mitkOtsuTool3D.cpp

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

The Medical Imaging Interaction Toolkit (MITK)

Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.

Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.

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

// MITK
#include "mitkOtsuTool3D.h"
#include "mitkImageAccessByItk.h"
#include "mitkLabelSetImage.h"
#include "mitkOtsuSegmentationFilter.h"
#include "mitkRenderingManager.h"
#include "mitkToolManager.h"
#include <mitkITKImageImport.h>
#include <mitkImageCast.h>
#include <mitkLevelWindowProperty.h>
#include <mitkLookupTableProperty.h>
#include <mitkRenderingModeProperty.h>
#include <mitkSliceNavigationController.h>

// ITK
#include <itkBinaryThresholdImageFilter.h>
#include <itkOrImageFilter.h>
#include <itkOtsuMultipleThresholdsImageFilter.h>

// us
#include <usGetModuleContext.h>
#include <usModule.h>
#include <usModuleContext.h>
#include <usModuleResource.h>

#include <mitkImageStatisticsHolder.h>

namespace mitk
{
  MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, OtsuTool3D, "Otsu Segmentation");
}

mitk::OtsuTool3D::OtsuTool3D()
{
}

mitk::OtsuTool3D::~OtsuTool3D()
{
}

void mitk::OtsuTool3D::Activated()
{
  Superclass::Activated();

  if (m_ToolManager)
  {
    m_OriginalImage = dynamic_cast<mitk::Image *>(m_ToolManager->GetReferenceData(0)->GetData());

    m_BinaryPreviewNode = mitk::DataNode::New();
    m_BinaryPreviewNode->SetName("Binary_Preview");
    m_BinaryPreviewNode->SetProperty("color", ColorProperty::New(0.0, 1.0, 0.0));
    m_BinaryPreviewNode->SetProperty("opacity", FloatProperty::New(0.3));
    // m_BinaryPreviewNode->SetBoolProperty("helper object", true);
    // m_BinaryPreviewNode->SetProperty("binary", mitk::BoolProperty::New(true));
    m_ToolManager->GetDataStorage()->Add(this->m_BinaryPreviewNode);

    m_MultiLabelResultNode = mitk::DataNode::New();
    m_MultiLabelResultNode->SetName("Otsu_Preview");
    // m_MultiLabelResultNode->SetBoolProperty("helper object", true);
    m_MultiLabelResultNode->SetVisibility(true);

    m_MaskedImagePreviewNode = mitk::DataNode::New();
    m_MaskedImagePreviewNode->SetName("Volume_Preview");
    // m_MultiLabelResultNode->SetBoolProperty("helper object", true);
    m_MaskedImagePreviewNode->SetVisibility(false);

    m_ToolManager->GetDataStorage()->Add(this->m_MultiLabelResultNode);
  }
}

void mitk::OtsuTool3D::Deactivated()
{
  m_ToolManager->GetDataStorage()->Remove(this->m_MultiLabelResultNode);
  m_MultiLabelResultNode = nullptr;
  m_ToolManager->GetDataStorage()->Remove(this->m_BinaryPreviewNode);
  m_BinaryPreviewNode = nullptr;
  m_ToolManager->GetDataStorage()->Remove(this->m_MaskedImagePreviewNode);
  m_MaskedImagePreviewNode = nullptr;

  Superclass::Deactivated();
}

const char **mitk::OtsuTool3D::GetXPM() const
{
  return nullptr;
}

us::ModuleResource mitk::OtsuTool3D::GetIconResource() const
{
  us::Module *module = us::GetModuleContext()->GetModule();
  us::ModuleResource resource = module->GetResource("Otsu_48x48.png");
  return resource;
}

void mitk::OtsuTool3D::RunSegmentation(int regions, bool useValley, int numberOfBins)
{
  // this->m_OtsuSegmentationDialog->setCursor(Qt::WaitCursor);

  int numberOfThresholds = regions - 1;

  unsigned int timestep = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetTime()->GetPos();

  mitk::Image::Pointer image3D = Get3DImage(m_OriginalImage, timestep);

  mitk::OtsuSegmentationFilter::Pointer otsuFilter = mitk::OtsuSegmentationFilter::New();
  otsuFilter->SetNumberOfThresholds(numberOfThresholds);
  otsuFilter->SetValleyEmphasis(useValley);
  otsuFilter->SetNumberOfBins(numberOfBins);
  otsuFilter->SetInput(image3D);

  try
  {
    otsuFilter->Update();
  }
  catch (...)
  {
    mitkThrow() << "itkOtsuFilter error (image dimension must be in {2, 3} and image must not be RGB)";
  }

  m_ToolManager->GetDataStorage()->Remove(this->m_MultiLabelResultNode);
  m_MultiLabelResultNode = nullptr;
  m_MultiLabelResultNode = mitk::DataNode::New();
  m_MultiLabelResultNode->SetName("Otsu_Preview");
  m_MultiLabelResultNode->SetVisibility(true);
  m_ToolManager->GetDataStorage()->Add(this->m_MultiLabelResultNode);
  m_MultiLabelResultNode->SetOpacity(1.0);

  mitk::LabelSetImage::Pointer resultImage = mitk::LabelSetImage::New();
  resultImage->InitializeByLabeledImage(otsuFilter->GetOutput());
  this->m_MultiLabelResultNode->SetData(resultImage);
  m_MultiLabelResultNode->SetProperty("binary", mitk::BoolProperty::New(false));
  mitk::RenderingModeProperty::Pointer renderingMode = mitk::RenderingModeProperty::New();
  renderingMode->SetValue(mitk::RenderingModeProperty::LOOKUPTABLE_LEVELWINDOW_COLOR);
  m_MultiLabelResultNode->SetProperty("Image Rendering.Mode", renderingMode);
  mitk::LookupTable::Pointer lut = mitk::LookupTable::New();
  mitk::LookupTableProperty::Pointer prop = mitk::LookupTableProperty::New(lut);
  vtkSmartPointer<vtkLookupTable> lookupTable = vtkSmartPointer<vtkLookupTable>::New();
  lookupTable->SetHueRange(1.0, 0.0);
  lookupTable->SetSaturationRange(1.0, 1.0);
  lookupTable->SetValueRange(1.0, 1.0);
  lookupTable->SetTableRange(-1.0, 1.0);
  lookupTable->Build();
  lut->SetVtkLookupTable(lookupTable);
  prop->SetLookupTable(lut);
  m_MultiLabelResultNode->SetProperty("LookupTable", prop);
  mitk::LevelWindowProperty::Pointer levWinProp = mitk::LevelWindowProperty::New();
  mitk::LevelWindow levelwindow;
  levelwindow.SetRangeMinMax(0, numberOfThresholds + 1);
  levWinProp->SetLevelWindow(levelwindow);
  m_MultiLabelResultNode->SetProperty("levelwindow", levWinProp);

  // m_BinaryPreviewNode->SetVisibility(false);
  //  m_MultiLabelResultNode->SetVisibility(true);
  // this->m_OtsuSegmentationDialog->setCursor(Qt::ArrowCursor);
  mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}

void mitk::OtsuTool3D::ConfirmSegmentation()
{
  mitk::LabelSetImage::Pointer resultImage = mitk::LabelSetImage::New();
  resultImage->InitializeByLabeledImage(dynamic_cast<mitk::Image *>(m_BinaryPreviewNode->GetData()));
  GetTargetSegmentationNode()->SetData(resultImage);

  m_ToolManager->ActivateTool(-1);
}

void mitk::OtsuTool3D::UpdateBinaryPreview(std::vector<int> regionIDs)
{
  m_MultiLabelResultNode->SetVisibility(false);
  mitk::Image::Pointer multiLabelSegmentation = dynamic_cast<mitk::Image *>(m_MultiLabelResultNode->GetData());
  AccessByItk_1(multiLabelSegmentation, CalculatePreview, regionIDs);
}

template <typename TPixel, unsigned int VImageDimension>
void mitk::OtsuTool3D::CalculatePreview(itk::Image<TPixel, VImageDimension> *itkImage, std::vector<int> regionIDs)
{
  typedef itk::Image<TPixel, VImageDimension> InputImageType;
  typedef itk::Image<mitk::Tool::DefaultSegmentationDataType, VImageDimension> OutputImageType;

  typedef itk::BinaryThresholdImageFilter<InputImageType, OutputImageType> FilterType;

  typename FilterType::Pointer filter = FilterType::New();

  // InputImageType::Pointer itkImage;
  typename OutputImageType::Pointer itkBinaryTempImage1;
  typename OutputImageType::Pointer itkBinaryTempImage2;
  typename OutputImageType::Pointer itkBinaryResultImage;

  // mitk::Image::Pointer multiLabelSegmentation = dynamic_cast<mitk::Image*>(m_MultiLabelResultNode->GetData());
  // mitk::CastToItkImage(multiLabelSegmentation, itkImage);

  filter->SetInput(itkImage);
  filter->SetLowerThreshold(regionIDs[0]);
  filter->SetUpperThreshold(regionIDs[0]);
  filter->SetInsideValue(1);
  filter->SetOutsideValue(0);
  filter->Update();
  itkBinaryTempImage2 = filter->GetOutput();

  typename itk::OrImageFilter<OutputImageType, OutputImageType>::Pointer orFilter =
    itk::OrImageFilter<OutputImageType, OutputImageType>::New();

  // if more than one region id is used compute the union of all given binary regions
  for (auto it = regionIDs.begin(); it != regionIDs.end(); ++it)
  {
    filter->SetLowerThreshold(*it);
    filter->SetUpperThreshold(*it);
    filter->SetInsideValue(1);
    filter->SetOutsideValue(0);
    filter->Update();
    itkBinaryTempImage1 = filter->GetOutput();

    orFilter->SetInput1(itkBinaryTempImage1);
    orFilter->SetInput2(itkBinaryTempImage2);

    orFilter->UpdateLargestPossibleRegion();
    itkBinaryResultImage = orFilter->GetOutput();
    itkBinaryTempImage2 = itkBinaryResultImage;
  }
  //----------------------------------------------------------------------------------------------------
  mitk::Image::Pointer binarySegmentation;
  mitk::CastToMitkImage(itkBinaryResultImage, binarySegmentation);
  m_BinaryPreviewNode->SetData(binarySegmentation);
  m_BinaryPreviewNode->SetVisibility(true);
  m_BinaryPreviewNode->SetProperty("outline binary", mitk::BoolProperty::New(false));

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

// void mitk::OtsuTool3D::UpdateBinaryPreview(int regionID)
//{
//  m_MultiLabelResultNode->SetVisibility(false);
//  //pixel with regionID -> binary image
//  const unsigned short dim = 3;
//  typedef unsigned char PixelType;
//
//  typedef itk::Image< PixelType, dim > InputImageType;
//  typedef itk::Image< PixelType, dim > OutputImageType;
//
//  typedef itk::BinaryThresholdImageFilter< InputImageType, OutputImageType > FilterType;
//
//  FilterType::Pointer filter = FilterType::New();
//
//  InputImageType::Pointer itkImage;
//
//  mitk::Image::Pointer multiLabelSegmentation = dynamic_cast<mitk::Image*>(m_MultiLabelResultNode->GetData());
//  mitk::CastToItkImage(multiLabelSegmentation, itkImage);
//
//  filter->SetInput(itkImage);
//  filter->SetLowerThreshold(regionID);
//  filter->SetUpperThreshold(regionID);
//  filter->SetInsideValue(1);
//  filter->SetOutsideValue(0);
//  filter->Update();
//  mitk::Image::Pointer binarySegmentation;
//  mitk::CastToMitkImage( filter->GetOutput(), binarySegmentation);
//  m_BinaryPreviewNode->SetData(binarySegmentation);
//  m_BinaryPreviewNode->SetVisibility(true);
//  m_BinaryPreviewNode->SetProperty("outline binary", mitk::BoolProperty::New(false));
//
//  mitk::RenderingManager::GetInstance()->RequestUpdateAll();
//}

const char *mitk::OtsuTool3D::GetName() const
{
  return "Otsu";
}

void mitk::OtsuTool3D::UpdateVolumePreview(bool volumeRendering)
{
  if (volumeRendering)
  {
    m_MaskedImagePreviewNode->SetBoolProperty("volumerendering", true);
    m_MaskedImagePreviewNode->SetBoolProperty("volumerendering.uselod", true);
  }
  else
  {
    m_MaskedImagePreviewNode->SetBoolProperty("volumerendering", false);
  }
  mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}

void mitk::OtsuTool3D::ShowMultiLabelResultNode(bool show)
{
  m_MultiLabelResultNode->SetVisibility(show);
  m_BinaryPreviewNode->SetVisibility(!show);
  mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}

int mitk::OtsuTool3D::GetNumberOfBins()
{
  ScalarType min = m_OriginalImage.GetPointer()->GetStatistics()->GetScalarValueMin();
  ScalarType max = m_OriginalImage.GetPointer()->GetStatistics()->GetScalarValueMaxNoRecompute();
  return static_cast<int>(max - min) + 1;
}