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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 "BrainModelVolumeNearToPlane.h"
#include "BrainSet.h"
#include "CommandVolumeNearToPlane.h"
#include "FileFilters.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "SureFitVectorFile.h"
#include "VolumeFile.h"
/**
* constructor.
*/
CommandVolumeNearToPlane::CommandVolumeNearToPlane()
: CommandBase("-volume-near-to-plane",
"VOLUME NEAR TO PLANE")
{
}
/**
* destructor.
*/
CommandVolumeNearToPlane::~CommandVolumeNearToPlane()
{
}
/**
* get the script builder parameters.
*/
void
CommandVolumeNearToPlane::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Input Mask Volume File Name", FileFilters::getVolumeGenericFileFilter());
paramsOut.addFile("Input Vector File Name", FileFilters::getSureFitVectorFileFilter());
paramsOut.addFile("Output Volume File Name", FileFilters::getVolumeGenericFileFilter());
paramsOut.addFloat("Sigma-N");
paramsOut.addFloat("Sigma-W");
paramsOut.addFloat("Offset");
paramsOut.addInt("Grad Sign");
paramsOut.addBoolean("Down Flag");
paramsOut.addBoolean("Mask Flag");
}
/**
* get full help information.
*/
QString
CommandVolumeNearToPlane::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<input-mask-volume-file-name>\n"
+ indent9 + "<input-vector-file-name>\n"
+ indent9 + "<output-volume-file-name>\n"
+ indent9 + "<Sigma-N>\n"
+ indent9 + "<Sigma-W>\n"
+ indent9 + "<Offset>\n"
+ indent9 + "<Grad-Sign>\n"
+ indent9 + "<Down-Flag>\n"
+ indent9 + "<Mask-Flag>\n"
+ indent9 + "\n"
+ indent9 + "Near to plane operation.\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandVolumeNearToPlane::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
const QString inputMaskVolumeFileName =
parameters->getNextParameterAsString("Input Mask Volume File Name");
const QString inputVectorFileName =
parameters->getNextParameterAsString("Input Vector File Name");
QString outputVolumeFileName, outputVolumeFileLabel;
parameters->getNextParameterAsVolumeFileNameAndLabel("Output Volume File Name/Label",
outputVolumeFileName,
outputVolumeFileLabel);
const float sigmaN =
parameters->getNextParameterAsFloat("Sigma N");
const float sigmaW =
parameters->getNextParameterAsFloat("Sigma W");
const float offset =
parameters->getNextParameterAsFloat("Offset");
const int gradSign =
parameters->getNextParameterAsInt("Grad Sign");
const bool downFlag =
parameters->getNextParameterAsFloat("Down Flag");
const bool maskFlag =
parameters->getNextParameterAsFloat("Mask Flag");
checkForExcessiveParameters();
//
// Read the input file
//
VolumeFile maskVolume;
maskVolume.readFile(inputMaskVolumeFileName);
//
// Read the vector file
//
SureFitVectorFile vectorFile;
vectorFile.readFile(inputVectorFileName);
VolumeFile outputVolume = maskVolume;
//
// perform near to plane
//
BrainSet bs;
BrainModelVolumeNearToPlane np(&bs,
&vectorFile,
sigmaN,
sigmaW,
offset,
downFlag,
gradSign,
maskFlag,
&maskVolume,
&outputVolume);
np.execute();
//
// Write the volume
//
writeVolumeFile(outputVolume, outputVolumeFileName, outputVolumeFileLabel);
}
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