QmitkAdaptiveRegionGrowingToolGUI.cpp

Go to the documentation of this file.

/*===================================================================

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 "QmitkAdaptiveRegionGrowingToolGUI.h"

#include "QmitkStdMultiWidget.h"

#include <qmessagebox.h>

#include "mitkITKImageImport.h"
#include "mitkImageAccessByItk.h"
#include "mitkImageTimeSelector.h"
#include "mitkNodePredicateDataType.h"
#include "mitkProperties.h"
#include "mitkTransferFunctionProperty.h"

#include "mitkImageStatisticsHolder.h"

#include "itkMaskImageFilter.h"
#include "itkNumericTraits.h"
#include <itkBinaryThresholdImageFilter.h>
#include <itkConnectedAdaptiveThresholdImageFilter.h>
#include <itkImageIterator.h>
#include <itkMinimumMaximumImageCalculator.h>

#include "QmitkConfirmSegmentationDialog.h"
#include "itkOrImageFilter.h"
#include "mitkImageCast.h"

#include "mitkImagePixelReadAccessor.h"
#include "mitkPixelTypeMultiplex.h"

#include "mitkImageCast.h"

MITK_TOOL_GUI_MACRO(, QmitkAdaptiveRegionGrowingToolGUI, "")

QmitkAdaptiveRegionGrowingToolGUI::QmitkAdaptiveRegionGrowingToolGUI(QWidget *parent)
  : QmitkToolGUI(),
    m_MultiWidget(nullptr),
    m_DataStorage(nullptr),
    m_UseVolumeRendering(false),
    m_UpdateSuggestedThreshold(true),
    m_SuggestedThValue(0.0)
{
  this->setParent(parent);

  m_Controls.setupUi(this);

  m_Controls.m_ThresholdSlider->setDecimals(1);
  m_Controls.m_ThresholdSlider->setSpinBoxAlignment(Qt::AlignVCenter);

  m_Controls.m_PreviewSlider->setEnabled(false);
  m_Controls.m_PreviewSlider->setSingleStep(0.5);
  // Not yet available
  // m_Controls.m_PreviewSlider->InvertedAppearance(true);

  this->CreateConnections();
  this->SetDataNodeNames("labeledRGSegmentation", "RGResult", "RGFeedbackSurface", "maskedSegmentation");

  connect(this, SIGNAL(NewToolAssociated(mitk::Tool *)), this, SLOT(OnNewToolAssociated(mitk::Tool *)));
}

QmitkAdaptiveRegionGrowingToolGUI::~QmitkAdaptiveRegionGrowingToolGUI()
{
  // Removing the observer of the PointSet node
  if (m_RegionGrow3DTool->GetPointSetNode().IsNotNull())
  {
    m_RegionGrow3DTool->GetPointSetNode()->GetData()->RemoveObserver(m_PointSetAddObserverTag);
    m_RegionGrow3DTool->GetPointSetNode()->GetData()->RemoveObserver(m_PointSetMoveObserverTag);
  }
  this->RemoveHelperNodes();
}

void QmitkAdaptiveRegionGrowingToolGUI::OnNewToolAssociated(mitk::Tool *tool)
{
  m_RegionGrow3DTool = dynamic_cast<mitk::AdaptiveRegionGrowingTool *>(tool);
  if (m_RegionGrow3DTool.IsNotNull())
  {
    SetInputImageNode(this->m_RegionGrow3DTool->GetReferenceData());
    this->m_DataStorage = this->m_RegionGrow3DTool->GetDataStorage();
    this->EnableControls(true);

    // Watch for point added or modified
    itk::SimpleMemberCommand<QmitkAdaptiveRegionGrowingToolGUI>::Pointer pointAddedCommand =
      itk::SimpleMemberCommand<QmitkAdaptiveRegionGrowingToolGUI>::New();
    pointAddedCommand->SetCallbackFunction(this, &QmitkAdaptiveRegionGrowingToolGUI::OnPointAdded);
    m_PointSetAddObserverTag =
      m_RegionGrow3DTool->GetPointSetNode()->GetData()->AddObserver(mitk::PointSetAddEvent(), pointAddedCommand);
    m_PointSetMoveObserverTag =
      m_RegionGrow3DTool->GetPointSetNode()->GetData()->AddObserver(mitk::PointSetMoveEvent(), pointAddedCommand);
  }
  else
  {
    this->EnableControls(false);
  }
}

void QmitkAdaptiveRegionGrowingToolGUI::RemoveHelperNodes()
{
  mitk::DataNode::Pointer imageNode = m_DataStorage->GetNamedNode(m_NAMEFORLABLEDSEGMENTATIONIMAGE);
  if (imageNode.IsNotNull())
  {
    m_DataStorage->Remove(imageNode);
  }

  mitk::DataNode::Pointer maskedSegmentationNode = m_DataStorage->GetNamedNode(m_NAMEFORMASKEDSEGMENTATION);
  if (maskedSegmentationNode.IsNotNull())
  {
    m_DataStorage->Remove(maskedSegmentationNode);
  }
}

void QmitkAdaptiveRegionGrowingToolGUI::CreateConnections()
{
  // Connecting GUI components
  connect((QObject *)(m_Controls.m_pbRunSegmentation), SIGNAL(clicked()), this, SLOT(RunSegmentation()));
  connect(m_Controls.m_PreviewSlider, SIGNAL(valueChanged(double)), this, SLOT(ChangeLevelWindow(double)));
  connect((QObject *)(m_Controls.m_pbConfirmSegementation), SIGNAL(clicked()), this, SLOT(ConfirmSegmentation()));
  connect((QObject *)(m_Controls.m_cbVolumeRendering), SIGNAL(toggled(bool)), this, SLOT(UseVolumeRendering(bool)));
  connect(
    m_Controls.m_ThresholdSlider, SIGNAL(maximumValueChanged(double)), this, SLOT(SetUpperThresholdValue(double)));
  connect(
    m_Controls.m_ThresholdSlider, SIGNAL(minimumValueChanged(double)), this, SLOT(SetLowerThresholdValue(double)));
}

void QmitkAdaptiveRegionGrowingToolGUI::SetDataNodeNames(std::string labledSegmentation,
                                                         std::string binaryImage,
                                                         std::string surface,
                                                         std::string maskedSegmentation)
{
  m_NAMEFORLABLEDSEGMENTATIONIMAGE = labledSegmentation;
  m_NAMEFORBINARYIMAGE = binaryImage;
  m_NAMEFORSURFACE = surface;
  m_NAMEFORMASKEDSEGMENTATION = maskedSegmentation;
}

void QmitkAdaptiveRegionGrowingToolGUI::SetDataStorage(mitk::DataStorage *dataStorage)
{
  m_DataStorage = dataStorage;
}

void QmitkAdaptiveRegionGrowingToolGUI::SetMultiWidget(QmitkStdMultiWidget *multiWidget)
{
  m_MultiWidget = multiWidget;
}

void QmitkAdaptiveRegionGrowingToolGUI::SetInputImageNode(mitk::DataNode *node)
{
  m_InputImageNode = node;
  mitk::Image *inputImage = dynamic_cast<mitk::Image *>(m_InputImageNode->GetData());
  if (inputImage)
  {
    mitk::ScalarType max = inputImage->GetStatistics()->GetScalarValueMax();
    mitk::ScalarType min = inputImage->GetStatistics()->GetScalarValueMin();
    m_Controls.m_ThresholdSlider->setMaximum(max);
    m_Controls.m_ThresholdSlider->setMinimum(min);
    // Just for initialization
    m_Controls.m_ThresholdSlider->setMaximumValue(max);
    m_Controls.m_ThresholdSlider->setMinimumValue(min);
  }
}

template <typename TPixel>
static void AccessPixel(mitk::PixelType /*ptype*/, const mitk::Image::Pointer im, mitk::Point3D p, int &val)
{
  mitk::ImagePixelReadAccessor<TPixel, 3> access(im);
  val = access.GetPixelByWorldCoordinates(p);
}

void QmitkAdaptiveRegionGrowingToolGUI::OnPointAdded()
{
  if (m_RegionGrow3DTool.IsNull())
    return;

  mitk::DataNode *node = m_RegionGrow3DTool->GetPointSetNode();

  if (node != NULL)
  {
    mitk::PointSet::Pointer pointSet = dynamic_cast<mitk::PointSet *>(node->GetData());

    if (pointSet.IsNull())
    {
      QMessageBox::critical(NULL, "QmitkAdaptiveRegionGrowingToolGUI", "PointSetNode does not contain a pointset");
      return;
    }

    m_Controls.m_lblSetSeedpoint->setText("");

    mitk::Image *image = dynamic_cast<mitk::Image *>(m_InputImageNode->GetData());

    mitk::Point3D seedPoint =
      pointSet
        ->GetPointSet(
          mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget1"))->GetTimeStep())
        ->GetPoints()
        ->ElementAt(0);

    if (image->GetGeometry()->IsInside(seedPoint))
      mitkPixelTypeMultiplex3(
        AccessPixel, image->GetChannelDescriptor().GetPixelType(), image, seedPoint, m_SeedpointValue) else return;

    /* In this case the seedpoint is placed e.g. in the lung or bronchialtree
     * The lowerFactor sets the windowsize depending on the regiongrowing direction
     */
    m_CurrentRGDirectionIsUpwards = true;
    if (m_SeedpointValue < -500)
    {
      m_CurrentRGDirectionIsUpwards = false;
    }

    // Initializing the region by the area around the seedpoint
    m_SeedPointValueMean = 0;

    itk::Index<3> currentIndex, runningIndex;
    mitk::ScalarType pixelValues[125];
    unsigned int pos(0);

    image->GetGeometry(0)->WorldToIndex(seedPoint, currentIndex);
    runningIndex = currentIndex;

    for (int i = runningIndex[0] - 2; i <= runningIndex[0] + 2; i++)
    {
      for (int j = runningIndex[1] - 2; j <= runningIndex[1] + 2; j++)
      {
        for (int k = runningIndex[2] - 2; k <= runningIndex[2] + 2; k++)
        {
          currentIndex[0] = i;
          currentIndex[1] = j;
          currentIndex[2] = k;

          if (image->GetGeometry()->IsIndexInside(currentIndex))
          {
            int component = 0;
            m_InputImageNode->GetIntProperty("Image.Displayed Component", component);
            mitkPixelTypeMultiplex4(mitk::FastSinglePixelAccess,
                                    image->GetChannelDescriptor().GetPixelType(),
                                    image,
                                    NULL,
                                    currentIndex,
                                    pixelValues[pos]);

            pos++;
          }
          else
          {
            pixelValues[pos] = std::numeric_limits<long>::min();
            pos++;
          }
        }
      }
    }

    // Now calculation mean of the pixelValues
    // Now calculation mean of the pixelValues
    unsigned int numberOfValues(0);
    for (auto &pixelValue : pixelValues)
    {
      if (pixelValue > std::numeric_limits<long>::min())
      {
        m_SeedPointValueMean += pixelValue;
        numberOfValues++;
      }
    }
    m_SeedPointValueMean = m_SeedPointValueMean / numberOfValues;

    mitk::ScalarType var = 0;
    if (numberOfValues > 1)
    {
      for (auto &pixelValue : pixelValues)
      {
        if (pixelValue > std::numeric_limits<mitk::ScalarType>::min())
        {
          var += (pixelValue - m_SeedPointValueMean) * (pixelValue - m_SeedPointValueMean);
        }
      }
      var /= numberOfValues - 1;
    }
    mitk::ScalarType stdDev = sqrt(var);

    /*
     * Here the upper- and lower threshold is calculated:
     * The windowSize is 20% of the maximum range of the intensity values existing in the current image
     * If the RG direction is upwards the lower TH is meanSeedValue-0.15*windowSize and upper TH is
     * meanSeedValue+0.85*windowsSize
     * if the RG direction is downwards the lower TH is meanSeedValue-0.85*windowSize and upper TH is
     * meanSeedValue+0.15*windowsSize
    */
    mitk::ScalarType min = image->GetStatistics()->GetScalarValueMin();
    mitk::ScalarType max = image->GetStatistics()->GetScalarValueMax();
    mitk::ScalarType windowSize = max - min;

    windowSize = 0.15 * windowSize;

    if (m_CurrentRGDirectionIsUpwards)
    {
      m_LOWERTHRESHOLD = m_SeedPointValueMean - stdDev;
      m_UPPERTHRESHOLD = m_SeedpointValue + windowSize;
      if (m_UPPERTHRESHOLD > max)
        m_UPPERTHRESHOLD = max;
      m_Controls.m_ThresholdSlider->setMaximumValue(m_UPPERTHRESHOLD);
      m_Controls.m_ThresholdSlider->setMinimumValue(m_LOWERTHRESHOLD);
    }
    else
    {
      m_UPPERTHRESHOLD = m_SeedPointValueMean;
      if (m_SeedpointValue > m_SeedPointValueMean)
        m_UPPERTHRESHOLD = m_SeedpointValue;
      m_LOWERTHRESHOLD = m_SeedpointValue - windowSize;
      if (m_LOWERTHRESHOLD < min)
        m_LOWERTHRESHOLD = min;
      m_Controls.m_ThresholdSlider->setMinimumValue(m_LOWERTHRESHOLD);
      m_Controls.m_ThresholdSlider->setMaximumValue(m_UPPERTHRESHOLD);
    }
  }
}

void QmitkAdaptiveRegionGrowingToolGUI::RunSegmentation()
{
  if (m_InputImageNode.IsNull())
  {
    QMessageBox::information(NULL, "Adaptive Region Growing functionality", "Please specify the image in Datamanager!");
    return;
  }

  mitk::DataNode::Pointer node = m_RegionGrow3DTool->GetPointSetNode();

  if (node.IsNull())
  {
    QMessageBox::information(NULL, "Adaptive Region Growing functionality", "Please insert a seed point inside the "
                                                                            "image.\n\nFirst press the \"Define Seed "
                                                                            "Point\" button,\nthen click left mouse "
                                                                            "button inside the image.");
    return;
  }

  // safety if no pointSet or pointSet empty
  mitk::PointSet::Pointer seedPointSet = dynamic_cast<mitk::PointSet *>(node->GetData());
  if (seedPointSet.IsNull())
  {
    m_Controls.m_pbRunSegmentation->setEnabled(true);
    QMessageBox::information(
      NULL, "Adaptive Region Growing functionality", "The seed point is empty! Please choose a new seed point.");
    return;
  }

  int timeStep =
    mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget1"))->GetTimeStep();

  if (!(seedPointSet->GetSize(timeStep)))
  {
    m_Controls.m_pbRunSegmentation->setEnabled(true);
    QMessageBox::information(
      NULL, "Adaptive Region Growing functionality", "The seed point is empty! Please choose a new seed point.");
    return;
  }

  QApplication::setOverrideCursor(QCursor(Qt::WaitCursor));

  mitk::PointSet::PointType seedPoint = seedPointSet->GetPointSet(timeStep)->GetPoints()->Begin().Value();

  mitk::Image::Pointer orgImage = dynamic_cast<mitk::Image *>(m_InputImageNode->GetData());

  if (orgImage.IsNotNull())
  {
    if (orgImage->GetDimension() == 4)
    {
      mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New();
      timeSelector->SetInput(orgImage);
      timeSelector->SetTimeNr(timeStep);
      timeSelector->UpdateLargestPossibleRegion();
      mitk::Image *timedImage = timeSelector->GetOutput();
      AccessByItk_2(timedImage, StartRegionGrowing, timedImage->GetGeometry(), seedPoint);
    }
    else if (orgImage->GetDimension() == 3)
    {
      // QApplication::setOverrideCursor(QCursor(Qt::WaitCursor)); //set the cursor to waiting
      AccessByItk_2(orgImage, StartRegionGrowing, orgImage->GetGeometry(), seedPoint);
      // QApplication::restoreOverrideCursor();//reset cursor
    }
    else
    {
      QApplication::restoreOverrideCursor(); // reset cursor
      QMessageBox::information(
        NULL, "Adaptive Region Growing functionality", "Only images of dimension 3 or 4 can be processed!");
      return;
    }
  }
  EnableControls(true); // Segmentation ran successfully, so enable all controls.
  node->SetVisibility(true);
  QApplication::restoreOverrideCursor(); // reset cursor
}

template <typename TPixel, unsigned int VImageDimension>
void QmitkAdaptiveRegionGrowingToolGUI::StartRegionGrowing(itk::Image<TPixel, VImageDimension> *itkImage,
                                                           mitk::BaseGeometry *imageGeometry,
                                                           mitk::PointSet::PointType seedPoint)
{
  typedef itk::Image<TPixel, VImageDimension> InputImageType;
  typedef typename InputImageType::IndexType IndexType;
  typedef itk::ConnectedAdaptiveThresholdImageFilter<InputImageType, InputImageType> RegionGrowingFilterType;
  typename RegionGrowingFilterType::Pointer regionGrower = RegionGrowingFilterType::New();
  typedef itk::MinimumMaximumImageCalculator<InputImageType> MinMaxValueFilterType;
  typedef itk::BinaryThresholdImageFilter<InputImageType, InputImageType> ThresholdFilterType;
  typedef itk::MaskImageFilter<InputImageType, InputImageType, InputImageType> MaskImageFilterType;

  if (!imageGeometry->IsInside(seedPoint))
  {
    QApplication::restoreOverrideCursor(); // reset cursor to be able to click ok with the regular mouse cursor
    QMessageBox::information(NULL,
                             "Segmentation functionality",
                             "The seed point is outside of the image! Please choose a position inside the image!");
    return;
  }

  IndexType seedIndex;
  imageGeometry->WorldToIndex(seedPoint, seedIndex); // convert world coordinates to image indices

  if (m_SeedpointValue > m_UPPERTHRESHOLD || m_SeedpointValue < m_LOWERTHRESHOLD)
  {
    QApplication::restoreOverrideCursor(); // reset cursor to be able to click ok with the regular mouse cursor
    QMessageBox::information(
      NULL,
      "Segmentation functionality",
      "The seed point is outside the defined thresholds! Please set a new seed point or adjust the thresholds.");
    MITK_INFO << "Mean: " << m_SeedPointValueMean;
    return;
  }

  // Setting the direction of the regiongrowing. For dark structures e.g. the lung the regiongrowing
  // is performed starting at the upper value going to the lower one
  regionGrower->SetGrowingDirectionIsUpwards(m_CurrentRGDirectionIsUpwards);
  regionGrower->SetInput(itkImage);
  regionGrower->AddSeed(seedIndex);
  // In some cases we have to subtract 1 for the lower threshold and add 1 to the upper.
  // Otherwise no region growing is done. Maybe a bug in the ConnectiveAdaptiveThresholdFilter
  regionGrower->SetLower(m_LOWERTHRESHOLD - 1);
  regionGrower->SetUpper(m_UPPERTHRESHOLD + 1);

  try
  {
    regionGrower->Update();
  }
  catch (itk::ExceptionObject &exc)
  {
    QMessageBox errorInfo;
    errorInfo.setWindowTitle("Adaptive RG Segmentation Functionality");
    errorInfo.setIcon(QMessageBox::Critical);
    errorInfo.setText("An error occurred during region growing!");
    errorInfo.setDetailedText(exc.what());
    errorInfo.exec();
    return; // can't work
  }
  catch (...)
  {
    QMessageBox::critical(NULL, "Adaptive RG Segmentation Functionality", "An error occurred during region growing!");
    return;
  }

  mitk::Image::Pointer resultImage = mitk::ImportItkImage(regionGrower->GetOutput())->Clone();
  // initialize slider
  m_Controls.m_PreviewSlider->setMinimum(m_LOWERTHRESHOLD);

  mitk::ScalarType max = m_SeedpointValue + resultImage->GetStatistics()->GetScalarValueMax();
  if (max < m_UPPERTHRESHOLD)
    m_Controls.m_PreviewSlider->setMaximum(max);
  else
    m_Controls.m_PreviewSlider->setMaximum(m_UPPERTHRESHOLD);

  this->m_DetectedLeakagePoint = regionGrower->GetLeakagePoint();

  if (m_CurrentRGDirectionIsUpwards)
  {
    m_Controls.m_PreviewSlider->setValue(m_SeedPointValueMean - 1);
  }
  else
  {
    m_Controls.m_PreviewSlider->setValue(m_SeedPointValueMean + 1);
  }
  this->m_SliderInitialized = true;

  // create new node and then delete the old one if there is one
  mitk::DataNode::Pointer newNode = mitk::DataNode::New();
  newNode->SetData(resultImage);

  // set some properties
  newNode->SetProperty("name", mitk::StringProperty::New(m_NAMEFORLABLEDSEGMENTATIONIMAGE));
  newNode->SetProperty("helper object", mitk::BoolProperty::New(true));
  newNode->SetProperty("color", mitk::ColorProperty::New(0.0, 1.0, 0.0));
  newNode->SetProperty("layer", mitk::IntProperty::New(1));
  newNode->SetProperty("opacity", mitk::FloatProperty::New(0.7));

  // delete the old image, if there was one:
  mitk::DataNode::Pointer binaryNode = m_DataStorage->GetNamedNode(m_NAMEFORLABLEDSEGMENTATIONIMAGE);
  m_DataStorage->Remove(binaryNode);

  // now add result to data tree
  m_DataStorage->Add(newNode, m_InputImageNode);

  typename InputImageType::Pointer inputImageItk;
  mitk::CastToItkImage<InputImageType>(resultImage, inputImageItk);
  // volume rendering preview masking
  typename ThresholdFilterType::Pointer thresholdFilter = ThresholdFilterType::New();
  thresholdFilter->SetInput(inputImageItk);
  thresholdFilter->SetInsideValue(1);
  thresholdFilter->SetOutsideValue(0);

  double sliderVal = this->m_Controls.m_PreviewSlider->value();
  if (m_CurrentRGDirectionIsUpwards)
  {
    thresholdFilter->SetLowerThreshold(sliderVal);
    thresholdFilter->SetUpperThreshold(itk::NumericTraits<TPixel>::max());
  }
  else
  {
    thresholdFilter->SetLowerThreshold(itk::NumericTraits<TPixel>::min());
    thresholdFilter->SetUpperThreshold(sliderVal);
  }
  thresholdFilter->SetInPlace(false);

  typename MaskImageFilterType::Pointer maskFilter = MaskImageFilterType::New();
  maskFilter->SetInput(inputImageItk);
  maskFilter->SetInPlace(false);
  maskFilter->SetMaskImage(thresholdFilter->GetOutput());
  maskFilter->SetOutsideValue(0);
  maskFilter->UpdateLargestPossibleRegion();

  mitk::Image::Pointer mitkMask;
  mitk::CastToMitkImage<InputImageType>(maskFilter->GetOutput(), mitkMask);
  mitk::DataNode::Pointer maskedNode = mitk::DataNode::New();
  maskedNode->SetData(mitkMask);

  // set some properties
  maskedNode->SetProperty("name", mitk::StringProperty::New(m_NAMEFORMASKEDSEGMENTATION));
  maskedNode->SetProperty("helper object", mitk::BoolProperty::New(true));
  maskedNode->SetProperty("color", mitk::ColorProperty::New(0.0, 1.0, 0.0));
  maskedNode->SetProperty("layer", mitk::IntProperty::New(1));
  maskedNode->SetProperty("opacity", mitk::FloatProperty::New(0.0));

  // delete the old image, if there was one:
  mitk::DataNode::Pointer deprecatedMask = m_DataStorage->GetNamedNode(m_NAMEFORMASKEDSEGMENTATION);
  m_DataStorage->Remove(deprecatedMask);

  // now add result to data tree
  m_DataStorage->Add(maskedNode, m_InputImageNode);

  this->InitializeLevelWindow();

  if (m_UseVolumeRendering)
    this->EnableVolumeRendering(true);

  m_UpdateSuggestedThreshold = true; // reset first stored threshold value
  // Setting progress to finished
  mitk::ProgressBar::GetInstance()->Progress(357);
  mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}

void QmitkAdaptiveRegionGrowingToolGUI::InitializeLevelWindow()
{
  // get the preview from the datatree
  mitk::DataNode::Pointer newNode = m_DataStorage->GetNamedNode(m_NAMEFORLABLEDSEGMENTATIONIMAGE);

  mitk::LevelWindow tempLevelWindow;
  newNode->GetLevelWindow(tempLevelWindow, NULL, "levelwindow");

  mitk::ScalarType *level = new mitk::ScalarType(0.0);
  mitk::ScalarType *window = new mitk::ScalarType(1.0);

  int upper;
  if (m_CurrentRGDirectionIsUpwards)
  {
    upper = m_UPPERTHRESHOLD - m_SeedpointValue;
  }
  else
  {
    upper = m_SeedpointValue - m_LOWERTHRESHOLD;
  }

  tempLevelWindow.SetRangeMinMax(mitk::ScalarType(0), mitk::ScalarType(upper));

  // get the suggested threshold from the detected leakage-point and adjust the slider

  if (m_CurrentRGDirectionIsUpwards)
  {
    this->m_Controls.m_PreviewSlider->setValue(m_SeedpointValue);
    *level = m_UPPERTHRESHOLD - (m_SeedpointValue) + 0.5;
  }
  else
  {
    this->m_Controls.m_PreviewSlider->setValue(m_SeedpointValue);
    *level = (m_SeedpointValue)-m_LOWERTHRESHOLD + 0.5;
  }

  tempLevelWindow.SetLevelWindow(*level, *window);
  newNode->SetLevelWindow(tempLevelWindow, NULL, "levelwindow");
  // update the widgets
  mitk::RenderingManager::GetInstance()->RequestUpdateAll();

  m_SliderInitialized = true;

  // inquiry need to fix bug#1828
  static int lastSliderPosition = 0;
  if ((this->m_SeedpointValue + this->m_DetectedLeakagePoint - 1) == lastSliderPosition)
  {
    this->ChangeLevelWindow(lastSliderPosition);
  }
  lastSliderPosition = this->m_SeedpointValue + this->m_DetectedLeakagePoint - 1;

  if (m_MultiWidget)
  {
    this->m_MultiWidget->levelWindowWidget->GetManager()->SetAutoTopMostImage(false);
    this->m_MultiWidget->levelWindowWidget->GetManager()->SetLevelWindowProperty(
      static_cast<mitk::LevelWindowProperty *>(newNode->GetProperty("levelwindow")));
  }

  if (m_UseVolumeRendering)
    this->UpdateVolumeRenderingThreshold((int)(*level + 0.5)); // lower threshold for labeled image
}

void QmitkAdaptiveRegionGrowingToolGUI::ChangeLevelWindow(double newValue)
{
  if (m_SliderInitialized)
  {
    // do nothing, if no preview exists
    mitk::DataNode::Pointer newNode = m_DataStorage->GetNamedNode(m_NAMEFORLABLEDSEGMENTATIONIMAGE);
    if (newNode.IsNull())
      return;

    mitk::LevelWindow tempLevelWindow;

    newNode->GetLevelWindow(tempLevelWindow, NULL, "levelwindow"); // get the levelWindow associated with the preview

    mitk::ScalarType level; // = this->m_UPPERTHRESHOLD - newValue + 0.5;
    mitk::ScalarType *window = new mitk::ScalarType(1);

    // adjust the levelwindow according to the position of the slider (newvalue)
    if (m_CurrentRGDirectionIsUpwards)
    {
      level = m_UPPERTHRESHOLD - newValue + 0.5;
      tempLevelWindow.SetLevelWindow(level, *window);
    }
    else
    {
      level = newValue - m_LOWERTHRESHOLD + 0.5;
      tempLevelWindow.SetLevelWindow(level, *window);
    }

    newNode->SetLevelWindow(tempLevelWindow, NULL, "levelwindow");

    if (m_UseVolumeRendering)
      this->UpdateVolumeRenderingThreshold((int)(level - 0.5)); // lower threshold for labeled image

    newNode->SetVisibility(true);
    mitk::RenderingManager::GetInstance()->RequestUpdateAll();
  }
}

void QmitkAdaptiveRegionGrowingToolGUI::DecreaseSlider()
{
  // moves the slider one step to the left, when the "-"-button is pressed
  if (this->m_Controls.m_PreviewSlider->value() != this->m_Controls.m_PreviewSlider->minimum())
  {
    int newValue = this->m_Controls.m_PreviewSlider->value() - 1;
    this->ChangeLevelWindow(newValue);
    this->m_Controls.m_PreviewSlider->setValue(newValue);
  }
}

void QmitkAdaptiveRegionGrowingToolGUI::IncreaseSlider()
{
  // moves the slider one step to the right, when the "+"-button is pressed
  if (this->m_Controls.m_PreviewSlider->value() != this->m_Controls.m_PreviewSlider->maximum())
  {
    int newValue = this->m_Controls.m_PreviewSlider->value() + 1;
    this->ChangeLevelWindow(newValue);
    this->m_Controls.m_PreviewSlider->setValue(newValue);
  }
}

void QmitkAdaptiveRegionGrowingToolGUI::ConfirmSegmentation()
{
  // get image node
  if (m_InputImageNode.IsNull())
  {
    QMessageBox::critical(NULL, "Adaptive region growing functionality", "Please specify the image in Datamanager!");
    return;
  }
  // get image data
  mitk::Image::Pointer orgImage = dynamic_cast<mitk::Image *>(m_InputImageNode->GetData());
  if (orgImage.IsNull())
  {
    QMessageBox::critical(NULL, "Adaptive region growing functionality", "No Image found!");
    return;
  }
  // get labeled segmentation
  mitk::Image::Pointer labeledSeg =
    (mitk::Image *)m_DataStorage->GetNamedObject<mitk::Image>(m_NAMEFORLABLEDSEGMENTATIONIMAGE);
  if (labeledSeg.IsNull())
  {
    QMessageBox::critical(NULL, "Adaptive region growing functionality", "No Segmentation Preview found!");
    return;
  }

  mitk::DataNode::Pointer newNode = m_DataStorage->GetNamedNode(m_NAMEFORLABLEDSEGMENTATIONIMAGE);
  if (newNode.IsNull())
    return;

  QmitkConfirmSegmentationDialog dialog;
  QString segName = QString::fromStdString(m_RegionGrow3DTool->GetCurrentSegmentationName());

  dialog.SetSegmentationName(segName);
  int result = dialog.exec();

  switch (result)
  {
    case QmitkConfirmSegmentationDialog::CREATE_NEW_SEGMENTATION:
      m_RegionGrow3DTool->SetOverwriteExistingSegmentation(false);
      break;
    case QmitkConfirmSegmentationDialog::OVERWRITE_SEGMENTATION:
      m_RegionGrow3DTool->SetOverwriteExistingSegmentation(true);
      break;
    case QmitkConfirmSegmentationDialog::CANCEL_SEGMENTATION:
      return;
  }

  mitk::Image::Pointer img = dynamic_cast<mitk::Image *>(newNode->GetData());
  AccessByItk(img, ITKThresholding);

  // disable volume rendering preview after the segmentation node was created
  this->EnableVolumeRendering(false);
  newNode->SetVisibility(false);
  m_Controls.m_cbVolumeRendering->setChecked(false);
  // TODO disable slider etc...

  if (m_RegionGrow3DTool.IsNotNull())
  {
    m_RegionGrow3DTool->ConfirmSegmentation();
  }
}

template <typename TPixel, unsigned int VImageDimension>
void QmitkAdaptiveRegionGrowingToolGUI::ITKThresholding(itk::Image<TPixel, VImageDimension> *itkImage)
{
  mitk::Image::Pointer originalSegmentation =
    dynamic_cast<mitk::Image *>(this->m_RegionGrow3DTool->GetTargetSegmentationNode()->GetData());

  int timeStep =
    mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget1"))->GetTimeStep();

  if (originalSegmentation)
  {
    typedef itk::Image<TPixel, VImageDimension> InputImageType;
    typedef itk::Image<mitk::Tool::DefaultSegmentationDataType, VImageDimension> SegmentationType;

    // select single 3D volume if we have more than one time step
    typename SegmentationType::Pointer originalSegmentationInITK = SegmentationType::New();
    if (originalSegmentation->GetTimeGeometry()->CountTimeSteps() > 1)
    {
      mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New();
      timeSelector->SetInput(originalSegmentation);
      timeSelector->SetTimeNr(timeStep);
      timeSelector->UpdateLargestPossibleRegion();
      CastToItkImage(timeSelector->GetOutput(), originalSegmentationInITK);
    }
    else // use original
    {
      CastToItkImage(originalSegmentation, originalSegmentationInITK);
    }

    // Fill current preiview image in segmentation image
    originalSegmentationInITK->FillBuffer(0);
    itk::ImageRegionIterator<SegmentationType> itOutput(originalSegmentationInITK,
                                                        originalSegmentationInITK->GetLargestPossibleRegion());
    itk::ImageRegionIterator<InputImageType> itInput(itkImage, itkImage->GetLargestPossibleRegion());
    itOutput.GoToBegin();
    itInput.GoToBegin();

    // calculate threhold from slider value
    int currentTreshold = 0;
    if (m_CurrentRGDirectionIsUpwards)
    {
      currentTreshold = m_UPPERTHRESHOLD - m_Controls.m_PreviewSlider->value() + 1;
    }
    else
    {
      currentTreshold = m_Controls.m_PreviewSlider->value() - m_LOWERTHRESHOLD;
    }

    // iterate over image and set pixel in segmentation according to thresholded labeled image
    while (!itOutput.IsAtEnd() && !itInput.IsAtEnd())
    {
      // Use threshold slider to determine if pixel is set to 1
      if (itInput.Value() != 0 && itInput.Value() >= currentTreshold)
      {
        itOutput.Set(1);
      }

      ++itOutput;
      ++itInput;
    }

    // combine current working segmentation image with our region growing result
    originalSegmentation->SetVolume((void *)(originalSegmentationInITK->GetPixelContainer()->GetBufferPointer()),
                                    timeStep);

    originalSegmentation->Modified();
    mitk::RenderingManager::GetInstance()->RequestUpdateAll();
  }
}

void QmitkAdaptiveRegionGrowingToolGUI::EnableControls(bool enable)
{
  if (m_RegionGrow3DTool.IsNull())
    return;

  // Check if seed point is already set, if not leave RunSegmentation disabled
  // if even m_DataStorage is NULL leave node NULL
  mitk::DataNode::Pointer node = m_RegionGrow3DTool->GetPointSetNode();
  if (node.IsNull())
  {
    this->m_Controls.m_pbRunSegmentation->setEnabled(false);
  }
  else
  {
    this->m_Controls.m_pbRunSegmentation->setEnabled(enable);
  }

  // Check if a segmentation exists, if not leave segmentation dependent disabled.
  // if even m_DataStorage is NULL leave node NULL
  node = m_DataStorage ? m_DataStorage->GetNamedNode(m_NAMEFORLABLEDSEGMENTATIONIMAGE) : NULL;
  if (node.IsNull())
  {
    this->m_Controls.m_PreviewSlider->setEnabled(false);
    this->m_Controls.m_pbConfirmSegementation->setEnabled(false);
  }
  else
  {
    this->m_Controls.m_PreviewSlider->setEnabled(enable);
    this->m_Controls.m_pbConfirmSegementation->setEnabled(enable);
  }

  this->m_Controls.m_cbVolumeRendering->setEnabled(enable);
}

void QmitkAdaptiveRegionGrowingToolGUI::EnableVolumeRendering(bool enable)
{
  mitk::DataNode::Pointer node = m_DataStorage->GetNamedNode(m_NAMEFORMASKEDSEGMENTATION);

  if (node.IsNull())
    return;

  if (m_MultiWidget)
    m_MultiWidget->SetWidgetPlanesVisibility(!enable);

  if (enable)
  {
    node->SetBoolProperty("volumerendering", enable);
    node->SetBoolProperty("volumerendering.uselod", true);
  }
  else
  {
    node->SetBoolProperty("volumerendering", enable);
  }

  double val = this->m_Controls.m_PreviewSlider->value();
  this->ChangeLevelWindow(val);

  mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}

void QmitkAdaptiveRegionGrowingToolGUI::UpdateVolumeRenderingThreshold(int thValue)
{
  typedef short PixelType;
  typedef itk::Image<PixelType, 3> InputImageType;
  typedef itk::BinaryThresholdImageFilter<InputImageType, InputImageType> ThresholdFilterType;
  typedef itk::MaskImageFilter<InputImageType, InputImageType, InputImageType> MaskImageFilterType;

  mitk::DataNode::Pointer grownImageNode = m_DataStorage->GetNamedNode(m_NAMEFORLABLEDSEGMENTATIONIMAGE);
  mitk::Image::Pointer grownImage = dynamic_cast<mitk::Image *>(grownImageNode->GetData());

  if (!grownImage)
  {
    MITK_ERROR << "Missing data node for labeled segmentation image.";
    return;
  }

  InputImageType::Pointer itkGrownImage;
  mitk::CastToItkImage(grownImage, itkGrownImage);

  ThresholdFilterType::Pointer thresholdFilter = ThresholdFilterType::New();
  thresholdFilter->SetInput(itkGrownImage);
  thresholdFilter->SetInPlace(false);

  double sliderVal = this->m_Controls.m_PreviewSlider->value();
  PixelType threshold = itk::NumericTraits<PixelType>::min();
  if (m_CurrentRGDirectionIsUpwards)
  {
    threshold = static_cast<PixelType>(m_UPPERTHRESHOLD - sliderVal + 0.5);

    thresholdFilter->SetLowerThreshold(threshold);
    thresholdFilter->SetUpperThreshold(itk::NumericTraits<PixelType>::max());
  }
  else
  {
    threshold = sliderVal - m_LOWERTHRESHOLD + 0.5;

    thresholdFilter->SetLowerThreshold(itk::NumericTraits<PixelType>::min());
    thresholdFilter->SetUpperThreshold(threshold);
  }
  thresholdFilter->UpdateLargestPossibleRegion();

  MaskImageFilterType::Pointer maskFilter = MaskImageFilterType::New();
  maskFilter->SetInput(itkGrownImage);
  maskFilter->SetInPlace(false);
  maskFilter->SetMaskImage(thresholdFilter->GetOutput());
  maskFilter->SetOutsideValue(0);
  maskFilter->UpdateLargestPossibleRegion();

  mitk::Image::Pointer mitkMaskedImage;
  mitk::CastToMitkImage<InputImageType>(maskFilter->GetOutput(), mitkMaskedImage);
  mitk::DataNode::Pointer maskNode = m_DataStorage->GetNamedNode(m_NAMEFORMASKEDSEGMENTATION);
  maskNode->SetData(mitkMaskedImage);
}

void QmitkAdaptiveRegionGrowingToolGUI::UseVolumeRendering(bool on)
{
  m_UseVolumeRendering = on;

  this->EnableVolumeRendering(on);
}

void QmitkAdaptiveRegionGrowingToolGUI::SetLowerThresholdValue(double lowerThreshold)
{
  m_LOWERTHRESHOLD = lowerThreshold;
}

void QmitkAdaptiveRegionGrowingToolGUI::SetUpperThresholdValue(double upperThreshold)
{
  m_UPPERTHRESHOLD = upperThreshold;
}

void QmitkAdaptiveRegionGrowingToolGUI::Deactivated()
{
  // make the segmentation preview node invisible
  mitk::DataNode::Pointer node = m_DataStorage->GetNamedNode(m_NAMEFORLABLEDSEGMENTATIONIMAGE);
  if (node.IsNotNull())
  {
    node->SetVisibility(false);
  }

  // disable volume rendering preview after the segmentation node was created
  this->EnableVolumeRendering(false);
  m_Controls.m_cbVolumeRendering->setChecked(false);
}

void QmitkAdaptiveRegionGrowingToolGUI::Activated()
{
}