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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 "BrainModelSurfaceBorderCutter.h"
#include "BrainSet.h"
#include "CommandSurfaceBorderCutter.h"
#include "CoordinateFile.h"
#include "FileFilters.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "TopologyFile.h"
/**
* constructor.
*/
CommandSurfaceBorderCutter::CommandSurfaceBorderCutter()
: CommandBase("-surface-border-cutter",
"SURFACE BORDER CUTTER")
{
}
/**
* destructor.
*/
CommandSurfaceBorderCutter::~CommandSurfaceBorderCutter()
{
}
/**
* get the script builder parameters.
*/
void
CommandSurfaceBorderCutter::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
std::vector<QString> cutModes, cutModeDescriptions;
cutModes.push_back("FLAT"); cutModeDescriptions.push_back("Cut Flat Surface");
cutModes.push_back("POS_Z"); cutModeDescriptions.push_back("Cut Only Parts of Surface with Positive Z-Coordinates");
cutModes.push_back("SPHERE"); cutModeDescriptions.push_back("Cut Anywhere on a Sphere");
paramsOut.clear();
paramsOut.addFile("Input Coordinate File", FileFilters::getCoordinateGenericFileFilter());
paramsOut.addFile("Input Topology File", FileFilters::getTopologyGenericFileFilter());
paramsOut.addFile("Output Coordinate File", FileFilters::getCoordinateGenericFileFilter());
paramsOut.addFile("Output Topology File", FileFilters::getTopologyGenericFileFilter());
paramsOut.addFile("Input Border Projection File", FileFilters::getBorderProjectionFileFilter());
paramsOut.addListOfItems("Cut Mode", cutModes, cutModeDescriptions);
}
/**
* get full help information.
*/
QString
CommandSurfaceBorderCutter::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<input-coordinate-file-name>\n"
+ indent9 + "<input-topology-file-name>\n"
+ indent9 + "<output-coordinate-file-name>\n"
+ indent9 + "<output-topology-file-name>\n"
+ indent9 + "<border-projection-file-name>\n"
+ indent9 + "<cut-mode>\n"
+ indent9 + "\n"
+ indent9 + "Cut the surface using as cuts all borders in the border\n"
+ indent9 + "projection file.\n"
+ indent9 + "\n"
+ indent9 + "\"cut-mode\" is one of:\n"
+ indent9 + " FLAT\n"
+ indent9 + " POS_Z\n"
+ indent9 + " SPHERE\n"
+ indent9 + "Use \"FLAT\" for cutting flat surfaces. Use \"POS_Z\" to\n"
+ indent9 + "apply the cuts only to nodes with positive Z-coordinates.\n"
+ indent9 + "Use \"SPHERE\" to process cuts anywhere on a sphere.\n"
+ indent9 + "\n"
+ indent9 + "If the \"output-coordinate-file-name\" or the\n"
+ indent9 + "\"output-topology-file-name\" is empty (consecutive \n"
+ indent9 + "double quotes), the respective file is not written.\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandSurfaceBorderCutter::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
//
// Get parameters
//
const QString inputCoordinateFileName =
parameters->getNextParameterAsString("Input Coordinate File Name");
const QString inputTopologyFileName =
parameters->getNextParameterAsString("Input Topology File Name");
const QString outputCoordinateFileName =
parameters->getNextParameterAsString("Output Coordinate File Name");
const QString outputTopologyFileName =
parameters->getNextParameterAsString("Output Topology File Name");
const QString inputBorderProjectionFileName =
parameters->getNextParameterAsString("Input Border Projection File Name");
const QString cutModeName =
parameters->getNextParameterAsString("Cut Mode");
checkForExcessiveParameters();
//
// Get cut mode
//
BrainModelSurfaceBorderCutter::CUTTING_MODE cutMode;
if (cutModeName == "FLAT") {
cutMode = BrainModelSurfaceBorderCutter::CUTTING_MODE_FLAT_SURFACE;
}
else if (cutModeName == "POS_Z") {
cutMode = BrainModelSurfaceBorderCutter::CUTTING_MODE_NON_NEGATIVE_Z_ONLY;
}
else if (cutModeName == "SPHERE") {
cutMode = BrainModelSurfaceBorderCutter::CUTTING_MODE_SPHERICAL_SURFACE;
}
else {
throw CommandException("Invalid cut mode: " + cutModeName);
}
//
// Create a brain set and find the surface
//
BrainSet brainSet(inputTopologyFileName,
inputCoordinateFileName,
"",
true);
BrainModelSurface* bms = brainSet.getBrainModelSurface(0);
if (bms == NULL) {
throw CommandException("Problem reading coordinate file.");
}
TopologyFile* tf = bms->getTopologyFile();
if (tf == NULL) {
throw CommandException("Problem reading topology file.");
}
//
// read the border projections
//
BorderProjectionFile borderProjectionFile;
borderProjectionFile.readFile(inputBorderProjectionFileName);
//
// Cut the surface
//
BrainModelSurfaceBorderCutter cmsbc(&brainSet,
bms,
&borderProjectionFile,
cutMode,
false);
cmsbc.execute();
//
// Write the topology file before the coordinate file
//
if (outputTopologyFileName.isEmpty() == false) {
brainSet.writeTopologyFile(outputTopologyFileName,
tf->getTopologyType(),
tf);
}
//
// Write the coordinate file
//
if (outputCoordinateFileName.isEmpty() == false) {
brainSet.writeCoordinateFile(outputCoordinateFileName,
bms->getSurfaceType(),
bms->getCoordinateFile(),
true);
}
}
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