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/*
//
// Copyright 1997-2009 Torsten Rohlfing
//
// Copyright 2004-2010, 2013 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 __cmtkFilterMask_h_included_
#define __cmtkFilterMask_h_included_
#include <cmtkconfig.h>
#include <Base/cmtkTypes.h>
#include <Base/cmtkUnits.h>
#include <Base/cmtkFixedVector.h>
#include <Base/cmtkMathUtil.h>
#include <System/cmtkSmartPtr.h>
#include <math.h>
#include <vector>
namespace
cmtk
{
/** \addtogroup Base */
//@{
/** Filter mask pixel entry.
* This class handles a single entry in a pre-computed filter mask for
* multidimensional images with relative coordinates and filter coeffiecient
* for a single pixel.
*/
template<int DIM>
class FilterMaskPixel
{
public:
/// This class.
typedef FilterMaskPixel Self;
/// Smart pointer.
typedef SmartPointer<Self> SmartPtr;
/// Default constructor.
FilterMaskPixel() {}
/// Explicit constructor.
FilterMaskPixel
( const FixedVector<DIM,int>& location, const int relativeIndex, const Types::DataItem coefficient )
: Location( location ),
RelativeIndex ( relativeIndex ),
Coefficient( coefficient ),
PixelIndex( 0 ),
Valid( false )
{}
/// Relative location of this pixel.
FixedVector<DIM,int> Location;
/// Relative index of this pixel in source image from center of kernel.
int RelativeIndex;
/// Filter coefficient.
Types::DataItem Coefficient;
/// Cached source index of image pixel for this element.
int PixelIndex;
/** Active flag.
* This flag can be used in client code to flag pixels in the filter mask as
* either valid (i.e., inside domain) or invalid (outsside domain). This
* eliminates repeated range checking in cases where there are multiple
* iterations over the filter mask at one location.
*/
bool Valid;
};
/** Filter mask.
* This class handles pre-computed filter masks for multidimensional images
* with relative pixel coordinates and filter coeffiecients.
*/
template<int DIM>
class FilterMask :
/// Inherit from STL container.
public std::vector< FilterMaskPixel<DIM> >
{
public:
/// This class type.
typedef FilterMask<DIM> Self;
/// Direct parent class.
typedef std::vector< FilterMaskPixel<DIM> > Superclass;
/// Smert pointer to this class.
typedef SmartPointer<Self> SmartPtr;
/// Constructor.
template<class F>
FilterMask( const FixedVector<DIM,int>& dims, const FixedVector<DIM,Types::Coordinate>& deltas, const Types::Coordinate radius, F filter )
{
FixedVector<DIM,int> pixel;
FixedVector<DIM,int> width;
FixedVector<DIM,Types::Coordinate> position;
for ( int dim = 0; dim < DIM; ++dim )
{
pixel[dim] = - (width[dim] = 1+static_cast<int>( radius / deltas[dim] ));
position[dim] = pixel[dim] * deltas[dim];
}
bool done = false;
while ( ! done )
{
// increment the DIM-digit pixel index counter including overflow.
for ( int dim = 0; dim < DIM; ++dim )
{
++pixel[dim];
if ( pixel[dim] <= width[dim] )
{
// no overflow, leave for loop since we're done
dim = DIM;
}
else
{
if ( dim+1 == DIM )
// was this the last dimension? if so, leave while() loop
done = true;
else
{
// no, then reset this dimension and repeat loop to increment next
pixel[dim] = -width[dim];
}
}
}
// are we done with the kernel?
if ( ! done )
{
// no, then compute Euclidean distance from center
Types::Coordinate distance = 0.0;
for ( int dim = 0; dim < DIM; ++dim )
{
position[dim] = pixel[dim] * deltas[dim];
distance += position[dim] * position[dim];
}
distance = sqrt( distance );
// if distance is within radius then add a pixel to the filter mask
if ( distance < radius )
{
const int index = pixel[0] + dims[0] * (pixel[1] + dims[1] * pixel[2] );
this->push_back( FilterMaskPixel<DIM>( pixel, index, filter( position ) ) );
}
}
}
}
/// Gaussian filter as an example of a concrete filter implementation.
class Gaussian
{
public:
/// Constructor.
Gaussian( const Units::GaussianSigma& standardDeviation )
{
InvStandardDeviation = 1.0 / standardDeviation.Value();
NormFactor = 1.0 / (sqrt(2.0 * M_PI) * standardDeviation.Value());
}
/// Get filter coefficient at relative location from filter center.
Types::DataItem operator() ( const FixedVector<DIM,Types::Coordinate>& relativePosition )
{
Types::Coordinate distance = 0;
for ( int i = 0; i < DIM; ++i )
distance += relativePosition[i] * relativePosition[i];
return static_cast<Types::DataItem>( NormFactor * exp( -distance * MathUtil::Square( InvStandardDeviation ) / 2 ) );
}
private:
/// Standard deviation.
Types::Coordinate InvStandardDeviation;
/// Gaussian normalization factor.
Types::Coordinate NormFactor;
};
};
} // namespace cmtk
#endif // #ifndef __cmtkFilterMask_h_included_
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