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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 "CommandVolumeMaskWithVolume.h"
#include "FileFilters.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "VolumeFile.h"
/**
* constructor.
*/
CommandVolumeMaskWithVolume::CommandVolumeMaskWithVolume()
: CommandBase("-volume-mask-with-volume",
"VOLUME MASK WITH VOLUME")
{
}
/**
* destructor.
*/
CommandVolumeMaskWithVolume::~CommandVolumeMaskWithVolume()
{
}
/**
* get the script builder parameters.
*/
void
CommandVolumeMaskWithVolume::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Input Volume File Name", FileFilters::getVolumeGenericFileFilter());
paramsOut.addFile("Input Mask Volume File Name", FileFilters::getVolumeGenericFileFilter());
paramsOut.addFile("Output Volume File Name", FileFilters::getVolumeGenericFileFilter());
paramsOut.addInt("Dilation Iterations");
}
/**
* get full help information.
*/
QString
CommandVolumeMaskWithVolume::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<input-volume-file-name>\n"
+ indent9 + "<input-mask-volume-file-name>\n"
+ indent9 + "<output-volume-file-name>\n"
+ indent9 + "<dilation-iterations>\n"
+ indent9 + "\n"
+ indent9 + "Clear all of the voxels in the input volume that map into\n"
+ indent9 + "a zero voxel in the mask volume. The mapping is performed\n"
+ indent9 + "using stereotaxic coordinates so the volumes do not need to have\n"
+ indent9 + "have the same voxel dimensions but must overlap in stereotaxic\n"
+ indent9 + "coordinates. Create a mask volume using this program with the\n"
+ indent9 + "\"-surfaces-to-segmentation-volume-mask\" option.\n"
+ indent9 + "\n"
+ indent9 + "If \"dilation-iterations\" is non-zero, the mask will be dilated\n"
+ indent9 + "the specified number of times prior to the application of the mask.\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandVolumeMaskWithVolume::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
const QString inputVolumeFileName =
parameters->getNextParameterAsString("Input Volume File Name");
const QString inputMaskVolumeFileName =
parameters->getNextParameterAsString("Input MaskVolume File Name");
QString outputVolumeFileName, outputVolumeFileLabel;
parameters->getNextParameterAsVolumeFileNameAndLabel("Output Volume File Name/Label",
outputVolumeFileName,
outputVolumeFileLabel);
const int dilationIterations =
parameters->getNextParameterAsInt("Dilation Iterations");
checkForExcessiveParameters();
//
// Read the input file
//
VolumeFile volume;
volume.readFile(inputVolumeFileName);
//
// Read the input mask file
//
VolumeFile maskVolume;
maskVolume.readFile(inputMaskVolumeFileName);
//
// Dilate mask volume
if (dilationIterations > 0) {
maskVolume.doVolMorphOps(dilationIterations, 0);
}
//
// mask the volume
//
volume.maskWithVolume(&maskVolume);
//
// Write the volume
//
writeVolumeFile(volume, outputVolumeFileName, outputVolumeFileLabel);
}
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