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itkBRAINSROIAutoImageFilter.h
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itkBRAINSROIAutoImageFilter.h
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/*=========================================================================
*
* Program: Insight Segmentation & Registration Toolkit
* Module: $RCSfile: itkBRAINSROIAutoImageFilter.h,v $
* Language: C++
* Date: $Date: 2008-10-16 19:33:40 $
* Version: $Revision: 1.7 $
*
* Copyright (c) Insight Software Consortium. All rights reserved.
* See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
*
* This software is distributed WITHOUT ANY WARRANTY; without even
* the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the above copyright notices for more information.
*
* =========================================================================*/
#ifndef __itkBRAINSROIAutoImageFilter_h
#define __itkBRAINSROIAutoImageFilter_h
// First make sure that the configuration is available.
// This line can be removed once the optimized versions
// gets integrated into the main directories.
#include "itkConfigure.h"
#include "itkImageToImageFilter.h"
#include "itkImage.h"
#include "itkImageMaskSpatialObject.h"
#include "itkLargestForegroundFilledMaskImageFilter.h"
#include "itkCastImageFilter.h"
typedef itk::SpatialObject<3> SpatialObjectType;
typedef SpatialObjectType::Pointer ImageMaskPointer;
namespace itk
{
/** \class BRAINSROIAutoImageFilter
* \brief This is a class to help with identifying common tissue
* Regions in an image.
*
* \sa Image
* \sa Neighborhood
*
* \ingroup IntensityImageFilters
*/
template <class TInputImage, class TOutputImage>
class ITK_EXPORT BRAINSROIAutoImageFilter :
public ImageToImageFilter<TInputImage, TOutputImage>
{
public:
/** Extract dimension from input and output image. */
itkStaticConstMacro(InputImageDimension, unsigned int,
TInputImage::ImageDimension);
itkStaticConstMacro(OutputImageDimension, unsigned int,
TOutputImage::ImageDimension);
/** Convenient typedefs for simplifying declarations. */
typedef TInputImage InputImageType;
typedef TOutputImage OutputImageType;
/** Standard class typedefs. */
typedef BRAINSROIAutoImageFilter Self;
typedef ImageToImageFilter<InputImageType, OutputImageType> Superclass;
typedef SmartPointer<Self> Pointer;
typedef SmartPointer<const Self> ConstPointer;
/** Method for creation through the object factory. */
itkNewMacro(Self);
/** Run-time type information (and related methods). */
itkTypeMacro(BRAINSROIAutoImageFilter, ImageToImageFilter);
/** Image typedef support. */
typedef typename InputImageType::PixelType InputPixelType;
typedef typename OutputImageType::PixelType OutputPixelType;
typedef typename InputImageType::RegionType InputImageRegionType;
typedef typename OutputImageType::RegionType OutputImageRegionType;
typedef typename InputImageType::SizeType InputSizeType;
typedef itk::Image<unsigned char, 3> UCHARIMAGE;
typedef itk::ImageMaskSpatialObject<UCHARIMAGE::ImageDimension> ImageMaskSpatialObjectType;
/** */
itkSetMacro(OtsuPercentileThreshold, double);
itkGetConstMacro(OtsuPercentileThreshold, double);
/** */
itkSetMacro(ThresholdCorrectionFactor, double);
itkGetConstMacro(ThresholdCorrectionFactor, double);
/** The closing size in mm, this is rounded up to the next closest number of
* voxel by taking Spacing into account */
itkSetMacro(ClosingSize, double);
itkGetConstMacro(ClosingSize, double);
/** The dilation size in mm, this is rounded up to the next closest number of
* voxel by taking Spacing into account */
itkSetMacro(DilateSize, double);
itkGetConstMacro(DilateSize, double);
// NOTE: This will generate a new spatial object each time it is called, and
// not return the previous spatial object
ImageMaskPointer GetSpatialObjectROI(void)
{
if( m_ResultMaskPointer.IsNull() ) // This is a cheap way to only create
// the mask once, note that this is made
// null when GenerateData is called.
{
typedef itk::CastImageFilter<OutputImageType, UCHARIMAGE> CastImageFilter;
typename CastImageFilter::Pointer castFilter = CastImageFilter::New();
castFilter->SetInput( this->GetOutput() );
castFilter->Update();
// convert mask image to mask
typename ImageMaskSpatialObjectType::Pointer mask = ImageMaskSpatialObjectType::New();
mask->SetImage( castFilter->GetOutput() );
mask->ComputeObjectToWorldTransform();
m_ResultMaskPointer = dynamic_cast<ImageMaskSpatialObjectType *>( mask.GetPointer() );
if( m_ResultMaskPointer.IsNull() )
{
itkGenericExceptionMacro(<< "failed conversion to MaskSpatialObject");
}
}
return m_ResultMaskPointer;
}
typename UCHARIMAGE::ConstPointer GetBinaryImageROI()
{
ImageMaskPointer tmp = this->GetSpatialObjectROI();
typename UCHARIMAGE::ConstPointer rval;
if( tmp.IsNotNull() )
{
const typename itk::ImageMaskSpatialObject<3>::ConstPointer imso =
dynamic_cast<itk::ImageMaskSpatialObject<3> *>(tmp.GetPointer() );
if( imso.IsNull() )
{
itkGenericExceptionMacro(<< "failed conversion to MaskSpatialObject");
}
if( imso.IsNotNull() )
{
rval = imso->GetImage();
}
}
return rval;
}
#ifdef ITK_USE_CONCEPT_CHECKING
/** Begin concept checking */
itkConceptMacro( SameDimensionCheck,
( Concept::SameDimension<InputImageDimension, OutputImageDimension> ) );
/** End concept checking */
#endif
protected:
BRAINSROIAutoImageFilter();
virtual ~BRAINSROIAutoImageFilter()
{
}
void PrintSelf(std::ostream & os, Indent indent) const;
void GenerateData();
private:
BRAINSROIAutoImageFilter(const Self &); // purposely not implemented
void operator=(const Self &); // purposely not implemented
double m_OtsuPercentileThreshold;
double m_ThresholdCorrectionFactor;
double m_ClosingSize;
double m_DilateSize;
ImageMaskPointer m_ResultMaskPointer;
};
} // end namespace itk
#ifndef ITK_MANUAL_INSTANTIATION
#include "itkBRAINSROIAutoImageFilter.hxx"
#endif
#endif