cmtkFilterVolume.h

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/*
//
//  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: 2752 $
//
//  $LastChangedDate: 2011-01-17 11:33:31 -0800 (Mon, 17 Jan 2011) $
//
//  $LastChangedBy: torstenrohlfing $
//
*/

#ifndef __cmtkFilterVolume_h_included_
#define __cmtkFilterVolume_h_included_

#include <cmtkconfig.h>

#define COUPE_BLOCK_SIZE 27
#define COUPE_BLOCK_RADIUS 1

#include <Base/cmtkUniformVolume.h>
#include <Base/cmtkTypedArray.h>
#include <Base/cmtkUnits.h>

namespace
cmtk
{


class FilterVolume
{
public:

  typedef Types::DataItem CoupeBlock[COUPE_BLOCK_SIZE];

  static TypedArray::SmartPtr GaussianFilter( const UniformVolume* volume, const Units::GaussianSigma& width, const Types::Coordinate radius = 1.0, const TypedArray* maskData = NULL );

  static TypedArray::SmartPtr CoupeFilter
  ( const UniformVolume* volume, 
    const int windowRadius,
    const float beta = 0.5 );

  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 );
  
  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 );

  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 );
private:
  static Types::DataItem Mean( CoupeBlock items );

  static Types::DataItem Variance( CoupeBlock items, const Types::DataItem mean );
 
  static void GetCoupeBlock( CoupeBlock block, const TypedArray* data, const int* dims, const int x, const int y, const int z );

  static double ComputeCoupeWeight
  ( const Types::DataItem smoothingParam,
    CoupeBlock centerBlock, 
    CoupeBlock outerBlock );

  static void BlockAddInPlace
  ( CoupeBlock v1, CoupeBlock v2 );

  static void BlockSubtract( CoupeBlock diff, CoupeBlock v1, CoupeBlock v2 );

  static void BlockConstMult( CoupeBlock prod, CoupeBlock items, const Types::DataItem mult );
  
  static double BlockSquaredDistance( CoupeBlock centerBlock, CoupeBlock outerBlock );
 
   static void ComputeNLWithinWindow
  ( CoupeBlock NL,
    const TypedArray* blockLocations,
    const TypedArray* data, const int* dims, const Types::DataItem smoothingParam,
    const int x, const int y, const int z, 
    const int windowRadius, 
    const float beta, 
    const TypedArray* localMeansMap, 
    const TypedArray* localVariancesMap, 
    CoupeBlock centerBlock );
};


} // namespace cmtk

#endif // #ifndef __cmtkFilterVolume_h_included_