLabel->show();
-
- // Clear statistics and histogram
- this->InvalidateStatisticsTableView();
- m_Controls->m_StatisticsWidgetStack->setCurrentIndex( 0 );
- m_CurrentStatisticsValid = false;
-
+ if (m_SelectedImage != nullptr) {
+ //all statistics are now computed also on planar figures (lines, paths...)!
// If a (non-closed) PlanarFigure is selected, display a line profile widget
- if ( m_SelectedPlanarFigure != nullptr )
- {
+ if (m_SelectedPlanarFigure != nullptr) {
// Check if the (closed) planar figure is out of bounds and so no image mask could be calculated--> Intensity Profile can not be calculated
bool outOfBounds = false;
if ( m_SelectedPlanarFigure->IsClosed() && m_SelectedImageMask == nullptr)
{
outOfBounds = true;
const QString message("<font color='red'>Planar figure is on a rotated image plane or outside the image bounds.</font>");
m_Controls->m_InfoLabel->setText(message);
}
// check whether PlanarFigure is initialized
const mitk::PlaneGeometry *planarFigurePlaneGeometry = m_SelectedPlanarFigure->GetPlaneGeometry();
+
if ( !(planarFigurePlaneGeometry == nullptr || outOfBounds))
{
unsigned int timeStep = this->GetRenderWindowPart()->GetTimeNavigationController()->GetTime()->GetPos();
mitk::Image::Pointer image;
if (this->m_CalculationThread->GetStatisticsImage()->GetDimension() == 4)
{
mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New();
timeSelector->SetInput(this->m_CalculationThread->GetStatisticsImage());
timeSelector->SetTimeNr(timeStep);
timeSelector->Update();
image = timeSelector->GetOutput();
}
else
{
image = this->m_CalculationThread->GetStatisticsImage();
}
mitk::IntensityProfile::ConstPointer intensityProfile = (mitk::IntensityProfile::ConstPointer)mitk::ComputeIntensityProfile(image, m_SelectedPlanarFigure);
auto intensityProfileList = ConvertIntensityProfileToVector(intensityProfile);
m_Controls->m_JSHistogram->SetChartType(QmitkChartWidget::ChartType::line);
m_Controls->m_JSHistogram->AddData1D(intensityProfileList);
- m_Controls->m_JSHistogram->SetDataLabels({ "Intensity profile" });
+ m_Controls->m_JSHistogram->SetDataLabels({ "Intensity profile " + m_Controls->m_SelectedMaskLabel->text().toStdString() });
m_Controls->m_JSHistogram->SetXAxisLabel("Distance");
m_Controls->m_JSHistogram->SetYAxisLabel("Intensity");
m_Controls->m_JSHistogram->Show(m_Controls->m_ShowSubchartCheckBox->isChecked());
m_Controls->m_lineRadioButton->setChecked(true);
m_Controls->m_lineRadioButton->setEnabled(false);
m_Controls->m_barRadioButton->setEnabled(false);
m_Controls->m_HistogramBinSizeSpinbox->setEnabled(false);
m_Controls->m_HistogramBinSizeCaptionLabel->setEnabled(false);
+ m_Controls->m_UseDefaultBinSizeBox->setEnabled(false);
//Reconnect OnLineRadioButtonSelected()
connect((QObject*)(this->m_Controls->m_JSHistogram), SIGNAL(PageSuccessfullyLoaded()), (QObject*) this, SLOT(OnLineRadioButtonSelected()));
+ auto statisticsVector = this->m_CalculationThread->GetStatisticsData();
+ //only one entry (current timestep)
+ this->FillLinearProfileStatisticsTableView(statisticsVector.front().GetPointer(), this->m_CalculationThread->GetStatisticsImage());
- this->FillLinearProfileStatisticsTableView(intensityProfile, this->m_CalculationThread->GetStatisticsImage().GetPointer());
-
- const QString message("<font color='red'>Only linegraph available for an intensity profile!</font>");
+ QString message("<font color='red'>Only linegraph available for an intensity profile!");
+ if (this->m_CalculationThread->GetStatisticsImage()->GetDimension() == 4) {
+ message += "Only current timestep displayed!";
+ }
+ message += "</font>";
m_Controls->m_InfoLabel->setText(message);
m_CurrentStatisticsValid = true;
}
else
{
// Clear statistics, histogram, and GUI
this->InvalidateStatisticsTableView();
m_Controls->m_StatisticsWidgetStack->setCurrentIndex( 0 );
m_CurrentStatisticsValid = false;
m_Controls->m_ErrorMessageLabel->hide();
m_Controls->m_SelectedMaskLabel->setText( "None" );
this->m_StatisticsUpdatePending = false;
m_Controls->m_lineRadioButton->setEnabled(true);
m_Controls->m_barRadioButton->setEnabled(true);
m_Controls->m_HistogramBinSizeSpinbox->setEnabled(true);
m_Controls->m_HistogramBinSizeCaptionLabel->setEnabled(true);
if (!outOfBounds)
m_Controls->m_InfoLabel->setText("");
- return; // Sebastian Wirkert: would suggest to remove this return, since it is an artifact of previous
- // code architecture. However, removing it will cause m_StatisticsUpdatePending to be set to false
- // in case of invalid statistics which it previously was not.
+ return;
}
}
+ else {
+ m_Controls->m_StatisticsWidgetStack->setCurrentIndex(0);
+ m_Controls->m_HistogramBinSizeSpinbox->setValue(this->m_CalculationThread->GetHistogramBinSize());
+ auto histogram = this->m_CalculationThread->GetTimeStepHistogram(this->m_CalculationThread->GetTimeStep()).GetPointer();
+
+ m_Controls->m_JSHistogram->AddData2D(ConvertHistogramToMap(histogram));
+ m_Controls->m_JSHistogram->SetChartType(QmitkChartWidget::ChartType::bar);
+ this->m_Controls->m_JSHistogram->SetDataLabels({ m_Controls->m_SelectedFeatureImageLabel->text().toStdString() });
+ this->m_Controls->m_JSHistogram->SetXAxisLabel("Gray value");
+ this->m_Controls->m_JSHistogram->SetYAxisLabel("Frequency");
+ m_Controls->m_JSHistogram->Show(this->m_Controls->m_ShowSubchartCheckBox->isChecked());
+
+ this->FillStatisticsTableView(this->m_CalculationThread->GetStatisticsData(), this->m_CalculationThread->GetStatisticsImage());
+ }
+ m_CurrentStatisticsValid = true;
+ }
+ }
+ else
+ {
+ m_Controls->m_SelectedMaskLabel->setText("None");
+ m_Controls->m_ErrorMessageLabel->setText(m_CalculationThread->GetLastErrorMessage().c_str());
+ m_Controls->m_ErrorMessageLabel->show();
+
+ // Clear statistics and histogram
+ this->InvalidateStatisticsTableView();
+ m_Controls->m_StatisticsWidgetStack->setCurrentIndex(0);
+ m_CurrentStatisticsValid = false;
+
}
berry::IPreferencesService* prefService = berry::WorkbenchPlugin::GetDefault()->GetPreferencesService();
m_StylePref = prefService->GetSystemPreferences()->Node(berry::QtPreferences::QT_STYLES_NODE);
this->m_StatisticsUpdatePending = false;
}
void QmitkImageStatisticsView::FillStatisticsTableView(
const std::vector<mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer> &statistics,
const mitk::Image *image )
{
this->m_Controls->m_StatisticsTable->setColumnCount(image->GetTimeSteps());
this->m_Controls->m_StatisticsTable->horizontalHeader()->setVisible(image->GetTimeSteps() > 1);
// Set Checkbox for complete copy of statistic table
if(image->GetTimeSteps()>1)
{
this->m_Controls->m_CheckBox4dCompleteTable->setEnabled(true);
}
else
{
this->m_Controls->m_CheckBox4dCompleteTable->setEnabled(false);
this->m_Controls->m_CheckBox4dCompleteTable->setChecked(false);
}
for (unsigned int t = 0; t < image->GetTimeSteps(); t++)
{
this->m_Controls->m_StatisticsTable->setHorizontalHeaderItem(t,
new QTableWidgetItem(QString::number(t)));
if (statistics.at(t)->GetMaxIndex().size()==3)
{
mitk::Point3D index, max, min;
index[0] = statistics.at(t)->GetMaxIndex()[0];
index[1] = statistics.at(t)->GetMaxIndex()[1];
index[2] = statistics.at(t)->GetMaxIndex()[2];
m_SelectedImage->GetGeometry()->IndexToWorld(index, max);
this->m_WorldMaxList.push_back(max);
index[0] = statistics.at(t)->GetMinIndex()[0];
index[1] = statistics.at(t)->GetMinIndex()[1];
index[2] = statistics.at(t)->GetMinIndex()[2];
m_SelectedImage->GetGeometry()->IndexToWorld(index, min);
this->m_WorldMinList.push_back(min);
}
auto statisticsVector = AssembleStatisticsIntoVector(statistics.at(t).GetPointer(), image);
unsigned int count = 0;
for (const auto& entry : statisticsVector) {
auto item = new QTableWidgetItem(entry);
this->m_Controls->m_StatisticsTable->setItem(count, t, item);
count++;
}
}
this->m_Controls->m_StatisticsTable->resizeColumnsToContents();
int height = STAT_TABLE_BASE_HEIGHT;
if (this->m_Controls->m_StatisticsTable->horizontalHeader()->isVisible())
height += this->m_Controls->m_StatisticsTable->horizontalHeader()->height();
if (this->m_Controls->m_StatisticsTable->horizontalScrollBar()->isVisible())
height += this->m_Controls->m_StatisticsTable->horizontalScrollBar()->height();
this->m_Controls->m_StatisticsTable->setMinimumHeight(height);
// make sure the current timestep's column is highlighted (and the correct histogram is displayed)
unsigned int t = this->GetRenderWindowPart()->GetTimeNavigationController()->GetTime()->
GetPos();
mitk::SliceNavigationController::GeometryTimeEvent timeEvent(this->m_SelectedImage->GetTimeGeometry(),
t);
this->OnTimeChanged(timeEvent);
t = std::min(image->GetTimeSteps() - 1, t);
// See bug 18340
/*QString hotspotMean; hotspotMean.append(QString("%1").arg(s[t].GetHotspotStatistics().GetMean(), 0, 'f', decimals));
hotspotMean += " (";
for (int i=0; i<s[t].GetHotspotIndex().size(); i++)
{
hotspotMean += QString::number(s[t].GetHotspotIndex()[i]);
if (i<s[t].GetHotspotIndex().size()-1)
hotspotMean += ",";
}
hotspotMean += ")";
this->m_Controls->m_StatisticsTable->setItem( 7, t, new QTableWidgetItem( hotspotMean ) );
QString hotspotMax; hotspotMax.append(QString("%1").arg(s[t].GetHotspotStatistics().GetMax(), 0, 'f', decimals));
hotspotMax += " (";
for (int i=0; i<s[t].GetHotspotStatistics().GetMaxIndex().size(); i++)
{
hotspotMax += QString::number(s[t].GetHotspotStatistics().GetMaxIndex()[i]);
if (i<s[t].GetHotspotStatistics().GetMaxIndex().size()-1)
hotspotMax += ",";
}
hotspotMax += ")";
this->m_Controls->m_StatisticsTable->setItem( 8, t, new QTableWidgetItem( hotspotMax ) );
QString hotspotMin; hotspotMin.append(QString("%1").arg(s[t].GetHotspotStatistics().GetMin(), 0, 'f', decimals));
hotspotMin += " (";
for (int i=0; i<s[t].GetHotspotStatistics().GetMinIndex().size(); i++)
{
hotspotMin += QString::number(s[t].GetHotspotStatistics().GetMinIndex()[i]);
if (i<s[t].GetHotspotStatistics().GetMinIndex().size()-1)
hotspotMin += ",";
}
hotspotMin += ")";
this->m_Controls->m_StatisticsTable->setItem( 9, t, new QTableWidgetItem( hotspotMin ) );*/
}
-std::vector<QString> QmitkImageStatisticsView::AssembleStatisticsIntoVectorForPlanarFigure(mitk::IntensityProfile::ConstPointer intensityProfile, mitk::Image::ConstPointer image)
+std::vector<QString> QmitkImageStatisticsView::AssembleStatisticsIntoVector(mitk::ImageStatisticsCalculator::StatisticsContainer::ConstPointer statistics, mitk::Image::ConstPointer image, bool noVolumeDefined) const
{
std::vector<QString> result;
- unsigned int decimals = 2;
- //statistics of higher order should have 5 decimal places because they used to be very small
- unsigned int decimalsHigherOrderStatistics = 5;
-
- if (image->GetPixelType().GetComponentType() == itk::ImageIOBase::DOUBLE || image->GetPixelType().GetComponentType() == itk::ImageIOBase::FLOAT)
- {
- decimals = 5;
- }
-
- mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer stats = mitk::ImageStatisticsCalculator::StatisticsContainer::New();
-
- mitk::ComputeIntensityProfileStatistics(intensityProfile, stats);
-
- result.push_back(GetFormattedString(stats->GetMean(), decimals));
- result.push_back(GetFormattedString(stats->GetMedian(), decimals));
- result.push_back(GetFormattedString(stats->GetStd(), decimals));
- result.push_back(GetFormattedString(stats->GetRMS(), decimals));
- result.push_back(GetFormattedString(stats->GetMax(), decimals));
- result.push_back(GetFormattedString(stats->GetMin(), decimals));
- result.push_back(GetFormattedString(stats->GetN(), 0));
- result.push_back(QString("NA")); //Volume can't be computed on a line
- result.push_back(GetFormattedString(stats->GetSkewness(), decimalsHigherOrderStatistics));
- result.push_back(GetFormattedString(stats->GetKurtosis(), decimalsHigherOrderStatistics));
- result.push_back(GetFormattedString(stats->GetUniformity(), decimalsHigherOrderStatistics));
- result.push_back(GetFormattedString(stats->GetEntropy(), decimalsHigherOrderStatistics));
- result.push_back(GetFormattedString(stats->GetMPP(), decimals));
- result.push_back(GetFormattedString(stats->GetUPP(), decimalsHigherOrderStatistics));
-
- return result;
- }
-
-std::vector<QString> QmitkImageStatisticsView::AssembleStatisticsIntoVector(mitk::ImageStatisticsCalculator::StatisticsContainer::ConstPointer statistics, mitk::Image::ConstPointer image) const
- {
- std::vector<QString> result;
-
unsigned int decimals = 2;
//statistics of higher order should have 5 decimal places because they used to be very small
unsigned int decimalsHigherOrderStatistics = 5;
if (image->GetPixelType().GetComponentType() == itk::ImageIOBase::DOUBLE || image->GetPixelType().GetComponentType() == itk::ImageIOBase::FLOAT)
{
decimals = 5;
}
result.push_back(GetFormattedString(statistics->GetMean(), decimals));
result.push_back(GetFormattedString(statistics->GetMedian(), decimals));
result.push_back(GetFormattedString(statistics->GetStd(), decimals));
result.push_back(GetFormattedString(statistics->GetRMS(), decimals));
result.push_back(GetFormattedString(statistics->GetMax(), decimals) + " " + GetFormattedIndex(statistics->GetMaxIndex()));
result.push_back(GetFormattedString(statistics->GetMin(), decimals) + " " + GetFormattedIndex(statistics->GetMinIndex()));
//to prevent large negative values of empty image statistics
if (statistics->GetN() != std::numeric_limits<long>::max() + 1) {
result.push_back(GetFormattedString(statistics->GetN(), 0));
const mitk::BaseGeometry *geometry = image->GetGeometry();
- if (geometry != NULL)
+ if (geometry != NULL && !noVolumeDefined)
{
const mitk::Vector3D &spacing = image->GetGeometry()->GetSpacing();
double volume = spacing[0] * spacing[1] * spacing[2] * static_cast<double>(statistics->GetN());
result.push_back(GetFormattedString(volume, decimals));
}
else {
result.push_back("NA");
}
}
else {
- result.push_back("0");
- result.push_back("0");
+ result.push_back("NA");
+ result.push_back("NA");
}
result.push_back(GetFormattedString(statistics->GetSkewness(), decimalsHigherOrderStatistics));
result.push_back(GetFormattedString(statistics->GetKurtosis(), decimalsHigherOrderStatistics));
result.push_back(GetFormattedString(statistics->GetUniformity(), decimalsHigherOrderStatistics));
result.push_back(GetFormattedString(statistics->GetEntropy(), decimalsHigherOrderStatistics));
result.push_back(GetFormattedString(statistics->GetMPP(), decimals));
result.push_back(GetFormattedString(statistics->GetUPP(), decimalsHigherOrderStatistics));
return result;
}
-void QmitkImageStatisticsView::FillLinearProfileStatisticsTableView( mitk::IntensityProfile::ConstPointer intensityProfile, mitk::Image::ConstPointer image )
+void QmitkImageStatisticsView::FillLinearProfileStatisticsTableView(mitk::ImageStatisticsCalculator::StatisticsContainer::ConstPointer statistics,
+ const mitk::Image *image)
{
this->m_Controls->m_StatisticsTable->setColumnCount(1);
this->m_Controls->m_StatisticsTable->horizontalHeader()->setVisible(false);
- m_PlanarFigureStatistics = this->AssembleStatisticsIntoVectorForPlanarFigure( intensityProfile, image);
+ m_PlanarFigureStatistics = this->AssembleStatisticsIntoVector(statistics, image, true);
for (unsigned int i = 0; i< m_PlanarFigureStatistics.size(); i++)
{
this->m_Controls->m_StatisticsTable->setItem( i, 0, new QTableWidgetItem(m_PlanarFigureStatistics[i] ));
}
this->m_Controls->m_StatisticsTable->resizeColumnsToContents();
int height = STAT_TABLE_BASE_HEIGHT;
if (this->m_Controls->m_StatisticsTable->horizontalHeader()->isVisible())
height += this->m_Controls->m_StatisticsTable->horizontalHeader()->height();
if (this->m_Controls->m_StatisticsTable->horizontalScrollBar()->isVisible())
height += this->m_Controls->m_StatisticsTable->horizontalScrollBar()->height();
this->m_Controls->m_StatisticsTable->setMinimumHeight(height);
}
void QmitkImageStatisticsView::InvalidateStatisticsTableView()
{
this->m_Controls->m_StatisticsTable->horizontalHeader()->setVisible(false);
this->m_Controls->m_StatisticsTable->setColumnCount(1);
for ( int i = 0; i < this->m_Controls->m_StatisticsTable->rowCount(); ++i )
{
{
this->m_Controls->m_StatisticsTable->setItem( i, 0, new QTableWidgetItem( "NA" ) );
}
}
this->m_Controls->m_StatisticsTable->setMinimumHeight(STAT_TABLE_BASE_HEIGHT);
}
void QmitkImageStatisticsView::Activated()
{
}
void QmitkImageStatisticsView::Deactivated()
{
}
void QmitkImageStatisticsView::Visible()
{
m_Visible = true;
mitk::IRenderWindowPart* renderWindow = GetRenderWindowPart();
if (renderWindow)
{
itk::ReceptorMemberCommand<QmitkImageStatisticsView>::Pointer cmdTimeEvent =
itk::ReceptorMemberCommand<QmitkImageStatisticsView>::New();
cmdTimeEvent->SetCallbackFunction(this, &QmitkImageStatisticsView::OnTimeChanged);
// It is sufficient to add the observer to the axial render window since the GeometryTimeEvent
// is always triggered by all views.
m_TimeObserverTag = renderWindow->GetQmitkRenderWindow("axial")->
GetSliceNavigationController()->
AddObserver(mitk::SliceNavigationController::GeometryTimeEvent(nullptr, 0), cmdTimeEvent);
}
if (m_DataNodeSelectionChanged)
{
if (this->IsCurrentSelectionValid())
{
this->SelectionChanged(this->GetCurrentSelection());
}
else
{
this->SelectionChanged(this->GetDataManagerSelection());
}
m_DataNodeSelectionChanged = false;
}
}
void QmitkImageStatisticsView::Hidden()
{
m_Visible = false;
// The slice navigation controller observer is removed here instead of in the destructor.
// If it was called in the destructor, the application would freeze because the view's
// destructor gets called after the render windows have been destructed.
if ( m_TimeObserverTag != 0 )
{
mitk::IRenderWindowPart* renderWindow = GetRenderWindowPart();
if (renderWindow)
{
renderWindow->GetQmitkRenderWindow("axial")->GetSliceNavigationController()->
RemoveObserver( m_TimeObserverTag );
}
m_TimeObserverTag = 0;
}
}
void QmitkImageStatisticsView::SetFocus()
{
}
std::map<double, double> QmitkImageStatisticsView::ConvertHistogramToMap(itk::Statistics::Histogram<double>::ConstPointer histogram) const
{
std::map<double, double> histogramMap;
auto endIt = histogram->End();
auto it = histogram->Begin();
// generating Lists of measurement and frequencies
for (; it != endIt; ++it)
{
double frequency = it.GetFrequency();
double measurement = it.GetMeasurementVector()[0];
histogramMap.emplace(measurement, frequency);
}
return histogramMap;
}
std::vector<double> QmitkImageStatisticsView::ConvertIntensityProfileToVector(mitk::IntensityProfile::ConstPointer intensityProfile) const
{
std::vector<double> intensityProfileList;
auto end = intensityProfile->End();
for (auto it = intensityProfile->Begin(); it != end; ++it)
{
intensityProfileList.push_back(it.GetMeasurementVector()[0]);
}
return intensityProfileList;
}
QString QmitkImageStatisticsView::GetFormattedString(double value, unsigned int decimals) const
{
typedef mitk::ImageStatisticsCalculator::StatisticsContainer::RealType RealType;
RealType maxVal = std::numeric_limits<RealType>::max();
if (value == maxVal)
{
return QString("NA");
}
else
{
return QString("%1").arg(value, 0, 'f', decimals);
}
}
QString QmitkImageStatisticsView::GetFormattedIndex(const vnl_vector<int>& vector) const
{
if (vector.empty()) {
return QString();
}
QString formattedIndex("(");
for (const auto& entry : vector)
{
formattedIndex += QString::number(entry);
formattedIndex += ",";
}
formattedIndex.chop(1);
formattedIndex += ")";
return formattedIndex;
}
diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.h b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.h
index b8080143ab..3e25b81b86 100644
--- a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.h
+++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.h
@@ -1,196 +1,194 @@
/*===================================================================
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 QmitkImageStatisticsView_H__INCLUDED
#define QmitkImageStatisticsView_H__INCLUDED
#include "ui_QmitkImageStatisticsViewControls.h"
// Qmitk includes
#include <QmitkAbstractView.h>
#include "QmitkStepperAdapter.h"
#include "QmitkImageStatisticsCalculationThread.h"
#include <berryIPartListener.h>
// mitk includes
#include "mitkILifecycleAwarePart.h"
#include "mitkPlanarLine.h"
#include <mitkIntensityProfile.h>
#include <berryIPreferences.h>
/*!
\brief QmitkImageStatisticsView is a bundle that allows statistics calculation from images. Three modes
are supported: 1. Statistics of one image, 2. Statistics of an image and a segmentation, 3. Statistics
of an image and a Planar Figure. The statistics calculation is realized in a seperate thread to keep the
gui accessable during calculation.
\ingroup Plugins/org.mitk.gui.qt.measurementtoolbox
*/
class QmitkImageStatisticsView : public QmitkAbstractView, public mitk::ILifecycleAwarePart, public berry::IPartListener
{
Q_OBJECT
private:
/*!
\ Convenient typedefs */
typedef mitk::DataStorage::SetOfObjects ConstVector;
typedef ConstVector::ConstPointer ConstVectorPointer;
typedef ConstVector::ConstIterator ConstVectorIterator;
typedef std::map< mitk::Image *, mitk::ImageStatisticsCalculator::Pointer > ImageStatisticsMapType;
typedef QList<mitk::DataNode*> SelectedDataNodeVectorType;
typedef itk::SimpleMemberCommand< QmitkImageStatisticsView > ITKCommandType;
std::map<double, double> ConvertHistogramToMap(itk::Statistics::Histogram<double>::ConstPointer histogram) const;
std::vector<double> ConvertIntensityProfileToVector(mitk::IntensityProfile::ConstPointer intensityProfile) const;
- std::vector<QString> AssembleStatisticsIntoVector(mitk::ImageStatisticsCalculator::StatisticsContainer::ConstPointer statistics, mitk::Image::ConstPointer image) const;
+ std::vector<QString> AssembleStatisticsIntoVector(mitk::ImageStatisticsCalculator::StatisticsContainer::ConstPointer statistics, mitk::Image::ConstPointer image, bool noVolumeDefined=false) const;
QString GetFormattedIndex(const vnl_vector<int>& vector) const;
QString GetFormattedString(double value, unsigned int decimals) const;
public:
/*!
\brief default constructor */
- QmitkImageStatisticsView(QObject *parent=nullptr, const char *name=nullptr);
+ QmitkImageStatisticsView(QObject *parent = nullptr, const char *name = nullptr);
/*!
\brief default destructor */
virtual ~QmitkImageStatisticsView();
/*!
\brief method for creating the widget containing the application controls, like sliders, buttons etc. */
virtual void CreateQtPartControl(QWidget *parent) override;
/*!
\brief method for creating the connections of main and control widget */
virtual void CreateConnections();
/*!
\brief Is called from the selection mechanism once the data manager selection has changed*/
void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList<mitk::DataNode::Pointer> &selectedNodes) override;
static const std::string VIEW_ID;
static const int STAT_TABLE_BASE_HEIGHT;
public slots:
- /** \brief Called when the statistics update is finished, sets the results to GUI.*/
- void OnThreadedStatisticsCalculationEnds();
+ /** \brief Called when the statistics update is finished, sets the results to GUI.*/
+ void OnThreadedStatisticsCalculationEnds();
- /** \brief Update bin size for histogram resolution. */
- void OnHistogramBinSizeBoxValueChanged();
+ /** \brief Update bin size for histogram resolution. */
+ void OnHistogramBinSizeBoxValueChanged();
- protected slots:
- /** \brief Saves the histogram to the clipboard */
- void OnClipboardHistogramButtonClicked();
- /** \brief Saves the statistics to the clipboard */
- void OnClipboardStatisticsButtonClicked();
- /** \brief Indicates if zeros should be excluded from statistics calculation */
- void OnIgnoreZerosCheckboxClicked( );
- /** \brief Checks if update is possible and calls StatisticsUpdate() possible */
- void RequestStatisticsUpdate();
- /** \brief Jump to coordinates stored in the double clicked cell */
- void JumpToCoordinates(int row, int col);
- /** \brief Toogle GUI elements if histogram default bin size checkbox value changed. */
- void OnDefaultBinSizeBoxChanged();
+ protected slots:
+ /** \brief Saves the histogram to the clipboard */
+ void OnClipboardHistogramButtonClicked();
+ /** \brief Saves the statistics to the clipboard */
+ void OnClipboardStatisticsButtonClicked();
+ /** \brief Indicates if zeros should be excluded from statistics calculation */
+ void OnIgnoreZerosCheckboxClicked();
+ /** \brief Checks if update is possible and calls StatisticsUpdate() possible */
+ void RequestStatisticsUpdate();
+ /** \brief Jump to coordinates stored in the double clicked cell */
+ void JumpToCoordinates(int row, int col);
+ /** \brief Toogle GUI elements if histogram default bin size checkbox value changed. */
+ void OnDefaultBinSizeBoxChanged();
- void OnShowSubchartBoxChanged();
+ void OnShowSubchartBoxChanged();
- void OnBarRadioButtonSelected();
+ void OnBarRadioButtonSelected();
- void OnLineRadioButtonSelected();
+ void OnLineRadioButtonSelected();
- void OnPageSuccessfullyLoaded();
+ void OnPageSuccessfullyLoaded();
signals:
- /** \brief Method to set the data to the member and start the threaded statistics update */
- void StatisticsUpdate();
+ /** \brief Method to set the data to the member and start the threaded statistics update */
+ void StatisticsUpdate();
protected:
/** \brief Writes the calculated statistics to the GUI */
void FillStatisticsTableView(const std::vector<mitk::ImageStatisticsCalculator::StatisticsContainer::Pointer> &statistics,
- const mitk::Image *image );
+ const mitk::Image *image);
- std::vector<QString> AssembleStatisticsIntoVectorForPlanarFigure(mitk::IntensityProfile::ConstPointer intensityProfile, mitk::Image::ConstPointer image);
-
- void FillLinearProfileStatisticsTableView(mitk::IntensityProfile::ConstPointer intensityProfile, mitk::Image::ConstPointer image);
+ void FillLinearProfileStatisticsTableView(mitk::ImageStatisticsCalculator::StatisticsContainer::ConstPointer statistics, const mitk::Image *image);
/** \brief Removes statistics from the GUI */
void InvalidateStatisticsTableView();
/** \brief Recalculate statistics for currently selected image and mask and
* update the GUI. */
void UpdateStatistics();
virtual void Activated() override;
virtual void Deactivated() override;
virtual void Visible() override;
virtual void Hidden() override;
virtual void SetFocus() override;
/** \brief Method called when itkModifiedEvent is called by selected data. */
void SelectedDataModified();
/** \brief Method called when the data manager selection changes */
void SelectionChanged(const QList<mitk::DataNode::Pointer> &selectedNodes);
/** \brief Method called to remove old selection when a new selection is present */
void ReinitData();
/** \brief writes the statistics to the gui*/
void WriteStatisticsToGUI();
void NodeRemoved(const mitk::DataNode *node) override;
/** \brief Is called right before the view closes (before the destructor) */
- virtual void PartClosed(const berry::IWorkbenchPartReference::Pointer& ) override;
+ virtual void PartClosed(const berry::IWorkbenchPartReference::Pointer&) override;
/** \brief Is called from the image navigator once the time step has changed */
- void OnTimeChanged( const itk::EventObject& );
+ void OnTimeChanged(const itk::EventObject&);
/** \brief Required for berry::IPartListener */
virtual Events::Types GetPartEventTypes() const override { return Events::CLOSED; }
// member variables
Ui::QmitkImageStatisticsViewControls *m_Controls;
// if you have a planar figure selected, the statistics values will be saved in this one.
std::vector<QString> m_PlanarFigureStatistics;
QmitkImageStatisticsCalculationThread* m_CalculationThread;
QmitkStepperAdapter* m_TimeStepperAdapter;
unsigned int m_CurrentTime;
QString m_Clipboard;
// Image and mask data
mitk::Image* m_SelectedImage;
mitk::Image* m_SelectedImageMask;
mitk::PlanarFigure* m_SelectedPlanarFigure;
// observer tags
long m_ImageObserverTag;
long m_ImageMaskObserverTag;
long m_PlanarFigureObserverTag;
long m_TimeObserverTag;
SelectedDataNodeVectorType m_SelectedDataNodes;
bool m_CurrentStatisticsValid;
bool m_StatisticsUpdatePending;
bool m_StatisticsIntegrationPending;
bool m_DataNodeSelectionChanged;
bool m_Visible;
double m_HistogramBinSize;
std::vector<mitk::Point3D> m_WorldMinList;
std::vector<mitk::Point3D> m_WorldMaxList;
berry::IPreferences::Pointer m_StylePref;
};
#endif // QmitkImageStatisticsView_H__INCLUDED