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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 "BrainModelSurfaceMetricOneAndPairedTTest.h"
#include "BrainSet.h"
#include "CommandMetricStatisticsPairedTTest.h"
#include "FileFilters.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
/**
* constructor.
*/
CommandMetricStatisticsPairedTTest::CommandMetricStatisticsPairedTTest()
: CommandBase("-metric-statistics-paired-t-test",
"METRIC STATISTICS PAIRED T-TEST")
{
}
/**
* destructor.
*/
CommandMetricStatisticsPairedTTest::~CommandMetricStatisticsPairedTTest()
{
}
/**
* get the script builder parameters.
*/
void
CommandMetricStatisticsPairedTTest::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Metric File Name A", FileFilters::getMetricShapeFileFilter());
paramsOut.addFile("Metric File Name B", FileFilters::getMetricShapeFileFilter());
paramsOut.addFile("Fiducial Coordinate File Name", FileFilters::getCoordinateFiducialFileFilter());
paramsOut.addFile("Open Topology File Name", FileFilters::getTopologyOpenFileFilter());
paramsOut.addFile("Distoration Metric File Name", FileFilters::getMetricShapeFileFilter());
paramsOut.addInt("Distortion Column Number");
paramsOut.addString("Output File Names Prefix");
paramsOut.addFloat("Negative Threshold");
paramsOut.addFloat("Positive Threshold");
paramsOut.addFloat("P-Value");
paramsOut.addInt("Variance Smoothing Iterations");
paramsOut.addFloat("Variance Smoothing Strength");
paramsOut.addInt("Iterations");
paramsOut.addInt("Number of Threads", 1);
}
/**
* get full help information.
*/
QString
CommandMetricStatisticsPairedTTest::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<metric-file-name-A> \n"
+ indent9 + "<metric-file-name-B> \n"
+ indent9 + "<fiducial-coordinate-file> \n"
+ indent9 + "<open-topology-file> \n"
+ indent9 + "<distortion-metric-file> \n"
+ indent9 + "<distortion-column-number> \n"
+ indent9 + "<output-file-names-prefix> \n"
+ indent9 + "<f-negative-threshold> \n"
+ indent9 + "<f-positive-threshold> \n"
+ indent9 + "<f-p-value> \n"
+ indent9 + "<i-variance-smoothing-iterations> \n"
+ indent9 + "<f-variance-smoothing-strength> \n"
+ indent9 + "<i-iterations> \n"
+ indent9 + "<number-of-threads> \n"
+ indent9 + " \n"
+ indent9 + "Perform a paired T-Test on the metric file. \n"
+ indent9 + " \n"
+ indent9 + "The distortion column number starts at 1. \n"
+ indent9 + " \n"
+ indent9 + "Number of threads is the number of concurrent processes run \n"
+ indent9 + "during the cluster search of the shuffled metric file. \n"
+ indent9 + "Use \"1\" if you are running on a single processor system. \n"
+ indent9 + "Users on systems with multiple processors or multi-core systems \n"
+ indent9 + "should set the number of threads to the number of processors \n"
+ indent9 + "and/or cores to reduce execution time. \n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandMetricStatisticsPairedTTest::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
const QString metricShapeFileA =
parameters->getNextParameterAsString("Metric or Shape File A");
const QString metricShapeFileB =
parameters->getNextParameterAsString("Metric or Shape File B");
const QString fiducialCoordFileName =
parameters->getNextParameterAsString("Fiducial Coordinate File Name");
const QString openTopoFileName =
parameters->getNextParameterAsString("Open Topology File Name");
const QString distortionMetricShapeFileName =
parameters->getNextParameterAsString("Distortion Metric/Shape File Name");
int distortionColumnNumber =
parameters->getNextParameterAsInt("Distortion Column Number");
const QString outputFileNamePrefix =
parameters->getNextParameterAsString("Output File Name Prefix");
const float negativeThreshold =
parameters->getNextParameterAsFloat("Negative Threshold");
const float positiveThreshold =
parameters->getNextParameterAsFloat("Positive Threshold");
const float pValue =
parameters->getNextParameterAsFloat("P-Value");
const int varianceSmoothingIterations =
parameters->getNextParameterAsInt("Variance Smoothing Iterations");
const float varianceSmoothingStrength =
parameters->getNextParameterAsFloat("Variance Smoothing Strength");
const int iterations =
parameters->getNextParameterAsInt("Iterations");
const int numberOfThreads =
parameters->getNextParameterAsInt("Number of Threads");
checkForExcessiveParameters();
if (distortionColumnNumber <= 0) {
throw CommandException("Distortion column number must be >= 1.");
}
distortionColumnNumber--; // algorithm starts at zero
const QString ext = metricShapeFileA.endsWith(SpecFile::getMetricFileExtension())
? SpecFile::getMetricFileExtension()
: SpecFile::getSurfaceShapeFileExtension();
const QString outputTMapFileName(outputFileNamePrefix + "_TMap" + ext);
const QString outputShuffledTMapFileName(outputFileNamePrefix + "_ShuffledTMap" + ext);
const QString outputPaintFileName(outputFileNamePrefix + "_TMapClusters" + SpecFile::getPaintFileExtension());
const QString outputMetricFileName(outputFileNamePrefix + "_TMapClusters" + SpecFile::getMetricFileExtension());
const QString outputReportFileName(outputFileNamePrefix + "_TMap_Significant_Clusters" + SpecFile::getTextFileExtension());
std::vector<QString> metricAndShapeFiles;
metricAndShapeFiles.push_back(metricShapeFileA);
metricAndShapeFiles.push_back(metricShapeFileB);
BrainSet bs;
BrainModelSurfaceMetricOneAndPairedTTest
oneSample(&bs,
BrainModelSurfaceMetricOneAndPairedTTest::T_TEST_MODE_PAIRED,
metricAndShapeFiles,
fiducialCoordFileName,
openTopoFileName,
distortionMetricShapeFileName,
outputTMapFileName,
outputShuffledTMapFileName,
outputPaintFileName,
outputMetricFileName,
outputReportFileName,
distortionColumnNumber,
negativeThreshold,
positiveThreshold,
pValue,
varianceSmoothingIterations,
varianceSmoothingStrength,
iterations,
0.0,
numberOfThreads);
oneSample.execute();
}
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