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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 "BrainModelVolumeGradient.h"
#include "BrainSet.h"
#include "CommandVolumeGradient.h"
#include "FileFilters.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "SureFitVectorFile.h"
#include "VolumeFile.h"
/**
* constructor.
*/
CommandVolumeGradient::CommandVolumeGradient()
: CommandBase("-volume-gradient",
"VOLUME GRADIENT")
{
}
/**
* destructor.
*/
CommandVolumeGradient::~CommandVolumeGradient()
{
}
/**
* get the script builder parameters.
*/
void
CommandVolumeGradient::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Input Volume File Name", FileFilters::getVolumeGenericFileFilter());
paramsOut.addFile("Mask Volume File Name", FileFilters::getVolumeGenericFileFilter());
paramsOut.addFile("Output Gradient Vector File", FileFilters::getSureFitVectorFileFilter());
paramsOut.addInt("Lambda");
paramsOut.addBoolean("Grad Flag");
paramsOut.addBoolean("Mask Flag");
}
/**
* get full help information.
*/
QString
CommandVolumeGradient::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<input-volume-file>\n"
+ indent9 + "<input-mask-volume-file>\n"
+ indent9 + "<gradient-vector-file-name>\n"
+ indent9 + "<lambda>\n"
+ indent9 + "<grad-flag>\n"
+ indent9 + "<mask-flag>\n"
+ indent9 + "\n"
+ indent9 + "Compute gradient.\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandVolumeGradient::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
const QString inputVolumeFileName =
parameters->getNextParameterAsString("Input Volume File Name");
const QString inputMaskVolumeFileName =
parameters->getNextParameterAsString("Input Mask Volume File Name");
const QString outputGradientFileName =
parameters->getNextParameterAsString("Output Gradient Vector File Name");
const int lambda =
parameters->getNextParameterAsInt("Lambda");
const int gradFlag =
parameters->getNextParameterAsBoolean("Grad Flag");
const int maskFlag =
parameters->getNextParameterAsBoolean("Mask Flag");
//
// Read the input and mask volume files
//
VolumeFile vf;
vf.readFile(inputVolumeFileName);
VolumeFile maskVolume;
maskVolume.readFile(inputMaskVolumeFileName);
//
// Gradient vector file
//
int xDim, yDim, zDim;
vf.getDimensions(xDim, yDim, zDim);
SureFitVectorFile gradFile(xDim, yDim, zDim);
//
// determine gradient
//
BrainSet bs;
BrainModelVolumeGradient grad(&bs,
lambda,
gradFlag,
maskFlag,
&vf,
&maskVolume,
&gradFile);
grad.execute();
//
// Write the gradient file
//
gradFile.writeFile(outputGradientFileName);
}
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