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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 <iostream>
#include <QTime>
#include "BrainModelVolumeTopologyGraphCorrector.h"
#include "BrainSet.h"
#include "CommandVolumeTopologyCorrector.h"
#include "FileFilters.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "VolumeFile.h"
/**
* constructor.
*/
CommandVolumeTopologyCorrector::CommandVolumeTopologyCorrector()
: CommandBase("-volume-topology-corrector",
"VOLUME TOPOLOGY CORRECTOR (in development - do not use)")
{
}
/**
* destructor.
*/
CommandVolumeTopologyCorrector::~CommandVolumeTopologyCorrector()
{
}
/**
* get the script builder parameters.
*/
void
CommandVolumeTopologyCorrector::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
std::vector<QString> mode;
mode.push_back("NORMAL");
mode.push_back("MINIMAL");
paramsOut.clear();
paramsOut.addFile("Input Segmentation Volume File Name",
FileFilters::getVolumeSegmentationFileFilter());
paramsOut.addFile("Output Corrected Segmentation Volume File Name",
FileFilters::getVolumeSegmentationFileFilter());
paramsOut.addListOfItems("Mode", mode, mode);
paramsOut.addFile("Paint Volume File Showing Corrections",
FileFilters::getVolumePaintFileFilter(),
"corrections.nii.gz",
"-correction-paint-volume");
}
/**
* get full help information.
*/
QString
CommandVolumeTopologyCorrector::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<input-segmentation-volume-file-name>\n"
+ indent9 + "<output-corrected-segmentation-volume-file-name>\n"
+ indent9 + "<correction-mode>\n"
+ indent9 + "[-correction-paint-volume <paint-volume-file-name>]\n"
+ indent9 + "\n"
+ indent9 + "Correct segmentation volume topology.\n"
+ indent9 + "\n"
+ indent9 + "correction-mode is one of:\n"
+ indent9 + " MINIMAL fix minimal number of voxels\n"
+ indent9 + " NORMAL normal correction\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandVolumeTopologyCorrector::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
//
// Get parameters
//
const QString segmentationVolumeFileName =
parameters->getNextParameterAsString("Input Segmentation Volume File Name");
const QString correctedSegmentationVolumeFileName =
parameters->getNextParameterAsString("Corrected Output Segmentation Volume File Name");
const QString correctionModeString =
parameters->getNextParameterAsString("Corrected Mode");
QString correctionsPaintVolumeFileName;
while (parameters->getParametersAvailable()) {
const QString paramName =
parameters->getNextParameterAsString("Optional Parameter");
if (paramName == "-correction-paint-volume") {
correctionsPaintVolumeFileName =
parameters->getNextParameterAsString("Paint Volume File Showing Corrections Name");
}
else {
throw CommandException("Unrecognized Parameter: " + paramName);
}
}
//
// Set the correction mode
//
BrainModelVolumeTopologyGraphCorrector::CORRECTION_MODE correctionMode =
BrainModelVolumeTopologyGraphCorrector::CORRECTION_MODE_NORMAL;
if (correctionModeString == "MINIMAL") {
correctionMode =
BrainModelVolumeTopologyGraphCorrector::CORRECTION_MODE_MINIMAL;
}
else if (correctionModeString == "NORMAL") {
correctionMode =
BrainModelVolumeTopologyGraphCorrector::CORRECTION_MODE_NORMAL;
}
else {
throw CommandException("Invalid correction mode: " + correctionModeString);
}
//
// Read volume
//
VolumeFile segmentationVolumeFile;
segmentationVolumeFile.readFile(segmentationVolumeFileName);
//
// Create graph of foreground
//
BrainSet bs;
BrainModelVolumeTopologyGraphCorrector corrector(&bs,
correctionMode,
&segmentationVolumeFile);
QTime timer;
timer.start();
corrector.execute();
const float totalTime = (static_cast<float>(timer.elapsed()) * 0.001);
//
// Save corrected volume file
//
if (corrector.getCorrectedSegmentationVolumeFile() != NULL) {
VolumeFile correctedVolumeFile(*corrector.getCorrectedSegmentationVolumeFile());
correctedVolumeFile.writeFile(correctedSegmentationVolumeFileName);
}
if (correctionsPaintVolumeFileName.isEmpty() == false) {
VolumeFile* paintVol = new VolumeFile(*corrector.getShowingCorrectionsPaintVolumeFile());
if (paintVol != NULL) {
paintVol->writeFile(correctionsPaintVolumeFileName);
delete paintVol;
}
}
//
// Print percent changed
//
const int numVoxels = segmentationVolumeFile.getTotalNumberOfVoxels();
const int numChanged = corrector.getNumberOfVoxelsChanged();
const float percentChanged =
(static_cast<float>(numChanged)
/ static_cast<float>(numVoxels))
* 100.0;
std::cout << numChanged
<< " of "
<< numVoxels
<< " ("
<< percentChanged
<< "%) voxels changed in correction."
<< std::endl;
std::cout << "Time to correct volume topology: "
<< totalTime
<< " seconds."
<< std::endl;
}
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