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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 "CommandVolumeTFCE.h"
#include "FileFilters.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "BrainModelVolumeTFCE.h"
#include "BrainSet.h"
#include "StringUtilities.h"
/**
* constructor.
*/
CommandVolumeTFCE::CommandVolumeTFCE()
: CommandBase("-volume-TFCE",
"VOLUME THRESHHOLD FREE CLUSTER ENHANCEMENT")
{
}
/**
* destructor.
*/
CommandVolumeTFCE::~CommandVolumeTFCE()
{
}
/**
* get the script builder parameters.
*/
void
CommandVolumeTFCE::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Input functional volume file name", FileFilters::getVolumeFunctionalFileFilter());
paramsOut.addFile("Output funtional volume file name", FileFilters::getVolumeFunctionalFileFilter());
paramsOut.addString("Output volume label");
paramsOut.addInt("Number of steps to approximate integral", BrainModelVolumeTFCE::defaultNumSteps(), 1);
paramsOut.addFloat("E (power to raise cluster mass to)", BrainModelVolumeTFCE::defaultE());
paramsOut.addFloat("H (power to raise threshhold to)", BrainModelVolumeTFCE::defaultH());
}
/**
* get full help information.
*/
QString
CommandVolumeTFCE::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 + "[number-of-steps = " + StringUtilities::fromNumber(BrainModelVolumeTFCE::defaultNumSteps()) + "]\n"
+ indent9 + "[E = " + StringUtilities::fromNumber(BrainModelVolumeTFCE::defaultE()) + "]\n"
+ indent9 + "[H = " + StringUtilities::fromNumber(BrainModelVolumeTFCE::defaultH()) + "]\n"
+ indent9 + "\n"
+ indent9 + "Enhance clusterlike signal using Threshhold Free Cluster Enhancement\n"
+ indent9 + "\n"
+ indent9 + " Optional parameters: (default value specified above)\n"
+ indent9 + " number-of-steps number of pieces used to approximate the integral\n"
+ indent9 + " using the value at the center of a piece as the\n"
+ indent9 + " height of the piece.\n"
+ indent9 + "\n"
+ indent9 + " E the power to raise the cluster mass (number of voxels) to in the\n"
+ indent9 + " integral.\n"
+ indent9 + "\n"
+ indent9 + " H the power to raise the threshhold to in the integral.\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandVolumeTFCE::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
const QString inputVolumeFileName =
parameters->getNextParameterAsString("Input Functional Volume File Name");
const QString outputVolumeFileName =
parameters->getNextParameterAsString("Output Functional Volume File Name");
const QString outputVolumeLabel =
parameters->getNextParameterAsString("Output Functional Volume Label");
int numSteps = BrainModelVolumeTFCE::defaultNumSteps();
float E = BrainModelVolumeTFCE::defaultE(),
H = BrainModelVolumeTFCE::defaultH();
if (parameters->getParametersAvailable())
{
numSteps =
parameters->getNextParameterAsInt("Number Of Steps (optional)");
}
if (parameters->getParametersAvailable())
{
E =
parameters->getNextParameterAsFloat("E (optional)");
}
if (parameters->getParametersAvailable())
{
H =
parameters->getNextParameterAsFloat("H (optional)");
}
checkForExcessiveParameters();
//
// Create a brain set
//
BrainSet brainSet;
//
// Read the volume file
//
VolumeFile inputVolume;
inputVolume.readFile(inputVolumeFileName);
//
// Create output volume file
//
VolumeFile outVolume(inputVolume);
//
// Create the Ligase object
//
BrainModelVolumeTFCE TFCEObject(&brainSet,
&inputVolume,
&outVolume,
outputVolumeFileName,
outputVolumeLabel,
numSteps,
E,
H);
//
// Execute Ligase
//
TFCEObject.execute();
//
// Write the file
//
outVolume.writeFile(outputVolumeFileName);
const QString warningMessages = TFCEObject.getWarningMessages();
if (warningMessages.isEmpty() == false) {
std::cout << "TFCE Warnings: " << warningMessages.toAscii().constData() << std::endl;
}
}
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