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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 "BrainModelSurfaceMetricCoordinateDifference.h"
#include "BrainSet.h"
#include "CommandMetricStatisticsCoordinateDifference.h"
#include "FileFilters.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
/**
* constructor.
*/
CommandMetricStatisticsCoordinateDifference::CommandMetricStatisticsCoordinateDifference()
: CommandBase("-metric-statistics-coordinate-difference",
"METRIC STATISTICS COORDINATE DIFFERENCE")
{
}
/**
* destructor.
*/
CommandMetricStatisticsCoordinateDifference::~CommandMetricStatisticsCoordinateDifference()
{
}
/**
* get the script builder parameters.
*/
void
CommandMetricStatisticsCoordinateDifference::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
std::vector<QString> values, descriptions;
values.push_back("COORD_DIFF"); descriptions.push_back("Use Coordinate Difference");
values.push_back("TMAP_DIFF"); descriptions.push_back("Perform T-Test of Coordinate Difference");
paramsOut.clear();
paramsOut.addListOfItems("Mode", values, descriptions);
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("Threshold");
paramsOut.addFloat("P-Value");
paramsOut.addInt("Number of Threads", 1);
paramsOut.addVariableListOfParameters("Coordinate Files");
}
/**
* get full help information.
*/
QString
CommandMetricStatisticsCoordinateDifference::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + " <mode> \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-threshold> \n"
+ indent9 + " <f-p-value> \n"
+ indent9 + " <i-number-of-threads> \n"
+ indent9 + " -groupA <one-or-more-coord-files-from-group-A> \n"
+ indent9 + " -groupB <one-or-more-coord-files-from-group-B> \n"
+ indent9 + " \n"
+ indent9 + "Find clusters in groups of coordinate files. \n"
+ indent9 + " \n"
+ indent9 + "mode is one of: \n"
+ indent9 + " COORD_DIFF - search for clusters in coordinate difference. \n"
+ indent9 + " TMAP_DIFF - search for clusters using T-Test of coordinate difference. \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
CommandMetricStatisticsCoordinateDifference::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
const QString modeName =
parameters->getNextParameterAsString("Mode");
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");
QString outputFileNamePrefix =
parameters->getNextParameterAsString("Output File Name Prefix");
const int iterations =
parameters->getNextParameterAsInt("Iterations");
const float threshold =
parameters->getNextParameterAsFloat("Threshold");
const float pValue =
parameters->getNextParameterAsFloat("P-Value");
const int numberOfThreads =
parameters->getNextParameterAsInt("Number of Threads");
std::vector<QString> coordFileNamesGroupA, coordFileNamesGroupB;
bool doingGroupA = false;
bool doingGroupB = false;
while (parameters->getParametersAvailable()) {
const QString arg = parameters->getNextParameterAsString("Coordinate File Names");
if (arg == "-groupA") {
doingGroupA = true;
doingGroupB = false;
}
else if (arg == "-groupB") {
doingGroupB = true;
doingGroupA = false;
}
else if (doingGroupA) {
coordFileNamesGroupA.push_back(arg);
}
else if (doingGroupB) {
coordFileNamesGroupB.push_back(arg);
}
else {
throw CommandException("Invalid parameter in groups of files: " + arg);
}
}
BrainModelSurfaceMetricCoordinateDifference::MODE mode;
if (modeName == "COORD_DIFF") {
mode = BrainModelSurfaceMetricCoordinateDifference::MODE_COORDINATE_DIFFERENCE;
}
else if (modeName == "TMAP_DIFF") {
mode = BrainModelSurfaceMetricCoordinateDifference::MODE_TMAP_DIFFERENCE;
}
else {
throw CommandException("Invalid mode: " + modeName);
}
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 ext = SpecFile::getMetricFileExtension();
const QString outputDistanceFileName(outputFileNamePrefix + "_DistanceOrTMap" + ext);
const QString outputShuffledDistanceFileName(outputFileNamePrefix + "_Shuffled_DistanceOrTMap" + ext);
const QString outputPaintFileName(outputFileNamePrefix + "_DistanceOrTMapClusters" + SpecFile::getPaintFileExtension());
const QString outputMetricFileName(outputFileNamePrefix + "_DistanceOrTMapClusters" + SpecFile::getMetricFileExtension());
const QString outputReportFileName(outputFileNamePrefix + "_DistanceOrTMap_Significant_Clusters" + SpecFile::getTextFileExtension());
BrainSet bs;
BrainModelSurfaceMetricCoordinateDifference
coordDiffAlg(&bs,
mode,
coordFileNamesGroupA,
coordFileNamesGroupB,
fiducialCoordFileName,
openTopoFileName,
distortionMetricShapeFileName,
outputDistanceFileName,
outputShuffledDistanceFileName,
outputPaintFileName,
outputMetricFileName,
outputReportFileName,
distortionColumnNumber,
iterations,
threshold,
pValue,
numberOfThreads);
coordDiffAlg.execute();
}
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