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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 "CommandVolumeSegmentationLigase.h"
#include "FileFilters.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "BrainModelVolumeLigaseSegmentation.h"
#include "BrainSet.h"
#include "StringUtilities.h"
/**
* constructor.
*/
CommandVolumeSegmentationLigase::CommandVolumeSegmentationLigase()
: CommandBase("-volume-segment-ligase",
"VOLUME SEGMENTATION LIGASE")
{
}
/**
* destructor.
*/
CommandVolumeSegmentationLigase::~CommandVolumeSegmentationLigase()
{
}
/**
* get the script builder parameters.
*/
void
CommandVolumeSegmentationLigase::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Input anatomy volume file name", FileFilters::getVolumeAnatomyFileFilter());
paramsOut.addFile("Output segmentation volume file name", FileFilters::getVolumeSegmentationFileFilter());
paramsOut.addString("Output volume label");
paramsOut.addInt("X index of seed", 128, 0);
paramsOut.addInt("Y index of seed", 128, 0);
paramsOut.addInt("Z index of seed", 128, 0);
paramsOut.addFloat("White minimum", 140.0f);
paramsOut.addFloat("White peak", 170.0f);
paramsOut.addFloat("White maximum", 200.0f);
paramsOut.addFloat("Difference cutoff base value", BrainModelVolumeLigaseSegmentation::defaultDiff());
paramsOut.addFloat("Gradient cutoff base value", BrainModelVolumeLigaseSegmentation::defaultGrad());
paramsOut.addFloat("Above peak probability minimum", BrainModelVolumeLigaseSegmentation::defaultHighBias());
paramsOut.addFloat("Below peak probability minimum", BrainModelVolumeLigaseSegmentation::defaultLowBias());
}
/**
* get full help information.
*/
QString
CommandVolumeSegmentationLigase::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<input-anatomy-volume-file-name>\n"
+ indent9 + "<output-segmentation-volume-file-name>\n"
+ indent9 + "<output-volume-label>\n"
+ indent9 + "<x-seed>\n"
+ indent9 + "<y-seed>\n"
+ indent9 + "<z-seed>\n"
+ indent9 + "<white-min>\n"
+ indent9 + "<white-peak>\n"
+ indent9 + "<white-max>\n"
+ indent9 + "[diff-base = " + StringUtilities::fromNumber(BrainModelVolumeLigaseSegmentation::defaultDiff()) + "]\n"
+ indent9 + "[grad-base = " + StringUtilities::fromNumber(BrainModelVolumeLigaseSegmentation::defaultGrad()) + "]\n"
+ indent9 + "[high-bias = " + StringUtilities::fromNumber(BrainModelVolumeLigaseSegmentation::defaultHighBias()) + "]\n"
+ indent9 + "[low-bias = " + StringUtilities::fromNumber(BrainModelVolumeLigaseSegmentation::defaultLowBias()) + "]\n"
+ indent9 + "\n"
+ indent9 + "Use LIGASE to segment the white matter.\n"
+ indent9 + "\n"
+ indent9 + " x-seed, y-seed, z-seed specify the voxel for LIGASE to grow\n"
+ indent9 + " from, make sure it is in the white\n"
+ indent9 + " matter.\n"
+ indent9 + "\n"
+ indent9 + " white-min specifies the minimum intensity of the white matter in\n"
+ indent9 + " the anatomy volume. \n"
+ indent9 + " \n"
+ indent9 + " white-peak specifies the intensity of the white matter peak in\n"
+ indent9 + " the anatomy volume. \n"
+ indent9 + " \n"
+ indent9 + " white-max specifies the maximum intensity of the white matter in\n"
+ indent9 + " the anatomy volume. \n"
+ indent9 + "\n"
+ indent9 + " Optional parameters: (default value specified above)\n"
+ indent9 + " diff-base specifies how much to rely on the difference from one\n"
+ indent9 + " voxel to the next when growing, higher numbers allow\n"
+ indent9 + " more growth. \n"
+ indent9 + "\n"
+ indent9 + " grad-base specifies how much to rely on the magnitude of the\n"
+ indent9 + " local 3D gradient when growing, higher numbers allow\n"
+ indent9 + " more growth.\n"
+ indent9 + "\n"
+ indent9 + " high-bias specifies how low a probability based on intensity\n"
+ indent9 + " is considered as no chance of being white matter\n"
+ indent9 + " when intensity is above peak, smaller numbers allow\n"
+ indent9 + " more growth.\n"
+ indent9 + "\n"
+ indent9 + " low-bias specifies how low a probability based on intensity\n"
+ indent9 + " is considered as no chance of being white matter\n"
+ indent9 + " when intensity is below peak, smaller numbers allow\n"
+ indent9 + " more growth.\n"
+ indent9 + "\n"
+ indent9 + "Note: This algorithm is generally conservative in estimating the\n"
+ indent9 + " gray/white boundary, try dilating the output if changing\n"
+ indent9 + " parameters doesn't give the desired results.\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandVolumeSegmentationLigase::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
const QString inputVolumeFileName =
parameters->getNextParameterAsString("Input Anatomy Volume File Name");
const QString outputVolumeFileName =
parameters->getNextParameterAsString("Output Segmentation Volume File Name");
const QString outputVolumeLabel =
parameters->getNextParameterAsString("Output Segmentation Volume Label");
const int xSeed =
parameters->getNextParameterAsInt("Seed Point X Index");
const int ySeed =
parameters->getNextParameterAsInt("Seed Point Y Index");
const int zSeed =
parameters->getNextParameterAsInt("Seed Point Z Index");
const float whiteMin =
parameters->getNextParameterAsFloat("White Minimum");
const float whitePeak =
parameters->getNextParameterAsFloat("White Peak");
const float whiteMax =
parameters->getNextParameterAsFloat("White Maximum");
float diffBase = BrainModelVolumeLigaseSegmentation::defaultDiff(),
gradBase = BrainModelVolumeLigaseSegmentation::defaultGrad(),
highBias = BrainModelVolumeLigaseSegmentation::defaultHighBias(),
lowBias = BrainModelVolumeLigaseSegmentation::defaultLowBias();
if (parameters->getParametersAvailable())
{
diffBase =
parameters->getNextParameterAsFloat("Difference Cutoff Base (optional)");
}
if (parameters->getParametersAvailable())
{
gradBase =
parameters->getNextParameterAsFloat("Gradient Cutoff Base (optional)");
}
if (parameters->getParametersAvailable())
{
highBias =
parameters->getNextParameterAsFloat("High Probability Bias (optional)");
}
if (parameters->getParametersAvailable())
{
lowBias =
parameters->getNextParameterAsFloat("Low Probability Bias (optional)");
}
checkForExcessiveParameters();
//
// Create a brain set
//
BrainSet brainSet;
//
// Read the volume file
//
VolumeFile inputVolume;
inputVolume.readFile(inputVolumeFileName);
//
// Create output volume file
//
VolumeFile segVolume(inputVolume);
segVolume.setVolumeType(VolumeFile::VOLUME_TYPE_SEGMENTATION);
//
// Create the Ligase object
//
BrainModelVolumeLigaseSegmentation ligaseObject(&brainSet,
&inputVolume,
&segVolume,
outputVolumeFileName,
outputVolumeLabel,
xSeed,
ySeed,
zSeed,
whiteMin,
whitePeak,
whiteMax,
diffBase,
gradBase,
highBias,
lowBias);
//
// Execute Ligase
//
ligaseObject.execute();
//
// Write the file
//
segVolume.writeFile(outputVolumeFileName);
const QString warningMessages = ligaseObject.getWarningMessages();
if (warningMessages.isEmpty() == false) {
std::cout << "Segmentation Warnings: " << warningMessages.toAscii().constData() << std::endl;
}
}
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