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/*
//
// Copyright 2016 Google, Inc.
//
// Copyright 1997-2009 Torsten Rohlfing
//
// Copyright 2004-2011 SRI International
//
// This file is part of the Computational Morphometry Toolkit.
//
// http://www.nitrc.org/projects/cmtk/
//
// The Computational Morphometry Toolkit is free software: you can
// redistribute it and/or modify it under the terms of the GNU General Public
// License as published by the Free Software Foundation, either version 3 of
// the License, or (at your option) any later version.
//
// The Computational Morphometry Toolkit is distributed in the hope that it
// will be useful, but WITHOUT ANY WARRANTY; without even the implied
// warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License along
// with the Computational Morphometry Toolkit. If not, see
// <http://www.gnu.org/licenses/>.
//
// $Revision: 5436 $
//
// $LastChangedDate: 2018-12-10 19:01:20 -0800 (Mon, 10 Dec 2018) $
//
// $LastChangedBy: torstenrohlfing $
//
*/
#ifndef __cmtkFilterVolume_h_included_
#define __cmtkFilterVolume_h_included_
#include <list>
#include <cmtkconfig.h>
#include <Base/cmtkUniformVolume.h>
#include <Base/cmtkTypedArray.h>
#include <Base/cmtkUnits.h>
namespace
cmtk
{
/** \addtogroup Base */
//@{
/// Class for filtering volume images.
class FilterVolume
{
public:
/** Apply Gaussian filter.
*\param volume Input 3D image.
*\param width Width (standard deviation) of the Gaussian kernel.
*\param radius Filter radius in multiples of the filter width. Outside the
* radius (Euclidean distance) the filter is truncated.
*\param maskData Optional binary mask data array.
*\return A newly allocated TypedArray object that can be used, for
* example, to replace the one held by the input image. The data type of the
* array is identical to the input array.
*/
static TypedArray::SmartPtr GaussianFilter( const UniformVolume* volume, const Units::GaussianSigma& width, const Types::Coordinate radius = 1.0, const TypedArray* maskData = NULL );
/** Apply Coupe denoising filter.
*\param volume Input 3D image.
*\param beta Smoothing adjustment parameter
*\param windowRadius Distance from center voxel to outer edge of window
*\return A newly allocated TypedArray object that can be used, for
* example, to replace the one held by the input image. The data type of the
* array is identical to the input array.
*/
static TypedArray::SmartPtr CoupeFilter
( const UniformVolume* volume,
const int windowRadius,
const float beta = 0.5 );
/** Apply Torsten Rohlfing's single-image intensity-consistent Gaussian filter.
*\param volume Input 3D image.
*\param subjectData Pixel array of the individual grey image from this
* subject.
*\param maskData Optional binary mask data array.
*\param iFilterSigma Width (standard deviation of the Gaussian kernel.
*\param filterWidth Width (standard deviation of the Gaussian kernel.
*\param filterRadius Filter radius in multiples of the filter width.
* Outside the radius (Euclidean distance) the filter is truncated.
*\return A newly allocated TypedArray object that can be used, for
* example, to replace the one held by the input image. The data type of the
* array is identical to the input array.
*/
static TypedArray::SmartPtr RohlfingFilter
( const UniformVolume* volume, const TypedArray* subjectData,
const TypedArray* maskData, const Units::GaussianSigma& iFilterSigma,
const Units::GaussianSigma& filterWidth, const Types::Coordinate filterRadius );
/** Apply Colin Studholme's Gaussian filter with registration-based weights.
*\param volume Input 3D image.
*\param subjectData Pixel array of the individual grey image from this
* subject.
*\param averageData Pixel array of the population average grey image.
*\param maskData Optional binary mask data array.
*\param imgList List of pixel arrays from matched 3D images. The consistency
* between these pixel arrays determines the relative weights of the
* otherwise Gaussian kernel. Consult Colin's NeuroImage (2003) paper for
* details.
*\param binWidth Bin width of the intensity histogram used to quantify the
* matching between all individuals.
*\param filterWidth Width (standard deviation of the Gaussian kernel.
*\param filterRadius Filter radius in multiples of the filter width.
* Outside the radius (Euclidean distance) the filter is truncated.
*\return A newly allocated TypedArray object that can be used, for
* example, to replace the one held by the input image. The data type of the
* array is identical to the input array.
*/
static TypedArray::SmartPtr StudholmeFilter
( const UniformVolume* volume, const TypedArray* subjectData,
const TypedArray* averageData, const TypedArray* maskData,
std::list<TypedArray::SmartPtr> imgList, const Types::DataItem binWidth,
const Units::GaussianSigma& filterWidth, const Types::Coordinate filterRadius );
/** Apply Colin Studholme's Gaussian filter using multiple time points.
*\param volume Input 3D image.
*\param subjectData List of pixel arrays of the individual grey images from
* this subject. Each list item corresponds to one time point. Ideally, there
* are two items in the list, which correspond to the time points between
* which the Jacobian map in "volume" was computed.
*\param averageData Pixel array of the population average grey image.
*\param maskData Optional binary mask data array.
*\param imgList List of pixel arrays from matched 3D images. The consistency
* between these pixel arrays determines the relative weights of the
* otherwise Gaussian kernel. Consult Colin's NeuroImage (2003) paper for
* details.
*\param binWidth Bin width of the intensity histogram used to quantify the
* matching between all individuals.
*\param filterWidth Width (standard deviation of the Gaussian kernel.
*\param filterRadius Filter radius in multiples of the filter width.
* Outside the radius (Euclidean distance) the filter is truncated.
*\return A newly allocated TypedArray object that can be used, for
* example, to replace the one held by the input image. The data type of the
* array is identical to the input array.
*/
static TypedArray::SmartPtr StudholmeFilter
( const UniformVolume* volume,
std::list<TypedArray::SmartPtr> subjectData,
const TypedArray* averageData, const TypedArray* maskData,
std::list<TypedArray::SmartPtr> imgList, const Types::DataItem binWidth,
const Units::GaussianSigma& filterWidth, const Types::Coordinate filterRadius );
};
//@}
} // namespace cmtk
#endif // #ifndef __cmtkFilterVolume_h_included_
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