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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 "BrainSetNodeAttribute.h"
#include "CommandSurfaceCrossoverCheck.h"
#include "FileFilters.h"
#include "FileUtilities.h"
#include "NodeRegionOfInterestFile.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "TopologyFile.h"
/**
* constructor.
*/
CommandSurfaceCrossoverCheck::CommandSurfaceCrossoverCheck()
: CommandBase("-surface-crossover-check",
"SURFACE CROSSOVER CHECK")
{
}
/**
* destructor.
*/
CommandSurfaceCrossoverCheck::~CommandSurfaceCrossoverCheck()
{
}
/**
* get the script builder parameters.
*/
void
CommandSurfaceCrossoverCheck::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Coordinate File Name",
FileFilters::getCoordinateGenericFileFilter());
paramsOut.addFile("Topology File Name",
FileFilters::getTopologyGenericFileFilter());
paramsOut.addVariableListOfParameters("Crossover Options");
}
/**
* get full help information.
*/
QString
CommandSurfaceCrossoverCheck::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<coordinate-file-name>\n"
+ indent9 + "<topology-file-name>\n"
+ indent9 + "[-roi-file roi-file-name]\n"
+ indent9 + "[-surface-type SURFACE-TYPE]\n"
+ indent9 + "\n"
+ indent9 + "Perform a crossover check on a surface.\n"
+ indent9 + "\n"
+ indent9 + "If a region of interest file name is supplied, the ROI is\n"
+ indent9 + "set to the nodes identified as crossovers.\n"
+ indent9 + "\n"
+ indent9 + "If a SURFACE-TYPE is specified it must be one of the \n"
+ indent9 + "types listed below. If no SURFACE-TYPE is supplied, the\n"
+ indent9 + "type contained in coordinate file will be used.\n");
std::vector<BrainModelSurface::SURFACE_TYPES> surfaceTypes;
std::vector<QString> surfaceTypeNames;
BrainModelSurface::getSurfaceTypesAndNames(surfaceTypes,
surfaceTypeNames);
for (int i = 0; i < static_cast<int>(surfaceTypeNames.size()); i++) {
helpInfo += (indent9
+ " "
+ surfaceTypeNames[i]
+ "\n");
}
helpInfo += "\n";
return helpInfo;
}
/**
* execute the command.
*/
void
CommandSurfaceCrossoverCheck::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
const QString coordinateFileName =
parameters->getNextParameterAsString("Coordinate File Name");
const QString topologyFileName =
parameters->getNextParameterAsString("Topology File Name");
//
// Create a brain set
//
BrainSet brainSet(topologyFileName,
coordinateFileName,
"",
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.");
}
//
// Check optional parameters
//
QString roiFileName;
while (parameters->getParametersAvailable()) {
const QString paramName = parameters->getNextParameterAsString("SURFACE CROSSOVER CHECK parameter");
if (paramName == "-roi-file") {
roiFileName =
parameters->getNextParameterAsString("SURFACE CROSSOVER ROI file name");
}
else if (paramName == "-surface-type") {
const QString surfaceTypeString =
parameters->getNextParameterAsString("SURFACE CROSSOVER SURFACE-TYPE");
const BrainModelSurface::SURFACE_TYPES surfaceType =
BrainModelSurface::getSurfaceTypeFromConfigurationID(surfaceTypeString);
bms->setSurfaceType(surfaceType);
}
else {
throw CommandException("unknown parameter: "
+ paramName);
}
}
//
// Do the crossover check
//
int tileCrossovers = 0;
int nodeCrossovers = 0;
bms->crossoverCheck(tileCrossovers,
nodeCrossovers,
bms->getSurfaceType());
//
// Create optional ROI file
//
if (roiFileName.isEmpty() == false) {
NodeRegionOfInterestFile roiFile;
roiFile.setNumberOfNodes(numNodes);
for (int i = 0; i < numNodes; i++) {
if (brainSet.getNodeAttributes(i)->getCrossover() ==
BrainSetNodeAttribute::CROSSOVER_YES) {
roiFile.setNodeSelected(i, true);
}
}
roiFile.writeFile(roiFileName);
}
//
// Print results
//
std::cout << "Crossover Check for "
<< FileUtilities::basename(coordinateFileName).toAscii().constData() << " "
<< FileUtilities::basename(topologyFileName).toAscii().constData() << std::endl;
std::cout << " Tile Crossovers: " << tileCrossovers << std::endl;
std::cout << " Node Crossovers: " << nodeCrossovers << std::endl;
}
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