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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 "BrainSet.h"
#include "BrainModelSurface.h"
#include "BrainModelSurfacePointProjector.h"
#include "CommandSurfaceSphereProjectUnproject.h"
#include "FileFilters.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "TopologyFile.h"
#include "TopologyHelper.h"
/**
* constructor.
*/
CommandSurfaceSphereProjectUnproject::CommandSurfaceSphereProjectUnproject()
: CommandBase("-surface-sphere-project-unproject",
"SURFACE SPHERE PROJECT/UNPROJECT")
{
}
/**
* destructor.
*/
CommandSurfaceSphereProjectUnproject::~CommandSurfaceSphereProjectUnproject()
{
}
/**
* get the script builder parameters.
*/
void
CommandSurfaceSphereProjectUnproject::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
}
/**
* get full help information.
*/
QString
CommandSurfaceSphereProjectUnproject::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<input-spherical-coordinate-file-name>\n"
+ indent9 + "<input-spherical-topology-file-name>\n"
+ indent9 + "<output-spherical-coordinate-file-name>\n"
+ indent9 + "<project-to-spherical-coordinate-file-name>\n"
+ indent9 + "<unproject-to-spherical-coordinate-file-name>\n"
+ indent9 + "<project-unproject-spherical-topology-file-name>\n"
+ indent9 + "\n"
+ indent9 + "Transform a spherical surface.\n"
+ indent9 + "\n"
+ indent9 + "The input spherical surface is projected to the \n"
+ indent9 + "\"project-to\" surface using barycentric projections\n"
+ indent9 + "and then unprojected using the \"unproject-to\" \n"
+ indent9 + "spherical surface. Typically the \"unproject-to\"\n"
+ indent9 + "surface is created during surface-based registration\n"
+ indent9 + "of the \"project-to\" spherical surface to some\n"
+ indent9 + "target.\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandSurfaceSphereProjectUnproject::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
const QString inputSphericalCoordinateFileName =
parameters->getNextParameterAsString("Input Spherical Coordinate File Name");
const QString inputSphericalTopologyFileName =
parameters->getNextParameterAsString("Input Spherical Topology File Name");
const QString outputSphericalCoordinateFileName =
parameters->getNextParameterAsString("Output Spherical Coordinate File Name");
const QString projectToSphericalCoordinateFileName =
parameters->getNextParameterAsString("Project To Spherical Coordinate File Name");
const QString unprojectToSphericalCoordinateFileName =
parameters->getNextParameterAsString("Unproject To Spherical Coordinate File Name");
const QString projectUnprojectSphericalTopologyFileName =
parameters->getNextParameterAsString("Project/Unproject Spherical Topology File Name");
checkForExcessiveParameters();
//
// Create a brain set for user surface
//
BrainSet brainSet(inputSphericalTopologyFileName,
inputSphericalCoordinateFileName,
"",
true);
BrainModelSurface* inputSphericalSurface = brainSet.getBrainModelSurface(0);
if (inputSphericalSurface == NULL) {
throw CommandException("unable to find input spherical surface after reading files.");
}
const TopologyFile* inputSphericalTopologyFile = inputSphericalSurface->getTopologyFile();
if (inputSphericalTopologyFile == NULL) {
throw CommandException("unable to find input spherical topology after reading files.");
}
const int inputSphereNumNodes = inputSphericalSurface->getNumberOfNodes();
if (inputSphereNumNodes == 0) {
throw CommandException("input spherical surface contains no nodes.");
}
//
// Create a brain set for project/unproject surfaces
//
BrainSet projectUnprojectBrainSet(projectUnprojectSphericalTopologyFileName,
projectToSphericalCoordinateFileName,
unprojectToSphericalCoordinateFileName,
true);
BrainModelSurface* projectSphericalSurface = projectUnprojectBrainSet.getBrainModelSurface(0);
if (projectSphericalSurface == NULL) {
throw CommandException("unable to find project to spherical surface after reading files.");
}
BrainModelSurface* unprojectSphericalSurface = projectUnprojectBrainSet.getBrainModelSurface(1);
if (unprojectSphericalSurface == NULL) {
throw CommandException("unable to find unproject to spherical surface after reading files.");
}
const CoordinateFile* unprojectCoordinateFile = unprojectSphericalSurface->getCoordinateFile();
const TopologyFile* projectTopologyFile = projectSphericalSurface->getTopologyFile();
if (projectTopologyFile == NULL) {
throw CommandException("unable to find project/unproject spherical topology after reading files.");
}
const int projectSphereNumNodes = projectSphericalSurface->getNumberOfNodes();
if (projectSphereNumNodes == 0) {
throw CommandException("input project to surface contains no nodes.");
}
//
// Topology Helper for input sphere
//
const TopologyHelper* inputSphereTopologyHelper =
inputSphericalTopologyFile->getTopologyHelper(false, true, false);
CoordinateFile* inputOutputCoordFile = inputSphericalSurface->getCoordinateFile();
//
// Make sure both surfaces are centered and of the same radius and unproject surface
//
unprojectSphericalSurface->translateMidpointToOrigin();
const float radius = unprojectSphericalSurface->getSphericalSurfaceRadius();
projectSphericalSurface->translateMidpointToOrigin();
projectSphericalSurface->convertToSphereWithRadius(radius);
inputSphericalSurface->translateMidpointToOrigin();
inputSphericalSurface->convertToSphereWithRadius(radius);
//
// Use a point projector to transform the surface nodes
//
BrainModelSurfacePointProjector pp(projectSphericalSurface,
BrainModelSurfacePointProjector::SURFACE_TYPE_HINT_SPHERE,
false);
for (int i = 0; i < inputSphereNumNodes; i++) {
if (inputSphereTopologyHelper->getNodeHasNeighbors(i)) {
float xyz[3];
inputOutputCoordFile->getCoordinate(i, xyz);
int nearestNode = -1;
int baryNodes[3];
float baryAreas[3];
int triangle = pp.projectBarycentric(xyz,
nearestNode,
baryNodes,
baryAreas,
false);
if (triangle >= 0) {
BrainModelSurfacePointProjector::unprojectPoint(baryNodes,
baryAreas,
unprojectCoordinateFile,
xyz);
}
else if (nearestNode >= 0) {
unprojectCoordinateFile->getCoordinate(nearestNode, xyz);
}
else {
throw CommandException("Sphere Project/Unproject failed for node index: "
+ QString::number(i));
}
inputOutputCoordFile->setCoordinate(i, xyz);
}
}
//
// Make spherical again
//
inputSphericalSurface->translateMidpointToOrigin();
inputSphericalSurface->convertToSphereWithRadius(radius);
//
// Write the output coordinate file
//
inputOutputCoordFile->writeFile(outputSphericalCoordinateFileName);
}
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