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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 "BrainModelSurface.h"
#include "BrainSet.h"
#include "CommandSurfaceInflate.h"
#include "FileFilters.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
/**
* constructor.
*/
CommandSurfaceInflate::CommandSurfaceInflate()
: CommandBase("-surface-inflate",
"SURFACE INFLATE")
{
}
/**
* destructor.
*/
CommandSurfaceInflate::~CommandSurfaceInflate()
{
}
/**
* get the script builder parameters.
*/
void
CommandSurfaceInflate::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Input FiducialCoordinate File", FileFilters::getCoordinateFiducialFileFilter());
paramsOut.addFile("Input Smoothing Coordinate File", FileFilters::getCoordinateGenericFileFilter());
paramsOut.addFile("Input Smoothing Topology File", FileFilters::getTopologyGenericFileFilter());
paramsOut.addFile("Output Smoothed Coordinate File", FileFilters::getCoordinateGenericFileFilter());
paramsOut.addInt("Smoothing Cycles", 2);
paramsOut.addFloat("Smoothing Strength", 1.0);
paramsOut.addInt("Smoothing Iterations", 100);
paramsOut.addFloat("Inflation Factor", 1.4);
paramsOut.addInt("Finger Smoothing Iterations", 30);
paramsOut.addFloat("Finger Smoothing Strength", 1.0);
paramsOut.addFloat("Finger Smoothing Compress/Stretch Threshold", 3.0);
}
/**
* get full help information.
*/
QString
CommandSurfaceInflate::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<input-fiducial-coordinate-file-name>\n"
+ indent9 + "<input-smoothing-coordinate-file-name>\n"
+ indent9 + "<input-smoothing-topology-file-name>\n"
+ indent9 + "<output-smoothed-coordinate-file-name>\n"
+ indent9 + "<number-of-smoothing-cycles>\n"
+ indent9 + "<smoothing-strength>\n"
+ indent9 + "<smoothing-iterations>\n"
+ indent9 + "<inflation-factor>\n"
+ indent9 + "<finger-smoothing-iterations>\n"
+ indent9 + "<finger-smoothing-strength>\n"
+ indent9 + "<finger-compress-stretch-threshold>\n"
+ indent9 + "\n"
+ indent9 + "Inflate a surface.\n"
+ indent9 + "\n"
+ indent9 + "Sequence to start with fiducial and create low smooth\n"
+ indent9 + "(low), inflated (INF), Very Inflated (VI), high smooth\n"
+ indent9 + "(high), and Ellipse Surfaces.\n"
+ indent9 + " low INF VI high Ellipse\n"
+ indent9 + "cycles 1 2 4 6 6\n"
+ indent9 + "strength 0.2 1.0 1.0 1.0 1.0\n"
+ indent9 + "iterations 50 30 30 60 50\n"
+ indent9 + "inflate-factor 1.0 1.4 1.1 1.6 1.4\n"
+ indent9 + "fing-iter 0 30 0 60 60\n"
+ indent9 + "fing-strength 1.0 1.0 1.0 1.0 1.0\n"
+ indent9 + "fing-cst 3.0 3.0 3.0 3.0 4.0\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandSurfaceInflate::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
const QString inputFiducialCoordinateFileName =
parameters->getNextParameterAsString("Input Fiducial Coordinate File Name");
const QString inputCoordinateFileName =
parameters->getNextParameterAsString("Input Smoothing Coordinate File Name");
const QString inputTopologyFileName =
parameters->getNextParameterAsString("Input Smoothing Topology File Name");
const QString outputCoordinateFileName =
parameters->getNextParameterAsString("Output Smoothed Coordinate File Name");
const int numberOfSmoothingCycles =
parameters->getNextParameterAsInt("Number of Smoothing Cycles");
const float smoothingStrength =
parameters->getNextParameterAsFloat("Smoothing Strength");
const int smoothingIterations =
parameters->getNextParameterAsInt("Smoothing Iterations");
const float inflationFactor =
parameters->getNextParameterAsFloat("Inflation Factor");
const int fingerSmoothingIterations =
parameters->getNextParameterAsInt("Finger Smoothing Iterations");
const float fingerSmoothingStrength =
parameters->getNextParameterAsFloat("Finger Smoothing Strength");
const float fingerSmoothingCompressStretchThreshold =
parameters->getNextParameterAsFloat("Finger Smoothing Compress Stretch Threshold");
//
// Create a brain set
//
BrainSet brainSet(inputTopologyFileName,
inputFiducialCoordinateFileName,
"",
true);
brainSet.readCoordinateFile(inputCoordinateFileName,
BrainModelSurface::SURFACE_TYPE_UNKNOWN,
false,
true,
false);
BrainModelSurface* fiducialSurface = brainSet.getBrainModelSurface(0);
BrainModelSurface* smoothingSurface = brainSet.getBrainModelSurface(1);
if ((fiducialSurface == NULL) ||
(smoothingSurface == NULL)) {
throw CommandException("Problem reading one or both surfaces.");
}
const TopologyFile* tf = smoothingSurface->getTopologyFile();
if (tf == NULL) {
throw CommandException("Problem reading topology file.");
}
//
// Smooth the surface
//
smoothingSurface->inflateSurfaceAndSmoothFingers(fiducialSurface,
numberOfSmoothingCycles,
smoothingStrength,
smoothingIterations,
inflationFactor,
fingerSmoothingCompressStretchThreshold,
fingerSmoothingStrength,
fingerSmoothingIterations,
NULL);
//
// Write the smoothed coordinate file
//
smoothingSurface->getCoordinateFile()->writeFile(outputCoordinateFileName);
}
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