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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 "BrainModelSurfaceMetricSmoothing.h"
#include "BrainSet.h"
#include "CommandMetricSmoothing.h"
#include "FileFilters.h"
#include "MetricFile.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
/**
* constructor.
*/
CommandMetricSmoothing::CommandMetricSmoothing()
: CommandBase("-metric-smoothing",
"METRIC SMOOTHING")
{
}
/**
* destructor.
*/
CommandMetricSmoothing::~CommandMetricSmoothing()
{
}
/**
* get the script builder parameters.
*/
void
CommandMetricSmoothing::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
std::vector<QString> values, descriptions;
values.push_back("AN"); descriptions.push_back("Average Neighbors");
values.push_back("DILATE"); descriptions.push_back("Dilation");
values.push_back("FWHM"); descriptions.push_back("Full Width Half Maximum");
values.push_back("GAUSS"); descriptions.push_back("Gaussian");
values.push_back("WAN"); descriptions.push_back("Weighted Average Neighbors");
paramsOut.clear();
paramsOut.clear();
paramsOut.addFile("Coordinate File Name", FileFilters::getCoordinateGenericFileFilter());
paramsOut.addFile("Topology File Name", FileFilters::getTopologyGenericFileFilter());
paramsOut.addFile("Input Metric File Name", FileFilters::getMetricFileFilter());
paramsOut.addFile("Output Metric File Name", FileFilters::getMetricFileFilter());
paramsOut.addListOfItems("Smoothing Algorithm", values, descriptions);
paramsOut.addInt("Smoothing Number of Iterations", 50, 1, 100000);
paramsOut.addFloat("Smoothing Strength", 1.0, 0.0, 1.0);
paramsOut.addVariableListOfParameters("Gaussian Options");
}
/**
* get full help information.
*/
QString
CommandMetricSmoothing::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<coordinate-file-name>\n"
+ indent9 + "<topology-file-name>\n"
+ indent9 + "<input-metric-file-name>\n"
+ indent9 + "<output-metric-file-name>\n"
+ indent9 + "<smoothing-algorithm>\n"
+ indent9 + "<smoothing-number-of-iterations>\n"
+ indent9 + "<smoothing-strength>\n"
+ indent9 + " \n"
+ indent9 + "[-fwhm desired-full-width-half-maximum] \n"
+ indent9 + " \n"
+ indent9 + "[-gauss spherical-coordinate-file-name\n"
+ indent9 + " sigma-norm\n"
+ indent9 + " sigma-tang\n"
+ indent9 + " norm below cutoff (mm)\n"
+ indent9 + " norm above cutoff (mm)\n"
+ indent9 + " tang-cutoff (mm)]\n"
+ indent9 + "\n"
+ indent9 + "Smooth metric data.\n"
+ indent9 + "\n"
+ indent9 + "\"smoothing-algorithm\" is one of:\n"
+ indent9 + " AN Average Neighbors\n"
+ indent9 + " DILATE Dilation\n"
+ indent9 + " FWHM Full-Width Half-Maximum\n"
+ indent9 + " GAUSS Gaussian\n"
+ indent9 + " WAN Weighted Average Neighbors\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandMetricSmoothing::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
const QString coordinateFileName =
parameters->getNextParameterAsString("Coordinate File Name");
const QString topologyFileName =
parameters->getNextParameterAsString("Topology File Name");
const QString inputMetricFileName =
parameters->getNextParameterAsString("Input Metric File Name");
const QString outputMetricFileName =
parameters->getNextParameterAsString("Output Metric File Name");
const QString algorithmName =
parameters->getNextParameterAsString("Smoothing Algorithm");
const int smoothingNumberOfIterations =
parameters->getNextParameterAsInt("Smoothing Number of Iterations");
const float smoothingStrength =
parameters->getNextParameterAsFloat("Smoothing Strength");
float desiredFullWidthHalfMaximum = 0.0;
QString gaussianSphericalSurfaceName;
float gaussSigmaNorm = 1.0;
float gaussSigmaTang = 1.0;
float gaussNormBelow = 1.0;
float gaussNormAbove = 1.0;
float gaussTangCutoff = 1.0;
while (parameters->getParametersAvailable()) {
const QString paramValue = parameters->getNextParameterAsString("Gaussian Parameter");
if (paramValue == "-fwhm") {
desiredFullWidthHalfMaximum =
parameters->getNextParameterAsFloat("Desired Full Width Half Maximum");
}
else if (paramValue == "-g") {
gaussianSphericalSurfaceName =
parameters->getNextParameterAsString("Guassian Spherical Surface");
gaussSigmaNorm =
parameters->getNextParameterAsFloat("Gaussian Sigma Norm");
gaussSigmaTang =
parameters->getNextParameterAsFloat("Gaussian Sigma Tangent");
gaussNormBelow =
parameters->getNextParameterAsFloat("Gaussina Norm Below Cutoff");
gaussNormAbove =
parameters->getNextParameterAsFloat("Gaussian Norm Above Cutoff");
gaussTangCutoff =
parameters->getNextParameterAsFloat("Gaussian Tangent Cutoff");
}
else {
throw CommandException("Unrecognized parameter: " + paramValue);
}
}
//
// Get algorithm
//
BrainModelSurfaceMetricSmoothing::SMOOTH_ALGORITHM smoothingAlgorithm;
if (algorithmName == "AN") {
smoothingAlgorithm = BrainModelSurfaceMetricSmoothing::SMOOTH_ALGORITHM_AVERAGE_NEIGHBORS;
}
else if (algorithmName == "DILATE") {
smoothingAlgorithm = BrainModelSurfaceMetricSmoothing::SMOOTH_ALGORITHM_DILATE;
}
else if (algorithmName == "FWHM") {
smoothingAlgorithm = BrainModelSurfaceMetricSmoothing::SMOOTH_ALGORITHM_FULL_WIDTH_HALF_MAXIMUM;
}
else if (algorithmName == "GAUSS") {
smoothingAlgorithm = BrainModelSurfaceMetricSmoothing::SMOOTH_ALGORITHM_SURFACE_NORMAL_GAUSSIAN;
}
else if (algorithmName == "WAN") {
smoothingAlgorithm = BrainModelSurfaceMetricSmoothing::SMOOTH_ALGORITHM_WEIGHTED_AVERAGE_NEIGHBORS;
}
else {
throw CommandException("Invalid algorithm: \""
+ algorithmName
+ "\"");
}
//
// Create a brain set
//
BrainSet brainSet(topologyFileName,
coordinateFileName,
gaussianSphericalSurfaceName,
true);
BrainModelSurface* surface = brainSet.getBrainModelSurface(0);
if (surface == NULL) {
throw CommandException("unable to find surface.");
}
const TopologyFile* tf = surface->getTopologyFile();
if (tf == NULL) {
throw CommandException("unable to find topology.");
}
BrainModelSurface* gaussianSphericalSurface = NULL;
if (gaussianSphericalSurfaceName.isEmpty() == false) {
gaussianSphericalSurface = brainSet.getBrainModelSurface(1);
if (gaussianSphericalSurface == NULL) {
throw CommandException("unable to find spherical surface.");
}
}
const int numNodes = surface->getNumberOfNodes();
if (numNodes == 0) {
throw CommandException("surface contains no nodes.");
}
//
// Read input metric file
//
MetricFile metricFile;
metricFile.readFile(inputMetricFileName);
//
// Perform smoothing
//
const int numberOfColumns = metricFile.getNumberOfColumns();
for (int i = 0; i < numberOfColumns; i++) {
BrainModelSurfaceMetricSmoothing smoothing(&brainSet,
surface,
gaussianSphericalSurface,
&metricFile,
smoothingAlgorithm,
i,
i,
metricFile.getColumnName(i),
smoothingStrength,
smoothingNumberOfIterations,
desiredFullWidthHalfMaximum,
gaussNormBelow,
gaussNormAbove,
gaussSigmaNorm,
gaussSigmaTang,
gaussTangCutoff);
smoothing.execute();
}
//
// Write the metric file
//
metricFile.writeFile(outputMetricFileName);
}
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