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#ifndef __BRAIN_MODEL_SURFACE_SHAPE_FIND_CLUSTERS_BASE_H__
#define __BRAIN_MODEL_SURFACE_SHAPE_FIND_CLUSTERS_BASE_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 "BrainModelAlgorithm.h"
class BrainModelSurface;
class BrainModelSurfaceMetricClustering;
class MetricFile;
class QTextStream;
/// base class for finding clusters in surface shape files
class BrainModelSurfaceMetricFindClustersBase : public BrainModelAlgorithm {
public:
// constructor
BrainModelSurfaceMetricFindClustersBase(BrainSet* bs,
const QString& fiducialCoordFileNameIn,
const QString& openTopoFileNameIn,
const QString& distortionShapeFileNameIn,
const QString& statisticalMapFileNameIn,
const QString& shuffledStatisticalMapFileNameIn,
const QString& clustersPaintFileNameIn,
const QString& clustersMetricFileNameIn,
const QString& reportFileNameIn,
const int distortionShapeFileColumnIn,
const float negativeThreshIn,
const float positiveThreshIn,
const float pValueIn,
const int tVarianceSmoothingIterationsIn,
const float tVarianceSmoothingStrengthIn,
const bool doStatisticalMapDOFIn,
const bool doStatisticalMapPValueIn,
const int numberOfThreadsIn);
// destructor
~BrainModelSurfaceMetricFindClustersBase();
// execute the algorithm
void execute() throw (BrainModelAlgorithmException);
protected:
/// class for cluster thresholding
class Cluster {
public:
QString name;
int column;
int numberOfNodes;
std::vector<int> nodes;
float area;
float areaCorrected;
float cogX;
float cogY;
float cogZ;
float pValue;
float threshMin;
float threshMax;
/// constructor
Cluster() {
name = "";
column = -1;
numberOfNodes = 0;
area = 0.0;
areaCorrected = 0.0;
cogX = 0.0;
cogY = 0.0;
cogZ = 0.0;
pValue = -1.0;
threshMin = 0.0;
threshMax = 0.0;
nodes.clear();
}
/// comparison operator using area corrected
bool operator<(const Cluster& c) const {
return (areaCorrected < c.areaCorrected);
}
/// set the name of a cluster
void setName() {
name = "";
if (threshMax < 0.0) {
name += "minus_";
}
else {
name += "plus_";
}
name += "cluster_area_";
name += QString::number(areaCorrected, 'f', 1);
name += "_nodes_";
name += QString::number(numberOfNodes);
}
};
/// must be implemented by subclasses
virtual void executeClusterSearch() throw (BrainModelAlgorithmException) = 0;
// free memory
virtual void cleanUp();
// find clusters in shape file
void findClusters(MetricFile* mf,
std::vector<Cluster>& clustersOut,
const QString& progressMessage,
const int limitToColumn,
const bool useLargestClusterPerColumnFlag) throw (BrainModelAlgorithmException);
// find clusters
void findClustersSingleThread(MetricFile* mf,
std::vector<Cluster>& clustersOut,
const QString& progressMessage,
const int limitToColumn,
const bool useLargestClusterPerColumnFlag) throw (BrainModelAlgorithmException);
// find clusters in shape file using multiple threads
void findClustersMultiThread(MetricFile* mf,
std::vector<Cluster>& clustersOut,
const QString& progressMessage,
const int limitToColumn,
const bool useLargestClusterPerColumnFlag,
const int numberOfThreads) throw (BrainModelAlgorithmException);
/// Get the clusters after the cluster finding algorithm has finished
void saveClusters(BrainModelSurfaceMetricClustering* bmsmc,
std::vector<Cluster>& clustersOut,
const int columnNumber,
const bool useLargestClusterPerColumnFlag);
// print the clusters
void printClusters(QTextStream& stream, const std::vector<Cluster>& clusters,
const float sigArea = -1.0);
/// create the clusters paint file
void createClustersPaintFile(const std::vector<Cluster>& clusters,
const float sigArea,
const int numNodes);
/// create the clusters metric file
void createClustersMetricFile(const std::vector<Cluster>& clusters,
const int statisticalMapColumn,
const int numNodes);
/// set names of all clusters
void setNamesForClusters(std::vector<Cluster>& clusters);
/// create the clusters report file
void createMetricShapeClustersReportFile(const std::vector<Cluster>& clusters,
const QString& metricShapeFileName);
/// name of fiducial coord file
QString fiducialCoordFileName;
/// name of open topo file
QString openTopoFileName;
/// name of area correction shape file
QString areaCorrectionShapeFileName;
/// name of Statistical Map file
QString statisticalMapFileName;
/// name of shuffled Statistical map file
QString shuffledStatisticalMapFileName;
/// name of clusters paint file
QString clustersPaintFileName;
/// name of clusters metric file name
QString clustersMetricFileName;
/// name of report file
QString reportFileName;
/// area correction shape file column
int areaCorrectionShapeFileColumn;
/// negative threshold
float negativeThresh;
/// positive threshold
float positiveThresh;
/// P-Value
float pValue;
/// brain set used by this algorithm
BrainSet* brain;
/// surface used by this algorithm
BrainModelSurface* bms;
// area correction shape file
MetricFile* areaCorrectionShapeFile;
/// shuffled statistical map file
MetricFile* shuffleStatisticalMapShapeFile;
/// statistical map shape fie
MetricFile* statisticalMapShapeFile;
/// t-map variance smoothing iterations
int tVarianceSmoothingIterations;
/// t-map variance smoothing strength
float tVarianceSmoothingStrength;
/// compute degrees of freedom for statistical map
bool doStatisticalMapDOF;
/// compute p-value for statistical map
bool doStatisticalMapPValue;
/// number of threads for cluster search
int numberOfThreads;
};
#endif // __BRAIN_MODEL_SURFACE_SHAPE_FIND_CLUSTERS_BASE_H__
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