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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 "BorderProjectionFile.h"
#include "BrainModelSurface.h"
#include "BrainModelSurfaceDeformationSphericalSlits.h"
#include "BrainSet.h"
#include "CommandSurfaceRegistrationPrepareSlits.h"
#include "FileFilters.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "SpecFile.h"
/**
* constructor.
*/
CommandSurfaceRegistrationPrepareSlits::CommandSurfaceRegistrationPrepareSlits()
: CommandBase("-surface-register-prepare-slits",
"SURFACE SPHERICAL REGISTRATION PREPARE SLIT LANDMARKS")
{
}
/**
* destructor.
*/
CommandSurfaceRegistrationPrepareSlits::~CommandSurfaceRegistrationPrepareSlits()
{
}
/**
* get the script builder parameters.
*/
void
CommandSurfaceRegistrationPrepareSlits::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Spec File Name", FileFilters::getSpecFileFilter());
paramsOut.addFile("Input Spherical Coordinate File Name", FileFilters::getCoordinateSphericalFileFilter());
paramsOut.addFile("Input Closed Topology File Name", FileFilters::getTopologyClosedFileFilter());
paramsOut.addFile("Input Border Projection File Name", FileFilters::getBorderProjectionFileFilter());
paramsOut.addFile("Output Cut Spherical Coordinate File Name", FileFilters::getCoordinateSphericalFileFilter());
paramsOut.addFile("Output Cut Topology File Name", FileFilters::getTopologyCutFileFilter());
paramsOut.addFile("Output Closed Smoothed Spherical Coordinate File Name", FileFilters::getCoordinateSphericalFileFilter());
paramsOut.addFile("Output Closed Topology File Name", FileFilters::getTopologyClosedFileFilter());
paramsOut.addFile("Output Border Projection File Name", FileFilters::getBorderProjectionFileFilter());
}
/**
* get full help information.
*/
QString
CommandSurfaceRegistrationPrepareSlits::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<spec-file-name>\n"
+ indent9 + "<input-spherical-coordinate-file-name>\n"
+ indent9 + "<input-closed-topology-file-name>\n"
+ indent9 + "<input-border-projection-file-name>\n"
+ indent9 + "<output-cut-spherical-coordinate-file-name>\n"
+ indent9 + "<output-cut-topology-file-name>\n"
+ indent9 + "<output-closed-smoothed-spherical-coordinate-file-name>\n"
+ indent9 + "<output-closed-topology-file-name>.\n"
+ indent9 + "<output-border-projection-file-name>\n"
+ indent9 + "\n"
+ indent9 + "For all borders that begin with the name \""
+ BrainModelSurfaceDeformationSphericalSlits::getSlitLandmarkBorderNamePrefix() + "\"\n"
+ indent9 + "in the input border projection file, use the border to cut\n"
+ indent9 + "the input spherical surface. The sphere is then smoothed\n"
+ indent9 + "to open up the holes caused by the cuts. For each of the\n"
+ indent9 + "slit borders, two new borders are created around the hole \n"
+ indent9 + "with the suffixes \"PatchA\" and \"PatchB\". The slit \n"
+ indent9 + "borders are deleted. Use the output-closed-smoothed-\n"
+ indent9 + "spherical-coordinate-file, the output-closed-topology-file,\n"
+ indent9 + "and the output-border-projection-file as inputs to the\n"
+ indent9 + "spherical registration command.\n"
+ indent9 + "\n"
+ indent9 + "When performing registration between species, there may\n"
+ indent9 + "be functional areas that are present in one species but \n"
+ indent9 + "not in the other. In this case, draw a border at the\n"
+ indent9 + "location of the \"missing\" area and use this command\n"
+ indent9 + "to open up that region. On the target subject, draw\n"
+ indent9 + "two corresponding borders, with the counter-clockwise\n"
+ indent9 + "half ending in \"PatchA\" and the clockwise half ending\n"
+ indent9 + "in \"PatchB\".\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandSurfaceRegistrationPrepareSlits::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
//
// Get the input parameters
//
const QString specFileName =
parameters->getNextParameterAsString("Spec File Name");
const QString inputSphericalCoordinateFileName =
parameters->getNextParameterAsString("Input Spherical Coordinate File Name");
const QString inputClosedTopologyFileName =
parameters->getNextParameterAsString("Input Closed Topology File Name");
const QString inputBorderProjectionFileName =
parameters->getNextParameterAsString("Input Border Projection File Name");
const QString outputCutSphericalCoordinateFileName =
parameters->getNextParameterAsString("Output Cut Spherical Coordinate File Name");
const QString outputCutTopologyFileName =
parameters->getNextParameterAsString("Output Cut Topology File Name");
const QString outputClosedSmoothedSphericalCoordinateFileName =
parameters->getNextParameterAsString("Output Closed Smoothed Spherical Coordinate File Name");
const QString outputClosedTopologyFileName =
parameters->getNextParameterAsString("Output Closed Topology File Name");
const QString outputBorderProjectionFileName =
parameters->getNextParameterAsString("Output Border Projection File Name");
checkForExcessiveParameters();
//
// Create a brain set
//
BrainSet brainSet(inputClosedTopologyFileName,
inputSphericalCoordinateFileName,
"",
true);
//
// Verify files read
//
BrainModelSurface* inputSphericalSurface =
brainSet.getBrainModelSurfaceOfType(BrainModelSurface::SURFACE_TYPE_SPHERICAL);
if (inputSphericalSurface == NULL) {
throw CommandException("Problem loading spherical surface.");
}
if (inputSphericalSurface->getTopologyFile() == NULL) {
throw CommandException("Topology is missing.");
}
//
// Read tje border projection file
//
brainSet.readBorderProjectionFile(inputBorderProjectionFileName, false, false);
BorderProjectionFile bpf;
BrainModelBorderSet* bmbs = brainSet.getBorderSet();
bmbs->copyBordersToBorderProjectionFile(bpf);
if (bpf.getNumberOfBorderProjections() <= 0) {
throw CommandException("Border projection file is empty.");
}
//
// Set the name of the spec file
//
brainSet.setSpecFileName(specFileName);
//
// Perform the deformation
//
BrainModelSurfaceDeformationSphericalSlits bmsdss(&brainSet,
inputSphericalSurface,
&bpf);
bmsdss.execute();
//
// Write the output files
// Do topology first so it gets the proper name that is used by coord writing
//
TopologyFile* outputCutTopologyFile = bmsdss.getCutSphericalSurfaceTopologyFile();
if (outputCutTopologyFile != NULL) {
if (outputCutTopologyFileName.isEmpty() == false) {
brainSet.writeTopologyFile(outputCutTopologyFileName,
TopologyFile::TOPOLOGY_TYPE_CUT,
outputCutTopologyFile);
}
}
BrainModelSurface* outputSphericalBMS = bmsdss.getCutSphericalSurface();
if (outputSphericalBMS != NULL) {
if (outputCutSphericalCoordinateFileName.isEmpty() == false) {
brainSet.writeCoordinateFile(outputCutSphericalCoordinateFileName,
BrainModelSurface::SURFACE_TYPE_SPHERICAL,
outputSphericalBMS->getCoordinateFile(),
true);
}
}
TopologyFile* outputClosedTopologyFile = bmsdss.getSmoothedClosedSphericalSurfaceTopologyFile();
if (outputClosedTopologyFile != NULL) {
if (outputClosedTopologyFileName.isEmpty() == false) {
brainSet.writeTopologyFile(outputClosedTopologyFileName,
TopologyFile::TOPOLOGY_TYPE_CLOSED,
outputClosedTopologyFile);
}
}
BrainModelSurface* outputSmoothedSphericalBMS = bmsdss.getSmoothedClosedSphericalSurface();
if (outputSmoothedSphericalBMS != NULL) {
if (outputClosedSmoothedSphericalCoordinateFileName.isEmpty() == false) {
brainSet.writeCoordinateFile(outputClosedSmoothedSphericalCoordinateFileName,
BrainModelSurface::SURFACE_TYPE_SPHERICAL,
outputSmoothedSphericalBMS->getCoordinateFile(),
true);
}
}
//
// Write the output border projection file
//
if (outputBorderProjectionFileName.isEmpty() == false) {
brainSet.writeBorderProjectionFile(outputBorderProjectionFileName,
"",
"",
false);
}
}
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