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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 "BrainModelVolumeSureFitSegmentation.h"
#include "BrainSet.h"
#include "CommandSurfaceIdentifySulci.h"
#include "FileFilters.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "SpecFile.h"
#include "VolumeFile.h"
/**
* constructor.
*/
CommandSurfaceIdentifySulci::CommandSurfaceIdentifySulci()
: CommandBase("-surface-identify-sulci",
"SURFACE IDENTIFY SULCI")
{
}
/**
* destructor.
*/
CommandSurfaceIdentifySulci::~CommandSurfaceIdentifySulci()
{
}
/**
* get the script builder parameters.
*/
void
CommandSurfaceIdentifySulci::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
std::vector<QString> values, descriptions;
values.push_back("NIFTI"); descriptions.push_back("NIFTI");
values.push_back("AFNI"); descriptions.push_back("AFNI");
values.push_back("SPM"); descriptions.push_back("SPM");
values.push_back("WUNIL"); descriptions.push_back("WUNIL");
std::vector<QString> structValues, structDescriptions;
structValues.push_back("LEFT"); structDescriptions.push_back("LEFT");
structValues.push_back("RIGHT"); structDescriptions.push_back("RIGHT");
paramsOut.clear();
paramsOut.addFile("Spec File Name", FileFilters::getSpecFileFilter());
paramsOut.addListOfItems("Structure", structValues, structDescriptions);
paramsOut.addFile("Segmentation Volume File Name", FileFilters::getVolumeSegmentationFileFilter());
paramsOut.addFile("Closed Topology File Name", FileFilters::getTopologyClosedFileFilter());
paramsOut.addFile("Raw Coordinate File Name", FileFilters::getCoordinateRawFileFilter());
paramsOut.addFile("Fiducial Coordinate File Name", FileFilters::getCoordinateFiducialFileFilter());
paramsOut.addListOfItems("Volume Write Type", values, descriptions);
}
/**
* get full help information.
*/
QString
CommandSurfaceIdentifySulci::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<spec-file-name>\n"
+ indent9 + "<structure>\n"
+ indent9 + "<segmentation-volume-file-name>\n"
+ indent9 + "<closed-topology-file-name>\n"
+ indent9 + "<raw-coordinate-file-name>\n"
+ indent9 + "<fiducial-coordinate-file-name>\n"
+ indent9 + "<volume-write-type>\n"
+ indent9 + "\n"
+ indent9 + "Identify Sulci with shape and paint.\n"
+ indent9 + "\n"
+ indent9 + "Create a surface shape file containing depth and curvature measurements,\n"
+ indent9 + "a paint file identifying the sulci, and an area color file. If there\n"
+ indent9 + "is no raw coordinate file, specify fiducial coordinate file instead.\n"
+ indent9 + "\n"
+ indent9 + "NOTE: This command MUST be run in the directory containing the files.\n"
+ indent9 + "\n"
+ indent9 + "structure Specifies the brain structure. \n"
+ indent9 + " Acceptable values are RIGHT or LEFT \n"
+ indent9 + " \n"
+ indent9 + "write-volume-type Type of volume files to write. \n"
+ indent9 + " Specifies the type of the volume files that will be written \n"
+ indent9 + " during the segmentation process. Valid values are: \n"
+ indent9 + " AFNI \n"
+ indent9 + " NIFTI \n"
+ indent9 + " NIFTI_GZIP (RECOMMENDED!!!!) \n"
+ indent9 + " SPM \n"
+ indent9 + " WUNIL \n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandSurfaceIdentifySulci::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
const QString specFileName =
parameters->getNextParameterAsString("Spec File Name");
const QString structureName =
parameters->getNextParameterAsString("Structure Name").toUpper();
const QString segmentationVolumeFileName =
parameters->getNextParameterAsString("Segmentation Volume File Name");
const QString closedTopologyFileName =
parameters->getNextParameterAsString("Closed Topology File Name");
const QString rawCoordinateFileName =
parameters->getNextParameterAsString("Raw Coordinate File Name");
const QString fiducialCoordinateFileName =
parameters->getNextParameterAsString("Fiducial Coordinate File Name");
const QString writeVolumeTypeString =
parameters->getNextParameterAsString("Write Volume Type");
checkForExcessiveParameters();
VolumeFile::FILE_READ_WRITE_TYPE writeVolumeType = VolumeFile::FILE_READ_WRITE_TYPE_NIFTI_GZIP;
if (writeVolumeTypeString == "AFNI") {
writeVolumeType = VolumeFile::FILE_READ_WRITE_TYPE_AFNI;
}
else if (writeVolumeTypeString == "NIFTI") {
writeVolumeType = VolumeFile::FILE_READ_WRITE_TYPE_NIFTI;
}
else if (writeVolumeTypeString == "NIFTI_GZIP") {
writeVolumeType = VolumeFile::FILE_READ_WRITE_TYPE_NIFTI_GZIP;
}
else if (writeVolumeTypeString == "SPM") {
writeVolumeType = VolumeFile::FILE_READ_WRITE_TYPE_SPM_OR_MEDX;
}
else if (writeVolumeTypeString == "WUNIL") {
writeVolumeType = VolumeFile::FILE_READ_WRITE_TYPE_WUNIL;
}
else {
throw CommandException("Invalid volume file write type: " +
+ writeVolumeType);
}
//
// Load the segmentation volume to get the data file name
//
VolumeFile volTest;
QString segmentationVolumeDataFileName;
volTest.readFileMetaDataOnly(segmentationVolumeFileName);
segmentationVolumeDataFileName = volTest.getDataFileName();
//
// Read spec file
//
SpecFile specFile;
specFile.readFile(specFileName);
//
// Set the selected files
//
specFile.setAllFileSelections(SpecFile::SPEC_FALSE);
specFile.addToSpecFile(SpecFile::getVolumeSegmentationFileTag(), segmentationVolumeFileName,
segmentationVolumeDataFileName, SpecFile::SPEC_FALSE);
specFile.addToSpecFile(SpecFile::getClosedTopoFileTag(), closedTopologyFileName,
"", SpecFile::SPEC_FALSE);
specFile.addToSpecFile(SpecFile::getRawCoordFileTag(), rawCoordinateFileName,
"", SpecFile::SPEC_FALSE);
specFile.addToSpecFile(SpecFile::getFiducialCoordFileTag(), fiducialCoordinateFileName,
"", SpecFile::SPEC_FALSE);
//
// Read the spec file into a brain set
//
QString errorMessage;
BrainSet brainSet(true);
if (brainSet.readSpecFile(specFile, specFileName, errorMessage)) {
throw CommandException("Reading spec file: " + errorMessage);
}
//
// Identify the sulci
//
Structure structure(structureName);
BrainModelVolumeSureFitSegmentation bmsf(&brainSet,
structure.getType(),
writeVolumeType,
true);
bmsf.executeIdentifySulci();
}
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