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/*
//
// Copyright 1997-2009 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 __cmtkImageSymmetryPlaneCommandLineBase_h_included_
#define __cmtkImageSymmetryPlaneCommandLineBase_h_included_
#include <cmtkconfig.h>
#include <Registration/cmtkImageSymmetryPlaneFunctionalBase.h>
#include <Base/cmtkInterpolator.h>
#include <System/cmtkCannotBeCopied.h>
#include <System/cmtkCommandLine.h>
namespace
cmtk
{
/** \addtogroup Registration */
//@{
/** Base class for symmetry plane computation command line tools.
*/
class ImageSymmetryPlaneCommandLineBase :
private CannotBeCopied
{
public:
/// Default constructor.
ImageSymmetryPlaneCommandLineBase();
/** Run the symmetry plane computation based on provided command line arguments.
*\return The return code for the symmetry plane program. This should be returned
* from main() via either "return" or "exit()".
*/
int Run( const int argc, const char* argv[] );
/// Get reference to command line parser object.
CommandLine& GetCommandLine()
{
return this->m_CommandLine;
}
protected:
/// Create functional for volume.
virtual ImageSymmetryPlaneFunctionalBase::SmartPtr CreateFunctional( UniformVolume::SmartPtr& volume ) = 0;
/// Create functional for volume and value range.
virtual ImageSymmetryPlaneFunctionalBase::SmartPtr CreateFunctional( UniformVolume::SmartPtr& volume, const Types::DataItemRange& range ) = 0;
private:
/// Parse the given command line.
bool ParseCommandLine ( const int argc, const char* argv[] );
/// The symmetry plane object.
ParametricPlane m_SymmetryPlane;
/// Minimum data value (lower threshold).
float m_MinValue;
/// Flag for valid (user-set) minimum data value.
bool m_MinValueSet;
/// Minimum data value (lower threshold).
float m_MaxValue;
/// Flag for valid (user-set) maximum data value.
bool m_MaxValueSet;
/// Image sampling (highest resampled resolution).
Types::Coordinate m_Sampling;
/// Optimization "accuracy" (really, precision)
Types::Coordinate m_Accuracy;
/// Interpolation method for reformatted image generation.
Interpolators::InterpolationEnum m_Interpolation;
/// Number of multi-resolution levels.
int m_Levels;
/// Flag to disable optimization.
bool m_DisableOptimization;
/// Symmetry plane "Rho" parameter (offset).
Types::Coordinate m_Rho;
/// Symmetry plane "Theta" angle parameter.
Units::Degrees m_Theta;
/// Symmetry plane "Phi" angle parameter.
Units::Degrees m_Phi;
/// Flag to fix symmetry plane offset parameter (i.e., do not optimize "Rho")
bool m_FixOffset;
/// Optional output path for mirrored file.
const char* m_MirrorOutFile;
/// Optional output path for aligned file.
const char* m_AlignedOutFile;
/// Flag for marking the symmetry plane in the aligned file.
bool m_MarkPlaneAligned;
/// Optional output path for file with marked symmetry plane.
const char* m_MarkedOutFile;
/// Optional output path for file with subtraction between input and mirrored input.
const char* m_DifferenceOutFile;
/// Optional output path for the alignment transformation.
const char* m_WriteXformPath;
/// Data value used for marking the symmetry plane in output images.
Types::DataItem m_MarkPlaneValue;
/// Flag for user-provided padding value.
bool m_PadOutValueSet;
/// User-provided padding value.
Types::DataItem m_PadOutValue;
/// Optional output path for symmetry plane.
const char* m_SymmetryOutFileName;
/// Optional output path for symmetry plane parameters.
const char* m_SymmetryParameters;
/// Optional input path for previously computed symmetry plane parameters.
const char* m_SymmetryParametersFile;
/// Input image file path.
std::string m_InFileName;
/// Constants for initial plane orientation.
typedef enum
{
/// XY plane (axial)
SYMPL_INIT_XY,
/// XZ plane (coronal)
SYMPL_INIT_XZ,
/// YZ plane (sagittal)
SYMPL_INIT_YZ
} InitialPlaneEnum;
/// Initial plane orientation: default to sagittal for human images.
InitialPlaneEnum m_InitialPlane;
/// Write difference image between original and mirrored image.
void WriteDifference( UniformVolume::SmartConstPtr& originalVolume ) const;
/// Write mirrored image.
void WriteMirror( UniformVolume::SmartConstPtr& originalVolume ) const;
/// Write original image with marked symmetry plane.
void WriteMarkPlane( UniformVolume::SmartConstPtr& originalVolume ) const;
/// Write image aligned w.r.t. the symmetry plane.
void WriteAligned( UniformVolume::SmartConstPtr& originalVolume ) const;
private:
CommandLine m_CommandLine;
};
} // namespace cmtk
#endif // #ifndef __cmtkImageSymmetryPlaneCommandLineBase_h_included_
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