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/*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*/
#ifndef __FOCI_FILE_TO_PALS_PROJECTOR_H__
#define __FOCI_FILE_TO_PALS_PROJECTOR_H__
#include <vector>
#include "BrainModelAlgorithm.h"
#include "Structure.h"
class CellProjection;
class FociProjectionFile;
class BrainModelSurfacePointProjector;
class BrainSet;
class MapFmriAtlasSpecFileInfo;
class StudyMetaDataFile;
/// This class is used to project a FocusFile to a BrainModelSurface and store the
/// results in a cell projection file.
class FociFileToPalsProjector : public BrainModelAlgorithm {
public:
/// Constructor
FociFileToPalsProjector(BrainSet* brainSetIn,
FociProjectionFile* fociProjectionFileIn,
const StudyMetaDataFile* studyMetaDataFileIn,
const int firstFocusIndexIn,
const int lastFocusIndexIn,
const float projectOntoSurfaceAboveDistanceIn,
const bool projectOntoSurfaceFlagIn,
const bool projectToCerebellumFlagIn,
const float cerebralCutoffIn,
const float cerebellumCutoffIn);
/// Destructor
~FociFileToPalsProjector();
/// project the foci
void execute() throw (BrainModelAlgorithmException);
/// default cutoff for distance to cerebral cortex
static float getDefaultCerebralCutoffDistance() { return 2.0; }
/// default cutoff for distance to cerebellum
static float getDefaultCerebellumCutoffDistance() { return 4.0; }
/// set the index of the first focus to project
void setFirstFocusIndex(const int firstFocusIndexIn,
const int lastFocusIndexIn);
protected:
//
// class for storing the point projectors
//
class PointProjector {
public:
/// constructor
PointProjector(const QString& spaceNameIn,
const Structure::STRUCTURE_TYPE structureTypeIn,
BrainModelSurfacePointProjector* pointProjectorIn,
BrainSet* bsIn,
BrainModelSurface* bmsIn);
/// destructor
~PointProjector();
/// get the space name
QString getSpaceName() const { return spaceName; }
/// get the structure
Structure::STRUCTURE_TYPE getStructureType() const { return structureType; }
/// equality operator
bool operator==(const PointProjector& pp) const;
/// brain set
BrainSet* bs;
/// surface used for projection
BrainModelSurface* bms;
/// original name of space
QString originalSpaceName;
/// name of space
QString spaceName;
/// structure
Structure::STRUCTURE_TYPE structureType;
/// the point projector
BrainModelSurfacePointProjector* pointProjector;
};
// project a single cell
void projectFocus(CellProjection& cp,
BrainModelSurface* bms,
BrainModelSurfacePointProjector* pointProjector,
const BrainModelSurface* searchSurface);
// convert space names to identical spaces
static void spaceNameConvert(QString& spaceName);
// load the needed point projectors
void loadNeededPointProjectors(const std::vector<PointProjector>& projectorsNeeded) throw (BrainModelAlgorithmException);
// find the surface for the specified space and structure
BrainModelSurface* findSearchSurface(const QString& spaceName,
const Structure::STRUCTURE_TYPE structure);
// get distance of focus from a surface
float getDistanceToSurface(const CellProjection* cp,
const PointProjector* pp) const;
// get point projector for space and structure
PointProjector* getPointProjector(const QString& spaceName,
const Structure::STRUCTURE_TYPE structure);
// spaces currently loaded
std::vector<PointProjector*> pointProjectors;
// the file that is to be projected
FociProjectionFile* fociProjectionFile;
// the study metadata file
const StudyMetaDataFile* studyMetaDataFile;
// the first focus that is to be projected
int firstFocusIndex;
// the last focus that is to be projected (if -1 do all)
int lastFocusIndex;
// project onto surface distance
const float projectOntoSurfaceAboveDistance;
// project onto surface flag
const bool projectOntoSurfaceFlag;
/// project to cerebellum flag
bool projectToCerebellumFlag;
/// cerebral cortext cutoff
float cerebralCutoff;
/// cerebellum cutoff
float cerebellumCutoff;
/// atlases available for mapping foci
std::vector<MapFmriAtlasSpecFileInfo> availableAtlases;
/// atlases need to be loaded flag
bool atlasesDirectoryLoadedFlag;
};
/*
bool
operator==(const FociFileToPalsProjector::PointProjector& pp1,
const FociFileToPalsProjector::PointProjector& pp2)
{
const bool val = ((pp1.getSpaceName() == pp2.getSpaceName()) &&
(pp1.getStructureType() == pp2.getStructureType()));
return val;
}
*/
#endif // __FOCI_FILE_TO_PALS_PROJECTOR_H__
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