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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 "BorderProjectionFile.h"
#include "BrainModelSurface.h"
#include "BrainModelSurfaceBorderToMetricConverter.h"
#include "BrainSet.h"
#include "CommandSurfaceBorderToMetric.h"
#include "FileFilters.h"
#include "FileUtilities.h"
#include "MetricFile.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
/**
* constructor.
*/
CommandSurfaceBorderToMetric::CommandSurfaceBorderToMetric()
: CommandBase("-surface-border-to-metric",
"SURFACE BORDER CONVERT TO METRIC")
{
}
/**
* destructor.
*/
CommandSurfaceBorderToMetric::~CommandSurfaceBorderToMetric()
{
}
/**
* get the script builder parameters.
*/
void
CommandSurfaceBorderToMetric::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Input Coordinates File",
FileFilters::getCoordinateGenericFileFilter());
paramsOut.addFile("Input Topology File",
FileFilters::getTopologyGenericFileFilter());
paramsOut.addFile("Input Border Projection File",
FileFilters::getBorderProjectionFileFilter());
paramsOut.addFile("Output Metric File",
FileFilters::getMetricFileFilter());
}
/**
* get full help information.
*/
QString
CommandSurfaceBorderToMetric::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<input-coordinate-file>\n"
+ indent9 + "<input-topology-file>\n"
+ indent9 + "<input-border-projection-file>\n"
+ indent9 + "<output-metric-file>\n"
+ indent9 + "\n"
+ indent9 + "Convert the border projection file to a metric file\n"
+ indent9 + "by assigning the border's variance to the surface \n"
+ indent9 + "nodes based upon the triangle which the border point\n"
+ indent9 + "falls within.\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandSurfaceBorderToMetric::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
//
// Get the inputs
//
const QString coordinateFileName =
parameters->getNextParameterAsString("Coordinate File");
const QString topologyFileName =
parameters->getNextParameterAsString("Topology File");
const QString borderProjectionFileName =
parameters->getNextParameterAsString("Border Projection File");
const QString metricFileName =
parameters->getNextParameterAsString("Metric File");
//
// Create a spec file to read in the data files
//
SpecFile sf;
sf.addToSpecFile(SpecFile::getUnknownCoordFileMatchTag(),
coordinateFileName,
"",
false);
sf.addToSpecFile(SpecFile::getUnknownTopoFileMatchTag(),
topologyFileName,
"",
false);
sf.addToSpecFile(SpecFile::getBorderProjectionFileTag(),
borderProjectionFileName,
"",
false);
//
// Read the files
//
QString errorMessage;
BrainSet brainSet;
brainSet.readSpecFile(sf,
"",
errorMessage);
if (errorMessage.isEmpty() == false) {
throw new CommandException(errorMessage);
}
BrainModelSurface* surface = brainSet.getBrainModelSurface(0);
if (surface == NULL) {
throw CommandException("Surface is invalid.");
}
//
// Get the border projections
//
BorderProjectionFile borderProjectionFile;
BrainModelBorderSet* bmbs = brainSet.getBorderSet();
bmbs->copyBordersToBorderProjectionFile(borderProjectionFile);
//
// Convert the borders to metric
//
MetricFile mf;
BrainModelSurfaceBorderToMetricConverter
converter(&brainSet,
surface,
&borderProjectionFile,
&mf,
0,
FileUtilities::basename(borderProjectionFileName));
converter.execute();
//
// Write the metric file
//
mf.writeFile(metricFileName);
}
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