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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 "BrainModelSurfaceMetricTwoSampleTTest.h"
#include "BrainSet.h"
#include "CommandMetricStatisticsTwoSampleTTest.h"
#include "FileFilters.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
/**
* constructor.
*/
CommandMetricStatisticsTwoSampleTTest::CommandMetricStatisticsTwoSampleTTest()
: CommandBase("-metric-statistics-two-sample-t-test",
"METRIC STATISTICS TWO SAMPLE T-TEST and WILCOXON")
{
}
/**
* destructor.
*/
CommandMetricStatisticsTwoSampleTTest::~CommandMetricStatisticsTwoSampleTTest()
{
}
/**
* get the script builder parameters.
*/
void
CommandMetricStatisticsTwoSampleTTest::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
std::vector<QString> transModeValues, transModeDescriptions;
transModeValues.push_back("NO_TRANSFORM");
transModeDescriptions.push_back("Node");
transModeValues.push_back("WILCOXON_TRANSFORM");
transModeDescriptions.push_back("Wilcoxon Rank-Sum input data then T-Test");
std::vector<QString> varModeValues, varModeDescriptions;
varModeValues.push_back("SIGMA");
varModeDescriptions.push_back("Donna's SIGMA Method");
varModeValues.push_back("POOLED");
varModeDescriptions.push_back("Use Pooled Variance in T Computation");
varModeValues.push_back("UNPOOLED");
varModeDescriptions.push_back("Use Unpooled Variance in T Computation");
paramsOut.clear();
paramsOut.addListOfItems("Data Transform Mode", transModeValues, transModeDescriptions);
paramsOut.addListOfItems("Variance Mode", varModeValues, varModeDescriptions);
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.addInt("Iterations");
paramsOut.addFloat("Negative Threshold");
paramsOut.addFloat("Positive Threshold");
paramsOut.addFloat("P-Value");
paramsOut.addInt("Variance Smoothing Iterations");
paramsOut.addFloat("Variance Smoothing Strength");
paramsOut.addBoolean("Do TMap Degrees of Freedom");
paramsOut.addBoolean("Do TMap P-Values");
paramsOut.addInt("Number of Threads", 1);
}
/**
* get full help information.
*/
QString
CommandMetricStatisticsTwoSampleTTest::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + " <data-transform-mode-name> \n"
+ indent9 + " <variance-mode-name> \n"
+ indent9 + " <metric-file-name-A> \n"
+ indent9 + " <metric-file-name-B> \n"
+ indent9 + " <fiducial-coord-file> \n"
+ indent9 + " <open-topo-file> \n"
+ indent9 + " <distortion-metric-shape-file> \n"
+ indent9 + " <distortion-column-number> \n"
+ indent9 + " <output-file-names-prefix> \n"
+ indent9 + " <i-iterations> \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 + " <b-do-tmap-DOF> \n"
+ indent9 + " <b-do-tmap-pvalue> \n"
+ indent9 + " <number-of-threads> \n"
+ indent9 + " \n"
+ indent9 + " Perform a two-sample T-Test or perform a Wilcoxon Rank-Sum of the \n"
+ indent9 + " data and then perform the T-Test. \n"
+ indent9 + " \n"
+ indent9 + " data-transform-mode-name one of: \n"
+ indent9 + " NO_TRANSFORM \n"
+ indent9 + " WILCOXON_TRANSFORM (Wilcoxon Rank-Sum input data then T-Test) \n"
+ indent9 + " \n"
+ indent9 + " variance-mode-name is one of: \n"
+ indent9 + " SIGMA - Use Donna's SIGMA method \n"
+ indent9 + " POOLED - Use pooled variance in T computation \n"
+ indent9 + " UNPOOLED - Use unpooled variance in T computation \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
CommandMetricStatisticsTwoSampleTTest::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
const QString dataTransformModeName =
parameters->getNextParameterAsString("Data Transform Mode Name");
const QString varianceModeName =
parameters->getNextParameterAsString("Variance Mode Name");
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 int iterations =
parameters->getNextParameterAsInt("Iterations");
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 bool doTMapDOF =
parameters->getNextParameterAsBoolean("Do T-MAP Degrees of Freedom");
const bool doTMapPValue =
parameters->getNextParameterAsBoolean("Do T-MAP P-Value");
const int numberOfThreads =
parameters->getNextParameterAsInt("Number of Threads");
checkForExcessiveParameters();
BrainModelSurfaceMetricTwoSampleTTest::DATA_TRANSFORM_MODE dataTransformMode;
if (dataTransformModeName == "NO_TRANSFORM") {
dataTransformMode = BrainModelSurfaceMetricTwoSampleTTest::DATA_TRANSFORM_NONE;
}
else if (dataTransformModeName == "WILCOXON_TRANSFORM") {
dataTransformMode = BrainModelSurfaceMetricTwoSampleTTest::DATA_TRANSFORM_WILCOXON_RANK_SUM_THEN_TWO_SAMPLE_T_TEST;
}
else {
throw CommandException("Invalid data transform mode: "
+ dataTransformModeName);
}
BrainModelSurfaceMetricTwoSampleTTest::VARIANCE_MODE varianceMode;
if (varianceModeName == "POOLED") {
varianceMode = BrainModelSurfaceMetricTwoSampleTTest::VARIANCE_MODE_POOLED;
}
else if (varianceModeName == "UNPOOLED") {
varianceMode = BrainModelSurfaceMetricTwoSampleTTest::VARIANCE_MODE_UNPOOLED;
}
else if (varianceModeName == "SIGMA") {
varianceMode = BrainModelSurfaceMetricTwoSampleTTest::VARIANCE_MODE_SIGMA;
}
else {
throw CommandException("Invalid variance mode: "
+ varianceModeName);
}
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());
BrainSet bs;
BrainModelSurfaceMetricTwoSampleTTest
twoSample(&bs,
dataTransformMode,
varianceMode,
metricShapeFileA,
metricShapeFileB,
fiducialCoordFileName,
openTopoFileName,
distortionMetricShapeFileName,
outputTMapFileName,
outputShuffledTMapFileName,
outputPaintFileName,
outputMetricFileName,
outputReportFileName,
distortionColumnNumber,
iterations,
negativeThreshold,
positiveThreshold,
pValue,
varianceSmoothingIterations,
varianceSmoothingStrength,
doTMapDOF,
doTMapPValue,
numberOfThreads);
twoSample.execute();
}
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