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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 "BrainModelSurfaceToVolumeSegmentationConverter.h"
#include "BrainSet.h"
#include "CommandSurfaceToCerebralHull.h"
#include "FileFilters.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "vtkPolyDataWriter.h"
/**
* constructor.
*/
CommandSurfaceToCerebralHull::CommandSurfaceToCerebralHull()
: CommandBase("-surface-to-cerebral-hull",
"SURFACE TO CEREBRAL HULL")
{
}
/**
* destructor.
*/
CommandSurfaceToCerebralHull::~CommandSurfaceToCerebralHull()
{
}
/**
* get the script builder parameters.
*/
void
CommandSurfaceToCerebralHull::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Fiducial Coordinate File Name",
FileFilters::getCoordinateFiducialFileFilter());
paramsOut.addFile("Closed Topology File Name",
FileFilters::getTopologyClosedFileFilter());
paramsOut.addFile("Input Volume File Name",
FileFilters::getVolumeGenericFileFilter());
paramsOut.addFile("Output Segmentation Volume File Name",
FileFilters::getVolumeSegmentationFileFilter());
paramsOut.addFile("Output Hull Volume File Name",
FileFilters::getVolumeGenericFileFilter());
paramsOut.addFile("Output Hull Surface VTK File Name",
FileFilters::getVtkSurfaceFileFilter());
}
/**
* get full help information.
*/
QString
CommandSurfaceToCerebralHull::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<fiducial-coordinate-file-name>\n"
+ indent9 + "<closed-topology-file-name>\n"
+ indent9 + "<input-volume-file-name>\n"
+ indent9 + "<output-segmentation-volume-file-name>\n"
+ indent9 + "<output-hull-volume-file-name>\n"
+ indent9 + "<output-cerebral-hull-surface-vtk-file-name>\n"
+ indent9 + "\n"
+ indent9 + "Generate a cerebral hull surface which is typically used\n"
+ indent9 + "for generating sulcal depth.\n"
+ indent9 + "\n"
+ indent9 + "Note: The \"input-volume-file-name\" must exist and be in\n"
+ indent9 + "the same stereotaxic space as the surface. The input\n"
+ indent9 + "volume is only used to get the stereotaxic space information \n"
+ indent9 + "and its data contents are ignored. If needed a volume can\n"
+ indent9 + "be created using this program with the command \n"
+ indent9 + "\"-volume-create\".\n"
+ indent9 + "\n"
+ indent9 + "\n"
+ indent9 + "\n"
+ indent9 + "\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandSurfaceToCerebralHull::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
//
// Get required parameters
//
const QString fiducialCoordinateFileName =
parameters->getNextParameterAsString("Fiducial Coordinate File Name");
const QString closedTopologyFileName =
parameters->getNextParameterAsString("Closed Topology File Name");
const QString inputVolumeFileName =
parameters->getNextParameterAsString("Input Volume File Name");
QString outputSegmentationVolumeFileName, outputSegmentationVolumeFileLabel;
parameters->getNextParameterAsVolumeFileNameAndLabel("Output Segmentation Volume File Name and Label",
outputSegmentationVolumeFileName,
outputSegmentationVolumeFileLabel);
QString outputHullVolumeFileName, outputHullVolumeFileLabel;
parameters->getNextParameterAsVolumeFileNameAndLabel("Output Hull Volume File Name and Label",
outputHullVolumeFileName,
outputHullVolumeFileLabel);
const QString outputCerebralHullVtkFileName =
parameters->getNextParameterAsString("Output Cerebral Hull VTK File Name");
checkForExcessiveParameters();
//
// Create a brain set
//
BrainSet brainSet(closedTopologyFileName,
fiducialCoordinateFileName,
"",
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 no nodes.");
}
//
// Read the volume file
//
VolumeFile volumeFile;
volumeFile.readFile(inputVolumeFileName);
// Create the segmentation volume
//
BrainModelSurfaceToVolumeSegmentationConverter bmssc(&brainSet,
bms,
&volumeFile,
false,
false);
bmssc.execute();
volumeFile.setDescriptiveLabel(outputSegmentationVolumeFileLabel);
volumeFile.writeFile(outputSegmentationVolumeFileName);
//
// Expand around edges with empty slices
//
VolumeFile segmentVolumeExpanded(volumeFile);
int expDim[3];
segmentVolumeExpanded.getDimensions(expDim);
const int expSlices = 7;
const int resizeCrop[6] = {
-expSlices, expDim[0] + expSlices,
-expSlices, expDim[1] + expSlices,
-expSlices, expDim[2] + expSlices
};
segmentVolumeExpanded.resize(resizeCrop);
//
// Generate the hull VTK file and volume
//
VolumeFile* hullVolume = NULL;
vtkPolyData* hullPolyData = NULL;
brainSet.generateCerebralHullVtkFile(&segmentVolumeExpanded,
hullVolume,
hullPolyData);
//
// Write the hull volume
//
hullVolume->setDescriptiveLabel(outputHullVolumeFileLabel);
hullVolume->writeFile(outputHullVolumeFileName);
delete hullVolume;
//
// Write the Hull VTK file
//
vtkPolyDataWriter* writer = vtkPolyDataWriter::New();
writer->SetInput(hullPolyData);
writer->SetHeader("Written by Caret");
writer->SetFileName((char*)outputCerebralHullVtkFileName.toAscii().constData());
writer->Write();
writer->Delete();
hullPolyData->Delete();
}
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