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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 "BrainModelVolumeSureFitSegmentation.h"
#include "CommandVolumeCreateCorpusCallosumSlice.h"
#include "FileFilters.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "Structure.h"
/**
* constructor.
*/
CommandVolumeCreateCorpusCallosumSlice::CommandVolumeCreateCorpusCallosumSlice()
: CommandBase("-volume-create-corpus-callosum-slice",
"VOLUME CREATE CORPUS CALLOSUM SLICE")
{
}
/**
* destructor.
*/
CommandVolumeCreateCorpusCallosumSlice::~CommandVolumeCreateCorpusCallosumSlice()
{
}
/**
* get the script builder parameters.
*/
void
CommandVolumeCreateCorpusCallosumSlice::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
std::vector<Structure::STRUCTURE_TYPE> structureTypes;
std::vector<QString> structureNames;
Structure::getAllTypesAndNames(structureTypes, structureNames, false);
paramsOut.clear();
paramsOut.addFile("Anatomy Volume File Name", FileFilters::getVolumeGenericFileFilter());
paramsOut.addFile("Output Volume File Name", FileFilters::getVolumeGenericFileFilter());
paramsOut.addListOfItems("Structure", structureNames, structureNames);
paramsOut.addVariableListOfParameters("Callosum Slice Options");
}
/**
* get full help information.
*/
QString
CommandVolumeCreateCorpusCallosumSlice::getHelpInformation() const
{
std::vector<Structure::STRUCTURE_TYPE> structureTypes;
std::vector<QString> structureNames;
Structure::getAllTypesAndNames(structureTypes, structureNames, false);
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + " <anatomy-volume-file-name>\n"
+ indent9 + " <output-volume-file-name>\n"
+ indent9 + " <structure>\n"
+ indent9 + " [-gray gray-matter-peak]\n"
+ indent9 + " [-white white-matter-peak]\n"
+ indent9 + "\n"
+ indent9 + "Create the corpus callosum slice from an anatomical volume.\n"
+ indent9 + "If the gray and white matter peaks are not specified, they\n"
+ indent9 + "will be estimated.\n"
+ indent9 + "\n");
helpInfo += (indent9 + "Examples of \"structure\" are: \n");
for (int i = 0; i < static_cast<int>(structureNames.size()); i++) {
helpInfo += (indent9 + " " + structureNames[i] + "\n");
}
helpInfo +=
(indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandVolumeCreateCorpusCallosumSlice::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
//
// Get the parameters
//
const QString inputVolumeFileName =
parameters->getNextParameterAsString("Anatomy Volume File Name");
QString outputVolumeFileName, outputVolumeFileLabel;
parameters->getNextParameterAsVolumeFileNameAndLabel("Output Volume File Name",
outputVolumeFileName,
outputVolumeFileLabel);
const Structure structure = parameters->getNextParameterAsStructure("Structure");
//
// Optional parameters
//
float grayMatterPeak = -1.0;
float whiteMatterPeak = -1.0;
while (parameters->getParametersAvailable()) {
const QString paramName = parameters->getNextParameterAsString("Volume Create Corpus Callosum Option");
if (paramName == "-gray") {
grayMatterPeak = parameters->getNextParameterAsFloat("Gray Matter Peak");
}
else if (paramName == "-white") {
whiteMatterPeak = parameters->getNextParameterAsFloat("White Matter Peak");
}
else {
throw CommandException("Volume Create Corpus Callosum invalid parameter "
+ paramName);
}
}
//
// Read input file
//
VolumeFile anatomyVolume;
anatomyVolume.readFile(inputVolumeFileName);
//
// Generate the corpus callosum slice volume
//
VolumeFile corpusCallosumVolume;
BrainModelVolumeSureFitSegmentation::generateCorpusCallosumSlice(
anatomyVolume,
corpusCallosumVolume,
structure,
grayMatterPeak,
whiteMatterPeak);
//
// Write the volume file
//
corpusCallosumVolume.setDescriptiveLabel(outputVolumeFileLabel);
corpusCallosumVolume.writeFile(outputVolumeFileName);
}
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