void QmitkImageStatisticsView::OnSelectionChanged( std::vector<mitk::DataNode*> nodes )
{
// Clear any unreferenced images
this->RemoveOrphanImages();
if ( !this->IsVisible() )
{
return;
}
// Check if selection makeup consists only of valid nodes:
// One image, segmentation or planarFigure
// One image and one of the other two
bool tooManyNodes( true );
bool invalidNodes( true );
if ( nodes.size() < 3 )
{
tooManyNodes = false;
}
if( !tooManyNodes )
{
unsigned int numberImages = 0;
unsigned int numberSegmentations = 0;
unsigned int numberPlanarFigures = 0;
for ( unsigned int index = 0; index < nodes.size(); index++ )
{
m_SelectedImageMask = dynamic_cast< mitk::Image * >( nodes[ index ]->GetData() );
m_SelectedPlanarFigure = dynamic_cast< mitk::PlanarFigure * >( nodes[ index ]->GetData() );
if ( m_SelectedImageMask != NULL )
{
bool isMask( false );
nodes[ index ]->GetPropertyValue("binary", isMask);
if ( !isMask )
{
numberImages++;
}
else
{
numberSegmentations++;
if ( numberImages != 0 ) // image should be last element
{
std::swap( nodes[ index ], nodes[ index - 1 ] );
}
}
}
else if ( m_SelectedPlanarFigure != NULL )
{
numberPlanarFigures++;
if ( numberImages != 0 ) // image should be last element
{
std::swap( nodes[ index ], nodes[ index - 1 ] );
}
}
}
if ( ( numberPlanarFigures + numberSegmentations + numberImages ) == nodes.size() && //No invalid nodes
( numberPlanarFigures + numberSegmentations ) < 2 && numberImages < 2
// maximum of one image and/or one of either planar figure or segmentation
)
{
invalidNodes = false;
}
}
if ( nodes.empty() || tooManyNodes || invalidNodes )
{
// Nothing to do: invalidate image, clear statistics, histogram, and GUI
m_SelectedImage = NULL;
this->InvalidateStatisticsTableView() ;
m_Controls->m_HistogramWidget->ClearItemModel();
m_Controls->m_LineProfileWidget->ClearItemModel();
m_CurrentStatisticsValid = false;
m_Controls->m_ErrorMessageLabel->hide();
m_Controls->m_SelectedMaskLabel->setText( "None" );
return;
}
// Get selected element
mitk::DataNode *selectedNode = nodes.front();
mitk::Image *selectedImage = dynamic_cast< mitk::Image * >( selectedNode->GetData() );
// Find the next parent/grand-parent node containing an image, if any
mitk::DataStorage::SetOfObjects::ConstPointer parentObjects;
mitk::DataNode *parentNode = NULL;
mitk::Image *parentImage = NULL;
// Possibly previous change listeners
if ( (m_SelectedPlanarFigure != NULL) && (m_PlanarFigureObserverTag >= 0) )
{
m_SelectedPlanarFigure->RemoveObserver( m_PlanarFigureObserverTag );
m_PlanarFigureObserverTag = -1;
}
if ( (m_SelectedImage != NULL) && (m_ImageObserverTag >= 0) )
{
m_SelectedImage->RemoveObserver( m_ImageObserverTag );
m_ImageObserverTag = -1;
}
if ( (m_SelectedImageMask != NULL) && (m_ImageMaskObserverTag >= 0) )
{
m_SelectedImageMask->RemoveObserver( m_ImageMaskObserverTag );
m_ImageMaskObserverTag = -1;
}
// Deselect all images and masks by default
m_SelectedImageNode = NULL;
m_SelectedImage = NULL;
m_SelectedMaskNode = NULL;
m_SelectedImageMask = NULL;
m_SelectedPlanarFigure = NULL;
{
unsigned int parentObjectIndex = 0;
parentObjects = this->GetDefaultDataStorage()->GetSources( selectedNode );
while( parentObjectIndex < parentObjects->Size() )
{
// Use first parent object (if multiple parents are present)
parentNode = parentObjects->ElementAt( parentObjectIndex );
parentImage = dynamic_cast< mitk::Image * >( parentNode->GetData() );
if( parentImage != NULL )
{
break;
}
parentObjectIndex++;
}
}
if ( nodes.size() == 2 )
{
parentNode = nodes.back();
parentImage = dynamic_cast< mitk::Image * >( parentNode->GetData() );
}
if ( parentImage != NULL )
{
m_SelectedImageNode = parentNode;
m_SelectedImage = parentImage;
// Check if a valid mask has been selected (Image or PlanarFigure)
m_SelectedImageMask = dynamic_cast< mitk::Image * >( selectedNode->GetData() );
m_SelectedPlanarFigure = dynamic_cast< mitk::PlanarFigure * >( selectedNode->GetData() );
// Check whether ImageMask is a binary segmentation
if ( (m_SelectedImageMask != NULL) )
{
bool isMask( false );
selectedNode->GetPropertyValue("binary", isMask);
if ( !isMask )
{
m_SelectedImageNode = selectedNode;
m_SelectedImage = selectedImage;
m_SelectedImageMask = NULL;
}
else
{
m_SelectedMaskNode = selectedNode;
}
}
else if ( (m_SelectedPlanarFigure != NULL) )
{
m_SelectedMaskNode = selectedNode;
}
}
else if ( selectedImage != NULL )
{
m_SelectedImageNode = selectedNode;
m_SelectedImage = selectedImage;
}
typedef itk::SimpleMemberCommand< QmitkImageStatisticsView > ITKCommandType;
ITKCommandType::Pointer changeListener;
changeListener = ITKCommandType::New();
changeListener->SetCallbackFunction( this, &QmitkImageStatisticsView::RequestStatisticsUpdate );
// Add change listeners to selected objects
if ( m_SelectedImage != NULL )
{
m_ImageObserverTag = m_SelectedImage->AddObserver(
itk::ModifiedEvent(), changeListener );
}
if ( m_SelectedImageMask != NULL )
{
m_ImageMaskObserverTag = m_SelectedImageMask->AddObserver(
itk::ModifiedEvent(), changeListener );
}
if ( m_SelectedPlanarFigure != NULL )
{
m_PlanarFigureObserverTag = m_SelectedPlanarFigure->AddObserver(
mitk::EndInteractionPlanarFigureEvent(), changeListener );
}
// Clear statistics / histogram GUI if nothing is selected
if ( m_SelectedImage == NULL )
{
// Clear statistics, histogram, and GUI
this->InvalidateStatisticsTableView();
m_Controls->m_HistogramWidget->ClearItemModel();
m_Controls->m_LineProfileWidget->ClearItemModel();
m_CurrentStatisticsValid = false;
m_Controls->m_ErrorMessageLabel->hide();
m_Controls->m_SelectedMaskLabel->setText( "None" );
}
else
{
// Else, request statistics and GUI update
this->RequestStatisticsUpdate();
}
}
void QmitkImageStatisticsView::UpdateStatistics()
{
// Remove any cached images that are no longer referenced elsewhere
this->RemoveOrphanImages();
QmitkStdMultiWidget *multiWidget = this->GetActiveStdMultiWidget();
if ( multiWidget == NULL )
{
return;
}
unsigned int timeStep = multiWidget->GetTimeNavigationController()->GetTime()->GetPos();
if ( m_SelectedImage != NULL )
{
// 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_Controls->m_HistogramWidget->ClearItemModel();
m_CurrentStatisticsValid = false;
return;
}
// Retrieve ImageStatisticsCalculator from has map (or create a new one
// for this image if non-existant)
ImageStatisticsMapType::iterator it =
m_ImageStatisticsMap.find( m_SelectedImage );
if ( it != m_ImageStatisticsMap.end() )
{
m_CurrentStatisticsCalculator = it->second;
MITK_INFO << "Retrieving StatisticsCalculator";
}
else
{
m_CurrentStatisticsCalculator = mitk::ImageStatisticsCalculator::New();
m_CurrentStatisticsCalculator->SetImage( m_SelectedImage );
m_ImageStatisticsMap[m_SelectedImage] = m_CurrentStatisticsCalculator;
MITK_INFO << "Creating StatisticsCalculator";
}
std::string maskName;
std::string maskType;
unsigned int maskDimension;
if ( m_SelectedImageMask != NULL )
{
m_CurrentStatisticsCalculator->SetImageMask( m_SelectedImageMask );
m_CurrentStatisticsCalculator->SetMaskingModeToImage();
maskName = m_SelectedMaskNode->GetName();
maskType = m_SelectedImageMask->GetNameOfClass();
maskDimension = 3;
}
else if ( m_SelectedPlanarFigure != NULL )
{
m_CurrentStatisticsCalculator->SetPlanarFigure( m_SelectedPlanarFigure );
m_CurrentStatisticsCalculator->SetMaskingModeToPlanarFigure();
maskName = m_SelectedMaskNode->GetName();
maskType = m_SelectedPlanarFigure->GetNameOfClass();
maskDimension = 2;
}
else
{
m_CurrentStatisticsCalculator->SetMaskingModeToNone();
maskName = "None";
maskType = "";
maskDimension = 0;
}
if(m_Controls->m_IgnoreZerosCheckbox->isChecked())
{
m_CurrentStatisticsCalculator->SetIgnorePixelValue(0);
m_CurrentStatisticsCalculator->SetDoIgnorePixelValue(true);
}
else
{
m_CurrentStatisticsCalculator->SetDoIgnorePixelValue(false);
}
std::stringstream maskLabel;
maskLabel << maskName;
if ( maskDimension > 0 )
{
maskLabel << " [" << maskDimension << "D " << maskType << "]";
}
m_Controls->m_SelectedMaskLabel->setText( maskLabel.str().c_str() );
bool statisticsChanged = false;
bool statisticsCalculationSuccessful = false;
// Initialize progress bar
mitk::ProgressBar::GetInstance()->AddStepsToDo( 100 );
// Install listener for progress events and initialize progress bar
typedef itk::SimpleMemberCommand< QmitkImageStatisticsView > ITKCommandType;
ITKCommandType::Pointer progressListener;
progressListener = ITKCommandType::New();
progressListener->SetCallbackFunction( this, &QmitkImageStatisticsView::UpdateProgressBar );
unsigned long progressObserverTag = m_CurrentStatisticsCalculator
->AddObserver( itk::ProgressEvent(), progressListener );
// show wait cursor
this->WaitCursorOn();
try
{
// Compute statistics
statisticsChanged =
m_CurrentStatisticsCalculator->ComputeStatistics( timeStep );
statisticsCalculationSuccessful = true;
}
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();
}
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();
}
m_CurrentStatisticsCalculator->RemoveObserver( progressObserverTag );
// Make sure that progress bar closes
mitk::ProgressBar::GetInstance()->Progress( 100 );
// remove wait cursor
this->WaitCursorOff();
if ( statisticsCalculationSuccessful )
{
if ( statisticsChanged )
{
// Do not show any error messages
m_Controls->m_ErrorMessageLabel->hide();
m_CurrentStatisticsValid = true;
}
m_Controls->m_StatisticsWidgetStack->setCurrentIndex( 0 );
m_Controls->m_HistogramWidget->SetHistogramModeToDirectHistogram();
m_Controls->m_HistogramWidget->SetHistogram(
m_CurrentStatisticsCalculator->GetHistogram( timeStep ) );
m_Controls->m_HistogramWidget->UpdateItemModelFromHistogram();
MITK_INFO << "UpdateItemModelFromHistogram()";
this->FillStatisticsTableView(
m_CurrentStatisticsCalculator->GetStatistics( timeStep ),
m_SelectedImage );
}
else
{
m_Controls->m_SelectedMaskLabel->setText( "None" );
// Clear statistics and histogram
this->InvalidateStatisticsTableView();
m_Controls->m_HistogramWidget->ClearItemModel();
m_CurrentStatisticsValid = false;
// If a (non-closed) PlanarFigure is selected, display a line profile widget
if ( m_SelectedPlanarFigure != NULL )
{
// check whether PlanarFigure is initialized
const mitk::Geometry2D *planarFigureGeometry2D = m_SelectedPlanarFigure->GetGeometry2D();
if ( planarFigureGeometry2D == NULL )
{
// Clear statistics, histogram, and GUI
this->InvalidateStatisticsTableView();
m_Controls->m_HistogramWidget->ClearItemModel();
m_Controls->m_LineProfileWidget->ClearItemModel();
m_CurrentStatisticsValid = false;
m_Controls->m_ErrorMessageLabel->hide();
m_Controls->m_SelectedMaskLabel->setText( "None" );
return;
}
// TODO: enable line profile widget
m_Controls->m_StatisticsWidgetStack->setCurrentIndex( 1 );
m_Controls->m_LineProfileWidget->SetImage( m_SelectedImage );
m_Controls->m_LineProfileWidget->SetPlanarFigure( m_SelectedPlanarFigure );
m_Controls->m_LineProfileWidget->UpdateItemModelFromPath();
}
}
}
}
void QmitkImageStatisticsView::UpdateStatistics()
{
mitk::IRenderWindowPart* renderPart = this->GetRenderWindowPart();
if ( renderPart == NULL )
{
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();
std::string maskType = std::string();
std::string featureImageName = std::string();
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 == NULL && 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 == NULL)
{
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 == NULL)
{
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 != NULL && m_SelectedImage == NULL)
{
mitk::DataStorage::SetOfObjects::ConstPointer parentSet = this->GetDataStorage()->GetSources(planarFigureNode);
for (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 == NULL)
{
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 != NULL && 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_Controls->m_JSHistogram->ClearHistogram();
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_HistogramBinSizeLabel->setEnabled(true);
m_Controls->m_InfoLabel->setText(QString(""));
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 != NULL)
{
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(")"));
}
//// 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 );
this->m_CalculationThread->SetHistogramBinSize(m_Controls->m_HistogramBinSizeSpinbox->value());
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;
}
}
