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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 "CommandMetricStatisticsTMap.h"
#include "FileFilters.h"
#include "MetricFile.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "TopologyFile.h"
/**
* constructor.
*/
CommandMetricStatisticsTMap::CommandMetricStatisticsTMap()
: CommandBase("-metric-statistics-t-map",
"METRIC STATISTICS T-MAP")
{
}
/**
* destructor.
*/
CommandMetricStatisticsTMap::~CommandMetricStatisticsTMap()
{
}
/**
* get the script builder parameters.
*/
void
CommandMetricStatisticsTMap::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Input Metric File Name A", FileFilters::getMetricShapeFileFilter());
paramsOut.addFile("Input Metric File Name B", FileFilters::getMetricShapeFileFilter());
paramsOut.addFile("Output Metric File Name", FileFilters::getMetricShapeFileFilter());
paramsOut.addFile("Topology File Name", FileFilters::getTopologyGenericFileFilter());
paramsOut.addInt("Variance Smoothing Iterations");
paramsOut.addFloat("Variance Smoothing Strength");
paramsOut.addFloat("False Discovery Rate Q");
paramsOut.addBoolean("Pool Variance Flag");
paramsOut.addBoolean("Do False Discovery Rate Flag");
paramsOut.addBoolean("Do Degrees of Freedom Flag");
paramsOut.addBoolean("Do P-Values Flag");
}
/**
* get full help information.
*/
QString
CommandMetricStatisticsTMap::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<input-metric-file-name-A>\n"
+ indent9 + "<input-metric-file-name-B>\n"
+ indent9 + "<output-metric-file-name>\n"
+ indent9 + "<topology-file-name>\n"
+ indent9 + "<variance-smoothing-iterations>\n"
+ indent9 + "<variance-smoothing-strength>\n"
+ indent9 + "<falseDiscoveryRateQ>\n"
+ indent9 + "<pool-the-variance-flag>\n"
+ indent9 + "<do-false-discovery-rate-flag>\n"
+ indent9 + "<do-degrees-of-freedom-flag>\n"
+ indent9 + "<do-p-values-flag>\n"
+ indent9 + "\n"
+ indent9 + "Compute a T-Map using the two input files.\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandMetricStatisticsTMap::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
const QString inputMetricFileNameA =
parameters->getNextParameterAsString("Input Metric File Name A");
const QString inputMetricFileNameB =
parameters->getNextParameterAsString("Input Metric File Name B");
const QString outputMetricFileName =
parameters->getNextParameterAsString("Output Metric File Name");
const QString topologyFileName =
parameters->getNextParameterAsString("Topology File Name");
const int varianceSmoothingIterations =
parameters->getNextParameterAsInt("Variance Smoothing Iterations");
const float varianceSmoothingStrength =
parameters->getNextParameterAsFloat("Variance Smoothing Strength");
const float falseDiscoveryRateQ =
parameters->getNextParameterAsFloat("False Discovery Rate Q");
const bool poolTheVarianceFlag =
parameters->getNextParameterAsBoolean("Pool Variance Flag");
const bool doFalseDiscoveryRateFlag =
parameters->getNextParameterAsBoolean("Do False Discovery Rate");
const bool doDegreesOfFreedomFlag =
parameters->getNextParameterAsBoolean("Do Degrees of Freedom");
const bool doPValuesFlag =
parameters->getNextParameterAsBoolean("Do P-Values Flag");
checkForExcessiveParameters();
MetricFile inputMetricFileA, inputMetricFileB;
inputMetricFileA.readFile(inputMetricFileNameA);
inputMetricFileB.readFile(inputMetricFileNameB);
TopologyFile topologyFile;
topologyFile.readFile(topologyFileName);
MetricFile* outputMetricFile =
MetricFile::computeStatisticalTMap(&inputMetricFileA,
&inputMetricFileB,
&topologyFile,
varianceSmoothingIterations,
varianceSmoothingStrength,
poolTheVarianceFlag,
falseDiscoveryRateQ,
doFalseDiscoveryRateFlag,
doDegreesOfFreedomFlag,
doPValuesFlag);
outputMetricFile->writeFile(outputMetricFileName);
delete outputMetricFile;
}
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