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#ifndef __BRAIN_MODEL_VOLUME_TO_SURFACE_MAPPER_ALGORITHM_PARAMETERS_H__
#define __BRAIN_MODEL_VOLUME_TO_SURFACE_MAPPER_ALGORITHM_PARAMETERS_H__
/*LICENSE_START*/
/*
* Copyright 1995-2002 Washington University School of Medicine
*
* http://brainmap.wustl.edu
*
* This file is part of CARET.
*
* CARET 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 2 of the License, or
* (at your option) any later version.
*
* CARET 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 CARET; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
*
*/
/*LICENSE_END*/
#include <vector>
#include <QString>
class PreferencesFile;
/// class for volume to surface algorithm parameters
class BrainModelVolumeToSurfaceMapperAlgorithmParameters {
public:
/// mapping algorithm
enum ALGORITHM {
/// metric average nodes mapping algorithm
ALGORITHM_METRIC_AVERAGE_NODES,
/// metric average voxel mapping algorithm
ALGORITHM_METRIC_AVERAGE_VOXEL,
/// metric enclosing voxel mapping algorithm
ALGORITHM_METRIC_ENCLOSING_VOXEL,
/// metric gaussian mapping algorithm
ALGORITHM_METRIC_GAUSSIAN,
/// metric interpolated voxel mapping algorithm
ALGORITHM_METRIC_INTERPOLATED_VOXEL,
/// metric maximum voxel mapping algorithm
ALGORITHM_METRIC_MAXIMUM_VOXEL,
/// metric MCW brainfish mapping algorithm
ALGORITHM_METRIC_MCW_BRAINFISH,
/// metric strongest voxel mapping algorithm
ALGORITHM_METRIC_STRONGEST_VOXEL,
/// paint enclosing voxel mapping algorithm
ALGORITHM_PAINT_ENCLOSING_VOXEL
};
// constructor
BrainModelVolumeToSurfaceMapperAlgorithmParameters();
// destructor
~BrainModelVolumeToSurfaceMapperAlgorithmParameters();
// transfer parameters from preferences file
void transferParametersFromPreferencesFile(const PreferencesFile* pf);
// transfer parameters to preferences file
void transferParametersToPreferncesFile(PreferencesFile* pf,
const bool writePreferencesFileFlag);
// get algorithm
ALGORITHM getAlgorithm() const;
// set algorithm
void setAlgorithm(const ALGORITHM alg);
// get the algorithm names and values
static void getAlgorithmNamesAndValues(std::vector<QString>& namesOut,
std::vector<ALGORITHM>& valuesOut);
// get the algorithm name
static QString getAlgorithmName(const ALGORITHM alg);
// get algorithm from string
static ALGORITHM getAlgorithmFromNameString(const QString& s);
// get algorithm parameter as string for comment usage
QString getAlgorithmParametersForComment() const;
// get the algorithm parameters as a equal and semicolon separated string
QString getAlgorithmParametersAsString() const;
// set the algorithm parameters from a string
void setAlgorithmParametersFromString(const QString& s);
// get the average voxel parameters
void getAlgorithmMetricAverageVoxelParameters(float& neighborsOut) const;
// set the average voxel parameters
void setAlgorithmMetricAverageVoxelParameters(const float neighborsIn);
// get the maximum voxel parameters
void getAlgorithmMetricMaximumVoxelParameters(float& neighborsOut) const;
// set the maximum voxel parameters
void setAlgorithmMetricMaximumVoxelParameters(const float neighborsIn);
// get the strongest voxel parameters
void getAlgorithmMetricStrongestVoxelParameters(float& neighborsOut) const;
// set the strongest voxel parameters
void setAlgorithmMetricStrongestVoxelParameters(const float neighborsIn);
// set gaussian algorithm parameters
void getAlgorithmMetricGaussianParameters(float& gaussianNeighborsOut,
float& gaussianSigmaNormOut,
float& gaussianSigmaTangOut,
float& gaussianNormBelowCutoffOut,
float& gaussianNormAboveCutoffOut,
float& gaussianTangCutoffOut) const;
// set gaussian algorithm parameters
void setAlgorithmMetricGaussianParameters(const float gaussianNeighborsIn,
const float gaussianSigmaNormIn,
const float gaussianSigmaTangIn,
const float gaussianNormBelowCutoffIn,
const float gaussianNormAboveCutoffIn,
const float gaussianTangCutoffIn);
// get the mcw brainfish algorithm parameters
void getAlgorithmMetricMcwBrainFishParameters(float& mcwBrainFishMaxDistanceOut,
int& mcwBrainFishSplatFactorOut) const;
// set the mcw brainfish algorithm parameters
void setAlgorithmMetricMcwBrainFishParameters(const float mcwBrainFishMaxDistanceIn,
const int mcwBrainFishSplatFactorIn);
/// get PALS metric average fiducial mapping enabled
bool getPalsMetricAverageFiducialMappingEnabled() const { return palsMetricAverageFiducialMappingEnabled; }
/// get PALS metric multi fiducial mapping enabled
bool getPalsMetricMultiFiducialMappingEnabled() const { return palsMetricMultiFiducialMappingEnabled; }
/// get PALS metric minimum enabled
bool getPalsMetricMinimumEnabled() const { return palsMetricMinimumEnabled; }
/// get PALS metric maximum enabled
bool getPalsMetricMaximumEnabled() const { return palsMetricMaximumEnabled; }
/// get PALS metric standard deviation enabled
bool getPalsMetricStandardDeviationEnabled() const { return palsMetricStandardDeviationEnabled; }
/// get PALS metric standard error enabled
bool getPalsMetricStandardErrorEnabled() const { return palsMetricStandardErrorEnabled; }
/// get PALS metric all cases enabled
bool getPalsMetricAllCasesEnabled() const { return palsMetricAllCasesEnabled; }
/// get PALS paint average fiducial mapping enabled
bool getPalsPaintAverageFiducialMappingEnabled() const { return palsPaintAverageFiducialMappingEnabled; }
/// get PALS paint most common enabled
bool getPalsPaintMostCommonEnabled() const { return palsPaintMostCommonEnabled; }
/// get PALS paint most common exlude unidentified enabled
bool getPalsPaintMostCommonExcludeUnidentifiedEnabled() const { return palsPaintMostCommonExcludeUnidentifiedEnabled; }
/// get PALS paint all cases enabled
bool getPalsPaintAllCasesEnabled() const { return palsPaintAllCasesEnabled; }
/// PALS metric average fiducial mapping enabled
void setPalsMetricAverageFiducialMappingEnabled(const bool b) { palsMetricAverageFiducialMappingEnabled = b; }
/// PALS metric multi fiducial mapping enabled
void setPalsMetricMultiFiducialMappingEnabled(const bool b) { palsMetricMultiFiducialMappingEnabled = b; }
/// PALS metric minimum enabled
void setPalsMetricMinimumEnabled(const bool b) { palsMetricMinimumEnabled = b; }
/// PALS metric maximum enabled
void setPalsMetricMaximumEnabled(const bool b) { palsMetricMaximumEnabled = b; }
/// PALS metric standard deviation enabled
void setPalsMetricStandardDeviationEnabled(const bool b) { palsMetricStandardDeviationEnabled = b; }
/// PALS metric standard error enabled
void setPalsMetricStandardErrorEnabled(const bool b) { palsMetricStandardErrorEnabled = b; }
/// PALS metric all cases enabled
void setPalsMetricAllCasesEnabled(const bool b) { palsMetricAllCasesEnabled = b; }
/// PALS paint average fiducial mapping enabled
void setPalsPaintAverageFiducialMappingEnabled(const bool b) { palsPaintAverageFiducialMappingEnabled = b; }
/// PALS paint most common enabled
void setPalsPaintMostCommonEnabled(const bool b) { palsPaintMostCommonEnabled = b; }
/// PALS paint most common exlude unidentified enabled
void setPalsPaintMostCommonExcludeUnidentifiedEnabled(const bool b) { palsPaintMostCommonExcludeUnidentifiedEnabled = b; }
/// PALS paint all cases enabled
void setPalsPaintAllCasesEnabled(const bool b) { palsPaintAllCasesEnabled = b; }
/// get the metric average nodes algorithm name
static QString getAlgorithmMetricAverageNodesName() { return "METRIC_AVERAGE_NODES"; }
/// get the metric average voxel algorithm name
static QString getAlgorithmMetricAverageVoxelName() { return "METRIC_AVERAGE_VOXEL"; }
/// get the metric enclosing voxel algorithm name
static QString getAlgorithmMetricEnclosingVoxelName() { return "METRIC_ENCLOSING_VOXEL"; }
/// get the metric gaussian algorithm name
static QString getAlgorithmMetricGaussianName() { return "METRIC_GAUSSIAN"; }
/// get the metric interpolated voxel algorithm name
static QString getAlgorithmMetricInterpolatedVoxelName() { return "METRIC_INTERPOLATED_VOXEL"; }
/// get the metric maximum voxel algorithm name
static QString getAlgorithmMetricMaximumVoxelName() { return "METRIC_MAXIMUM_VOXEL"; }
/// get the metric mcw brainfish algorithm name
static QString getAlgorithmMetricMcwBrainFishName() { return "METRIC_MCW_BRAIN_FISH"; }
/// get the metric strongest voxel algorithm name
static QString getAlgorithmMetricStrongestVoxelName() { return "METRIC_STRONGEST_VOXEL"; }
/// get the paint enclosing voxel algorithm name
static QString getAlgorithmPaintEnclosingVoxel() { return "PAINT_ENCLOSING_VOXEL"; }
protected:
/// algorithm used for mapping
ALGORITHM algorithm;
/// average voxel neighbors
float averageVoxelNeighbors;
/// maximum voxel neighbors
float maximumVoxelNeighbors;
/// strongest voxel neighbors
float strongestVoxelNeighbors;
/// gaussian neighbors
float gaussianNeighbors;
/// gaussian sigma norm
float gaussianSigmaNorm;
/// gaussian sigma tang
float gaussianSigmaTang;
/// gaussian norm below cutoff
float gaussianNormBelowCutoff;
/// gaussian norm above cutoff
float gaussianNormAboveCutoff;
/// gaussian tang cutoff
float gaussianTangCutoff;
/// mcw brain fish max distance
float mcwBrainFishMaxDistance;
/// mcw brain fish splat factor
int mcwBrainFishSplatFactor;
/// PALS metric average fiducial mapping enabled
bool palsMetricAverageFiducialMappingEnabled;
/// PALS metric multi fiducial mapping enabled
bool palsMetricMultiFiducialMappingEnabled;
/// PALS metric minimum enabled
bool palsMetricMinimumEnabled;
/// PALS metric maximum enabled
bool palsMetricMaximumEnabled;
/// PALS metric standard deviation enabled
bool palsMetricStandardDeviationEnabled;
/// PALS metric standard error enabled
bool palsMetricStandardErrorEnabled;
/// PALS metric all cases enabled
bool palsMetricAllCasesEnabled;
/// PALS paint average fiducial mapping enabled
bool palsPaintAverageFiducialMappingEnabled;
/// PALS paint most common enabled
bool palsPaintMostCommonEnabled;
/// PALS paint most common exlude unidentified enabled
bool palsPaintMostCommonExcludeUnidentifiedEnabled;
/// PALS paint all cases enabled
bool palsPaintAllCasesEnabled;
};
#endif // __BRAIN_MODEL_VOLUME_TO_SURFACE_MAPPER_ALGORITHM_PARAMETERS_H__
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