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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 "CommandVolumeMapToSurfaceROIFile.h"
#include "FileFilters.h"
#include "NodeRegionOfInterestFile.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "TransformationMatrixFile.h"
#include "VolumeFile.h"
/**
* constructor.
*/
CommandVolumeMapToSurfaceROIFile::CommandVolumeMapToSurfaceROIFile()
: CommandBase("-volume-map-to-surface-roi-file",
"VOLUME MAP TO SURFACE ROI FILE")
{
}
/**
* destructor.
*/
CommandVolumeMapToSurfaceROIFile::~CommandVolumeMapToSurfaceROIFile()
{
}
/**
* get the script builder parameters.
*/
void
CommandVolumeMapToSurfaceROIFile::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Input Volume File Name", FileFilters::getVolumeGenericFileFilter());
paramsOut.addFile("Input Coordinate File Name", FileFilters::getCoordinateGenericFileFilter());
paramsOut.addFile("Input Topology File Name", FileFilters::getTopologyGenericFileFilter());
paramsOut.addFile("Output Region of Interest File Name", FileFilters::getRegionOfInterestFileFilter());
paramsOut.addVariableListOfParameters("Volume Map Options");
}
/**
* get full help information.
*/
QString
CommandVolumeMapToSurfaceROIFile::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<input-volume-file-name>\n"
+ indent9 + "<input-coordinate-file-name> \n"
+ indent9 + "<input-topology-file-name>\n"
+ indent9 + "<output-region-of-interest-file-name>\n"
+ indent9 + "[-surface-offset X Y Z]\n"
+ indent9 + "\n"
+ indent9 + "Intersect a volume with a surface and for all nodes that are\n"
+ indent9 + "within a non-zero voxel, assign the node as selcted in the\n"
+ indent9 + "region of interest file.\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandVolumeMapToSurfaceROIFile::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
//
// Get parameters
//
const QString inputVolumeFileName =
parameters->getNextParameterAsString("Input Volume File Name");
const QString inputCoordinateFileName =
parameters->getNextParameterAsString("Input Coordinate File Name");
const QString inputTopologyFileName =
parameters->getNextParameterAsString("Input Topology File Name");
const QString outputROIFileName =
parameters->getNextParameterAsString("Output Node Region of Interest File Name");
//
// Get optional parmameters
//
float surfaceOffset[3] = { 0.0, 0.0, 0.0 };
while (parameters->getParametersAvailable()) {
const QString paramName = parameters->getNextParameterAsString("Volume Map to Surface ROI Parameter");
if (paramName == "-surfaceOffset") {
surfaceOffset[0] = parameters->getNextParameterAsFloat("Surface Offset X");
surfaceOffset[1] = parameters->getNextParameterAsFloat("Surface Offset Y");
surfaceOffset[2] = parameters->getNextParameterAsFloat("Surface Offset Z");
}
else {
throw CommandException("unknown parameter "
+ paramName);
}
}
//
// Create a brain set
//
BrainSet brainSet(inputTopologyFileName,
inputCoordinateFileName,
"",
true);
BrainModelSurface* surface = brainSet.getBrainModelSurface(0);
if (surface == NULL) {
throw CommandException("unable to find surface.");
}
const TopologyFile* tf = surface->getTopologyFile();
if (tf == NULL) {
throw CommandException("unable to find topology.");
}
const int numNodes = surface->getNumberOfNodes();
if (numNodes == 0) {
throw CommandException("surface contains no nodes.");
}
//
// Read the volume file
//
VolumeFile volumeFile;
volumeFile.readFile(inputVolumeFileName);
//
// Apply the surface translation
//
TransformationMatrix matrix;
matrix.translate(surfaceOffset);
surface->applyTransformationMatrix(matrix);
//
// Create the region of interest file
//
NodeRegionOfInterestFile roiFile;
roiFile.setNumberOfNodes(numNodes);
//
// Assign the roi
//
roiFile.assignSelectedNodesWithVolumeFile(&volumeFile,
surface->getCoordinateFile(),
surface->getTopologyFile());
//
// Write the roi file
//
roiFile.writeFile(outputROIFileName);
}
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