mitkAutoCropImageFilter.h

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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.

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

#ifndef __mitkAutoCropImageFilter_h_
#define __mitkAutoCropImageFilter_h_

#include "MitkAlgorithmsExtExports.h"
#include "mitkCommon.h"
#include "mitkImageTimeSelector.h"
#include "mitkSubImageSelector.h"

#include <itkImage.h>
#include <itkImageRegion.h>

namespace mitk
{
  class MITKALGORITHMSEXT_EXPORT AutoCropImageFilter : public SubImageSelector
  {
  public:
    typedef itk::ImageRegion<3> RegionType;

    mitkClassMacro(AutoCropImageFilter, SubImageSelector);

    itkFactorylessNewMacro(Self);

    itkCloneMacro(Self);

    itkGetConstMacro(BackgroundValue, float);
    itkSetMacro(BackgroundValue, float);

    itkGetConstMacro(MarginFactor, float);
    itkSetMacro(MarginFactor, float);

    itkGetMacro(CroppingRegion, RegionType);

    // Use this method to manually set a region
    void SetCroppingRegion(RegionType overrideRegion);

    virtual const PixelType GetOutputPixelType();

  protected:
    // default constructor
    AutoCropImageFilter();

    // default destructor
    ~AutoCropImageFilter() override;

    // This method calculates the actual smallest box
    void ComputeNewImageBounds();

    // Crops the image using the itk::RegionOfInterestImageFilter and creates the new output image
    template <typename TPixel, unsigned int VImageDimension>
    void ITKCrop3DImage(itk::Image<TPixel, VImageDimension> *inputItkImage, unsigned int timestep);

    // Here, the output image is initialized by the input and the newly calculated region
    void GenerateOutputInformation() override;

    // Purposely not implemented
    void GenerateInputRequestedRegion() override;

    // Crops the image on all time steps
    void GenerateData() override;

    float m_BackgroundValue;

    RegionType m_CroppingRegion;

    float m_MarginFactor;

    typedef itk::Image<float, 3> ImageType;
    typedef ImageType::Pointer ImagePointer;

    RegionType::SizeType m_RegionSize;
    RegionType::IndexType m_RegionIndex;

    mitk::ImageTimeSelector::Pointer m_TimeSelector;

    mitk::SlicedData::RegionType m_InputRequestedRegion;
    itk::TimeStamp m_TimeOfHeaderInitialization;

    bool m_OverrideCroppingRegion;
  };

} // namespace mitk

#endif