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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*/
#include <QFileInfo>
#include "BrainModelSurfaceDeformationSpherical.h"
#include "BrainSet.h"
#include "CommandSurfaceRegistrationSpherical.h"
#include "DeformationMapFile.h"
#include "FileFilters.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "SpecFile.h"
/**
* constructor.
*/
CommandSurfaceRegistrationSpherical::CommandSurfaceRegistrationSpherical()
: CommandBase("-surface-register-sphere",
"SURFACE SPHERICAL REGISTRATION")
{
}
/**
* destructor.
*/
CommandSurfaceRegistrationSpherical::~CommandSurfaceRegistrationSpherical()
{
}
/**
* get the script builder parameters.
*/
void
CommandSurfaceRegistrationSpherical::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addString("Options", "N");
paramsOut.addFile("Deformation Map File Name", FileFilters::getDeformationMapFileFilter());
paramsOut.addFile("Individual Spec File Name", FileFilters::getSpecFileFilter());
paramsOut.addFile("Individual Border Projection File Name", FileFilters::getBorderProjectionFileFilter());
paramsOut.addFile("Individual Closed Topology File Name", FileFilters::getTopologyClosedFileFilter());
paramsOut.addFile("Individual Cut Topology File Name", FileFilters::getTopologyCutFileFilter());
paramsOut.addFile("Individual Fiducial Coordinate File Name", FileFilters::getCoordinateFiducialFileFilter());
paramsOut.addFile("Individual Spherical Coordinate File Name", FileFilters::getCoordinateSphericalFileFilter());
paramsOut.addFile("Individual Flat Coordinate File Name", FileFilters::getCoordinateFlatFileFilter());
paramsOut.addFile("Atlas Spec File Name", FileFilters::getSpecFileFilter());
paramsOut.addFile("Atlas Border Projection File Name", FileFilters::getBorderProjectionFileFilter());
paramsOut.addFile("Atlas Closed Topology File Name", FileFilters::getTopologyClosedFileFilter());
paramsOut.addFile("Atlas Cut Topology File Name", FileFilters::getTopologyCutFileFilter());
paramsOut.addFile("Atlas Fiducial Coordinate File Name", FileFilters::getCoordinateFiducialFileFilter());
paramsOut.addFile("Atlas Spherical Coordinate File Name", FileFilters::getCoordinateSphericalFileFilter());
paramsOut.addFile("Atlas Flat Coordinate File Name", FileFilters::getCoordinateFlatFileFilter());
}
/**
* get full help information.
*/
QString
CommandSurfaceRegistrationSpherical::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<options>\n"
+ indent9 + "<deformation-map-file-name-containing-registration-parameters>\n"
+ indent9 + "<individual-spec-file-name>\n"
+ indent9 + "<atlas-spec-file-name>\n"
+ indent9 + "\n"
+ indent9 + "The above method requires that the each of the spec file have one and only\n"
+ indent9 + "one border projection file, closed topology file,fiducial coordinate file,\n"
+ indent9 + "and spherical coordinate file. The spec files may have zero or one\n"
+ indent9 + "cut topology file and flat coordinate file.\n"
+ indent9 + "\n"
+ indent9 + "Each of the individual or atlas data files MUST be listed\n"
+ indent9 + "in the respective individual or atlas spec files.\n"
+ indent9 + "\n"
+ indent9 + "<options>\n"
+ indent9 + "<deformation-map-file-name-containing-registration-parameters>\n"
+ indent9 + "<individual-spec-file-name>\n"
+ indent9 + "<individual-border-projection-file-name>\n"
+ indent9 + "<individual-closed-topology-file-name>\n"
+ indent9 + "<individual-cut-topology-file-name>\n"
+ indent9 + "<individual-fiducial-coordinate-file-name>\n"
+ indent9 + "<individual-spherical-coordinate-file-name>\n"
+ indent9 + "<individual-flat-coordiante-file-name>\n"
+ indent9 + "<atlas-spec-file-name>\n"
+ indent9 + "<atlas-border-projection-file-name>\n"
+ indent9 + "<atlas-closed-topology-file-name>\n"
+ indent9 + "<atlas-cut-topology-file-name>\n"
+ indent9 + "<atlas-fiducial-coordinate-file-name>\n"
+ indent9 + "<atlas-spherical-coordinate-file-name>\n"
+ indent9 + "<atlas-flat-coordiante-file-name>\n"
+ indent9 + "\n"
+ indent9 + "Peform spherical registration.\n"
+ indent9 + "\n"
+ indent9 + "Some files, such as the flat coordinate files or deformation map file\n"
+ indent9 + "are optional and in this case the name should be specified with two\n"
+ indent9 + "consecutive double quotes (eg: \"\").\n"
+ indent9 + "\n"
+ indent9 + "options - a single character either 'Y' or 'N' \n"
+ indent9 + " Y - deform the individual to the atlas and the atlas to the individual.\n"
+ indent9 + " N - deform the individual to the atlas only.\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandSurfaceRegistrationSpherical::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
const QString options =
parameters->getNextParameterAsString("Options");
const QString defMapFileName =
parameters->getNextParameterAsString("Deformation Map File Name");
QString individualSpecFileName =
parameters->getNextParameterAsString("Individual Spec File Name");
const QString indivBorderFileName =
parameters->getNextParameterAsString("Individual Border Projection File Name");
const QString indivClosedTopoFileName =
parameters->getNextParameterAsString("Individual Closed Topology File Name");
const QString indivCutTopologyFileName =
parameters->getNextParameterAsString("Individual Cut Topology File Name");
const QString indivFiducialCoordFileName =
parameters->getNextParameterAsString("Individual Fiducial Coordinate File Name");
const QString indivSphericalCoordFileName =
parameters->getNextParameterAsString("Individual Spherical Coordinate File Name");
const QString indivFlatCoordFileName =
parameters->getNextParameterAsString("Individual Flat Coordinate File Name");
QString atlasSpecFileName =
parameters->getNextParameterAsString("Atlas Spec File Name");
const QString atlasBorderFileName =
parameters->getNextParameterAsString("Atlas Border Projection File Name");
const QString atlasClosedTopoFileName =
parameters->getNextParameterAsString("Atlas Closed Topology File Name");
const QString atlasCutTopologyFileName =
parameters->getNextParameterAsString("Atlas Cut Topology File Name");
const QString atlasFiducialCoordFileName =
parameters->getNextParameterAsString("Atlas Fiducial Coordinate File Name");
const QString atlasSphericalCoordFileName =
parameters->getNextParameterAsString("Atlas Spherical Coordinate File Name");
const QString atlasFlatCoordFileName =
parameters->getNextParameterAsString("Atlas Flat Coordinate File Name");
//
// Read in the deformation map (if specified)
//
DeformationMapFile defMapFile;
if (defMapFileName.isEmpty() == false) {
defMapFile.readFile(defMapFileName);
}
//
// Process options
//
defMapFile.setDeformBothWays(false);
if (options.length() > 0) {
if (options[0] == 'Y') {
defMapFile.setDeformBothWays(true);
}
}
//
// Spherical deformation
//
defMapFile.setFlatOrSphereSelection(DeformationMapFile::DEFORMATION_TYPE_SPHERE);
//
// Make paths absolute
//
if (QFileInfo(individualSpecFileName).isRelative()) {
individualSpecFileName = QFileInfo(individualSpecFileName).absoluteFilePath();
}
if (QFileInfo(atlasSpecFileName).isRelative()) {
atlasSpecFileName = QFileInfo(atlasSpecFileName).absoluteFilePath();
}
//
// Set the files
//
defMapFile.setSourceSpecFileName(individualSpecFileName);
defMapFile.setSourceBorderFileName(indivBorderFileName, DeformationMapFile::BORDER_FILE_PROJECTION);
defMapFile.setSourceClosedTopoFileName(indivClosedTopoFileName);
defMapFile.setSourceCutTopoFileName(indivCutTopologyFileName);
defMapFile.setSourceFiducialCoordFileName(indivFiducialCoordFileName);
defMapFile.setSourceSphericalCoordFileName(indivSphericalCoordFileName);
defMapFile.setSourceDeformedFlatCoordFileName(indivFlatCoordFileName);
defMapFile.setTargetSpecFileName(atlasSpecFileName);
defMapFile.setTargetBorderFileName(0, atlasBorderFileName, DeformationMapFile::BORDER_FILE_PROJECTION);
defMapFile.setTargetClosedTopoFileName(atlasClosedTopoFileName);
defMapFile.setTargetCutTopoFileName(atlasCutTopologyFileName);
defMapFile.setTargetFiducialCoordFileName(atlasFiducialCoordFileName);
defMapFile.setTargetSphericalCoordFileName(atlasSphericalCoordFileName);
defMapFile.setTargetFlatCoordFileName(atlasFlatCoordFileName);
//
// Run the deformation
//
BrainSet bs;
BrainModelSurfaceDeformationSpherical alg(&bs,
&defMapFile);
alg.execute();
}
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