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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 "BrainModelSurfaceROINodeSelection.h"
#include "BrainSet.h"
#include "CommandSurfaceSmoothing.h"
#include "FileFilters.h"
#include "NodeRegionOfInterestFile.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
/**
* constructor.
*/
CommandSurfaceSmoothing::CommandSurfaceSmoothing()
: CommandBase("-surface-smoothing",
"SURFACE SMOOTHING")
{
}
/**
* destructor.
*/
CommandSurfaceSmoothing::~CommandSurfaceSmoothing()
{
}
/**
* get the script builder parameters.
*/
void
CommandSurfaceSmoothing::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Input Coordinate File Name",
FileFilters::getCoordinateGenericFileFilter());
paramsOut.addFile("Output Coordinate File Name",
FileFilters::getCoordinateGenericFileFilter());
paramsOut.addFile("Topology File Name",
FileFilters::getTopologyGenericFileFilter());
paramsOut.addFloat("Strength", 1.0, 0.0, 1.0);
paramsOut.addInt("Iterations", 10, 0, 100000);
paramsOut.addInt("Edge Iterations", 0, 0, 100000);
paramsOut.addVariableListOfParameters("Smoothing Options");
}
/**
* get full help information.
*/
QString
CommandSurfaceSmoothing::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + " <input-coordinate-file-name>\n"
+ indent9 + " <output-coordinate-file-name>\n"
+ indent9 + " <topology-file-name>\n"
+ indent9 + " <smoothing-strength>\n"
+ indent9 + " <smoothing-iterations>\n"
+ indent9 + " <smoothing-edge-iterations>\n"
+ indent9 + " [-project-to-sphere every-x-iterations]\n"
+ indent9 + " [-roi-file roi-file-name]\n"
+ indent9 + "\n"
+ indent9 + "Smooth a surface.\n"
+ indent9 + "\n"
+ indent9 + "Use \"-project-to-sphere\" to project the surface to a\n"
+ indent9 + "sphere \"every-x-iterations\".\n"
+ indent9 + "\n"
+ indent9 + "Use \"-roi-file\" to limit smoothing to a region of \n"
+ indent9 + "interest (subset of the surface).\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandSurfaceSmoothing::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
//
// Get coord, topo, and roi file names
//
const QString inputCoordinateFileName =
parameters->getNextParameterAsString("Input Coordinate File Name");
const QString outputCoordinateFileName =
parameters->getNextParameterAsString("Output Coordinate File Name");
const QString topoFileName =
parameters->getNextParameterAsString("Input Topology File Name");
const float smoothingStrength =
parameters->getNextParameterAsFloat("Smoothing Strength");
const int smoothingIterations =
parameters->getNextParameterAsInt("Smoothing Iterations");
const int smoothingEdgeIterations =
parameters->getNextParameterAsInt("Smoothing Edge Iterations");
//
// Create a brain set
//
BrainSet brainSet(topoFileName,
inputCoordinateFileName,
"",
true);
BrainModelSurface* bms = brainSet.getBrainModelSurface(0);
if (bms == NULL) {
throw CommandException("unable to find surface.");
}
const TopologyFile* tf = bms->getTopologyFile();
if (tf == NULL) {
throw CommandException("unable to find topology.");
}
const int numNodes = bms->getNumberOfNodes();
if (numNodes == 0) {
throw CommandException("surface contains not nodes.");
}
//
// Create an ROI of all nodes
//
BrainModelSurfaceROINodeSelection roi(&brainSet);
roi.selectAllNodes(bms);
int projectToSphereIterations = -1;
//
// Process the parameters for node selection
//
while (parameters->getParametersAvailable()) {
//
// Get the parameter
//
const QString parameterName =
parameters->getNextParameterAsString("SURFACE SMOOTHING option");
if (parameterName == "-project-to-sphere") {
projectToSphereIterations =
parameters->getNextParameterAsInt("SURFACE SMOOTHING Project to Sphere Every X Iterations");
}
else if (parameterName == "-roi-file") {
const QString roiFileName =
parameters->getNextParameterAsString("SURFACE SMOOTHING roi-file-name");
NodeRegionOfInterestFile roiFile;
roiFile.readFile(roiFileName);
roi.getRegionOfInterestFromFile(roiFile);
}
else {
throw CommandException("Unrecognized operation = \""
+ parameterName
+ "\".");
}
}
//
// Set nodes for smoothing
//
std::vector<bool> nodesToBeSmoothed(numNodes);
for (int i = 0; i < numNodes; i++) {
nodesToBeSmoothed[i] = roi.getNodeSelected(i);
}
//
// Smooth the surface
//
bms->arealSmoothing(smoothingStrength,
smoothingIterations,
smoothingEdgeIterations,
&nodesToBeSmoothed,
projectToSphereIterations);
//
// Write the coordinate file
//
CoordinateFile* outputCoordFile = bms->getCoordinateFile();
outputCoordFile->writeFile(outputCoordinateFileName);
}
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