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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 "CommandVolumeBiasCorrection.h"
#include "FileFilters.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "VolumeFile.h"
/**
* constructor.
*/
CommandVolumeBiasCorrection::CommandVolumeBiasCorrection()
: CommandBase("-volume-bias-correction",
"VOLUME BIAS CORRECTION")
{
}
/**
* destructor.
*/
CommandVolumeBiasCorrection::~CommandVolumeBiasCorrection()
{
}
/**
* get the script builder parameters.
*/
void
CommandVolumeBiasCorrection::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addInt("Gray Minimum", 0);
paramsOut.addInt("White Maximum", 255);
paramsOut.addInt("Iterations", 5);
paramsOut.addFile("Input Volume File", FileFilters::getVolumeAnatomyFileFilter());
paramsOut.addFile("Output Volume File", FileFilters::getVolumeAnatomyFileFilter());
}
/**
* get full help information.
*/
QString
CommandVolumeBiasCorrection::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<gray-minimum-value>\n"
+ indent9 + "<white-maximum-value>\n"
+ indent9 + "<iterations>\n"
+ indent9 + "<input-volume-file-name>\n"
+ indent9 + "<output-volume-file-name>\n"
+ indent9 + "\n"
+ indent9 + "Perform bias (non-uniformity) correction on an anatomy\n"
+ indent9 + "volume.\n"
+ indent9 + "\n"
+ indent9 + "\"gray-minimum-value\" is an integer that is the minimum\n"
+ indent9 + "value of the gray matter voxels. \n"
+ indent9 + "\n"
+ indent9 + "\"white-maximum-value\" is an integer that is the maximum\n"
+ indent9 + "value of the white matter voxels. \n"
+ indent9 + "\n"
+ indent9 + "\"iterations\" is the number of iterations used in the bias\n"
+ indent9 + "correction algorithm. A value of 5 is sufficient in most\n"
+ indent9 + "cases. \n"
+ indent9 + "\n"
+ indent9 + "This algorithm (and code) is taken directly from AFNI's \n"
+ indent9 + "3dUniformize program. \n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandVolumeBiasCorrection::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
const int grayMinimum =
parameters->getNextParameterAsInt("Gray Minimum Value");
const int whiteMaximum =
parameters->getNextParameterAsInt("White Maximum Value");
const int iterations =
parameters->getNextParameterAsInt("Iterations");
const QString inputVolumeFileName =
parameters->getNextParameterAsString("Input Volume File Name");
QString outputVolumeFileName =
parameters->getNextParameterAsString("Output Volume File Name");
QString outputVolumeFileLabel;
splitOutputVolumeNameIntoNameAndLabel(outputVolumeFileName, outputVolumeFileLabel);
checkForExcessiveParameters();
VolumeFile volumeFile;
volumeFile.readFile(inputVolumeFileName);
volumeFile.biasCorrectionWithAFNI(grayMinimum,
whiteMaximum,
iterations);
writeVolumeFile(volumeFile,
outputVolumeFileName,
outputVolumeFileLabel);
}
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