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#ifndef __BRAIN_MODEL_SURFACE_METRIC_COORDINATE_DIFFERENCE_H__
#define __BRAIN_MODEL_SURFACE_METRIC_COORDINATE_DIFFERENCE_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 <QString>
#include <vector>
#include "BrainModelSurfaceMetricFindClustersBase.h"
class BrainModelSurface;
class CoordinateFile;
class MetricFile;
class QTextStream;
/// find significant clusters in metric files that contain coordinate differences
class BrainModelSurfaceMetricCoordinateDifference : public BrainModelSurfaceMetricFindClustersBase {
public:
/// the mode of the algorithm
enum MODE {
/// coordinate difference mode
MODE_COORDINATE_DIFFERENCE,
/// t-map difference mode
MODE_TMAP_DIFFERENCE
};
// constructor
BrainModelSurfaceMetricCoordinateDifference(BrainSet* bs,
const MODE modeIn,
const std::vector<QString>& coordFileGroupAIn,
const std::vector<QString>& coordFileGroupBIn,
const QString& fiducialCoordFileNameIn,
const QString& openTopoFileNameIn,
const QString& distortionShapeFileNameIn,
const QString& distanceMetricFileNameIn,
const QString& shuffledDistanceMetricFileNameIn,
const QString& clustersPaintFileNameIn,
const QString& clustersMetricFileNameIn,
const QString& reportFileNameIn,
const int distortionShapeFileColumnIn,
const int iterationsIn,
const float thresholdIn,
const float pValueIn,
const int numberOfThreadsIn);
// destructor
~BrainModelSurfaceMetricCoordinateDifference();
protected:
/// must be implemented by subclasses
void executeClusterSearch() throw (BrainModelAlgorithmException);
// free memory
void cleanUp();
/// compute coordinate deviation
void computeCoordinateDeviation(const std::vector<CoordinateFile*>& coordFiles,
const CoordinateFile& averageCoordFile,
MetricFile& deviationFile);
/// mode of the algorithm
MODE mode;
/// names of coordinate files for group A
std::vector<QString> coordFileNameGroupA;
/// names of coordinate files for group B
std::vector<QString> coordFileNameGroupB;
/// group A coordinate files
std::vector<CoordinateFile*> coordGroupA;
/// group B coordinate files
std::vector<CoordinateFile*> coordGroupB;
/// iterations for shuffling average coord files
int iterations;
/// name of distance metric file
//QString& distanceMetricFileName;
/// name of shuffled distance metric file
//QString& shuffledDistanceMetricFileName;
};
#endif // __BRAIN_MODEL_SURFACE_METRIC_COORDINATE_DIFFERENCE_H__
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