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/*
//
// Copyright 2016 Google, Inc.
//
// Copyright 1997-2010 Torsten Rohlfing
//
// Copyright 2004-2013 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 __cmtkVolume_h_included_
#define __cmtkVolume_h_included_
#include <cmtkconfig.h>
#include <Base/cmtkDataGrid.h>
#include <Base/cmtkMacros.h>
#include <Base/cmtkMathUtil.h>
#include <Base/cmtkFixedVector.h>
#include <Base/cmtkVector3D.h>
#include <Base/cmtkAffineXform.h>
#include <Base/cmtkProbeInfo.h>
#include <Base/cmtkLandmarkList.h>
#include <Base/cmtkAnatomicalOrientation.h>
#include <System/cmtkSmartPtr.h>
#include <System/cmtkThreads.h>
#include <System/cmtkMemory.h>
#include <algorithm>
namespace
cmtk
{
/** \addtogroup Base */
//@{
/** General 3D volume.
* This class handles three-dimensional volume data with a coordinate
* transformation and associated distance measure. Methods to retrieve data and
* general structural information are provided.
*\author Torsten Rohlfing
*/
class Volume :
/// Inherit from 3-D data grid.
public DataGrid
{
public:
/// This class type.
typedef Volume Self;
/// Superclass.
typedef DataGrid Superclass;
/// Smart pointer to Volume.
typedef SmartPointer<Self> SmartPtr;
/// Region type.
typedef Region<3,Types::Coordinate> CoordinateRegionType;
/// Index type.
typedef CoordinateRegionType::IndexType CoordinateVectorType;
/** Volume offset (coordinate of first voxel in RAS standard space).
*\note This offset is NOT included in the volume size, m_Size.
*/
Self::CoordinateVectorType m_Offset;
/// Set volume offset.
void SetOffset( const Vector3D& o )
{
this->m_Offset = o;
}
/** Spatial extent of the volume in world coordinates
*\note This is the actual size of the volume between first and last pixel. Therefore,
* if a non-zero volume coordinate offset is set in m_Offset, this does not affect
* this field, because the volume size as the product of pixel size times number of pixels
* per dimension minus one remains unaffected.
*/
Self::CoordinateVectorType m_Size;
/// Check whether a location is inside the image.
bool IsInside( const Self::CoordinateVectorType& v ) const
{
return (this->m_Offset <= v) && ((v-this->m_Offset) < this->m_Size);
}
/// Copy constructor.
Volume( const Self& other ) : Superclass( other ), m_Offset( other.m_Offset ), m_Size( other.m_Size ) {}
/// Grid and data constructor.
Volume( const Self::IndexType& dims, const Self::CoordinateVectorType& size, TypedArray::SmartPtr& data = TypedArray::SmartPtr::Null() ) : DataGrid( dims, data ), m_Offset( 0.0 ), m_Size( size ) {}
/** Destructor.
* Do nothing really; just be present and virtual.
*/
virtual ~Volume () {};
/** Get total volume.
*\return Product of the spatial extents in all three coordinate directions.
*/
virtual Types::Coordinate TotalVolume () const
{
return m_Size[0] * m_Size[1] * m_Size[2];
}
/// Return average volume of all voxels.
virtual Types::Coordinate AverageVoxelVolume () const
{
return ( (m_Size[0]*m_Size[1]*m_Size[2]) / ((this->m_Dims[0]-1)*(this->m_Dims[1]-1)*(this->m_Dims[2]-1)) );
}
/** Calculate volume center.
*\return Returned is the center of the bounding box.
*/
Vector3D GetCenter () const;
protected:
/** Get information needed for trilinear interpolation.
*\return 1 if operation was successful, 0 if no valid data could be found
* at the given location.
*/
bool GetTrilinear ( ProbeInfo&, const Types::GridIndexType, const Types::GridIndexType, const Types::GridIndexType, const Vector3D&, const Types::Coordinate*, const Types::Coordinate* ) const;
};
//@}
} // namespace cmtk
#endif
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