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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 "CommandVolumeFslToVector.h"
#include "FileFilters.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "TransformationMatrixFile.h"
#include "VectorFile.h"
#include "VolumeFile.h"
/**
* constructor.
*/
CommandVolumeFslToVector::CommandVolumeFslToVector()
: CommandBase("-volume-fsl-to-vector",
"VOLUME FSL TO VECTOR")
{
}
/**
* destructor.
*/
CommandVolumeFslToVector::~CommandVolumeFslToVector()
{
}
/**
* get the script builder parameters.
*/
void
CommandVolumeFslToVector::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Input XYZ Volume File Name", FileFilters::getVolumeGenericFileFilter());
paramsOut.addFile("Input Magnitude Volume File Name", FileFilters::getVolumeGenericFileFilter());
paramsOut.addFile("Input FSL Diffusion to Structureal Matrix File Name", "*.mat");
paramsOut.addFile("Volume in Output Stereotaxic Space", FileFilters::getVolumeGenericFileFilter());
paramsOut.addFile("Output Vector File Name", FileFilters::getGiftiVectorFileFilter());
paramsOut.addVariableListOfParameters("", "");
}
/**
* get full help information
*/
QString
CommandVolumeFslToVector::getHelpInformation() const
{
float rgba[4];
VectorFile::getDefaultColorRGBA(rgba);
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<input-xyz-volume-file-name>\n"
+ indent9 + "<input-magnitude-volume-file-name>\n"
+ indent9 + "<input-fsl-diffusion-to-structural-matrix>\n"
+ indent9 + "<volume-in-output-stereotaxic-space-file-name>\n"
+ indent9 + "<output-vector-file-name>\n"
+ indent9 + "[-output-matrix output-transformation-matrix-file-name]\n"
+ indent9 + "[-rgb red green blue]\n"
+ indent9 + "\n"
+ indent9 + "Create a vector file from a vector volume file and .\n"
+ indent9 + "a magnitude volume file. All of the volumes must have \n"
+ indent9 + "the same IJK dimensions. A vector is created for each\n"
+ indent9 + "voxel whose magnitude is greater than zero.\n"
+ indent9 + "\n"
+ indent9 + "\"input-xyz-volume-file-name\" is a volume file that\n"
+ indent9 + "contains three sub-volumes containing the X, Y, and Z\n"
+ indent9 + "components of a unit vector.\n"
+ indent9 + "\n"
+ indent9 + "\"input-magnitude-volume-file-name\" is a volume \n"
+ indent9 + "containing the magnitude of the vectors.\n"
+ indent9 + "\n"
+ indent9 + "\"volume-in-output-stereotaxic-space-file-name\" is a \n"
+ indent9 + "volume whose stereotaxic coordinates are in the \n"
+ indent9 + "destination space.\n"
+ indent9 + "\n"
+ indent9 + "\"input-fsl-diffusion-to-structural-matrix\" is the FSL\n"
+ indent9 + "diffusion space to structural space matrix file, typically\n"
+ indent9 + "named \"diff2str.mat\". It contains a 4x4 transformation\n"
+ indent9 + "matrix with each row of the matrix on a separate line.\n"
+ indent9 + "\n"
+ indent9 + "The file name extension for a vector file is \"\n"
+ indent9 + SpecFile::getGiftiVectorFileExtension() + "\".\n"
+ indent9 + "\n"
+ indent9 + "If \"-output-matrix\" is specified, the matrix used to \n"
+ indent9 + "transform from the input volume to output volume space\n"
+ indent9 + "is placed in the output transformation matrix file.\n"
+ indent9 + "\n"
+ indent9 + "Use the \"-rgb\" option to set the colors of the \n"
+ indent9 + "vectors. The red, green, and blue components are\n"
+ indent9 + "specified as floating point number swith a range of \n"
+ indent9 + "zero to one. The default color is "
+ indent9 + "(" + QString::number(rgba[0])
+ ", " + QString::number(rgba[1])
+ ", " + QString::number(rgba[2]) + ")\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandVolumeFslToVector::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
float rgba[4];
VectorFile::getDefaultColorRGBA(rgba);
QString outputMatrixFileName;
const QString inputXYZVolumeFileName =
parameters->getNextParameterAsString("Input XYZ Volume File Name");
const QString inputMagnitudeVolumeFileName =
parameters->getNextParameterAsString("Input Magnitude Volume File Name");
const QString fslTransformationMatrixFileName =
parameters->getNextParameterAsString("FSL Diffusion to Structural Matrix File Name");
const QString outputSpaceVolumeFileName =
parameters->getNextParameterAsString("Volume in Output Stereotaxic Space File Name");
const QString outputVectorFileName =
parameters->getNextParameterAsString("Output Vector File Name");
while (parameters->getParametersAvailable()) {
const QString param = parameters->getNextParameterAsString("Optional Parameter");
if (param == "-output-matrix") {
outputMatrixFileName =
parameters->getNextParameterAsString("Output Matrix File Name");
}
else if (param == "-rgb") {
rgba[0] = parameters->getNextParameterAsFloat("Red Color Component");
rgba[1] = parameters->getNextParameterAsFloat("Green Color Component");
rgba[2] = parameters->getNextParameterAsFloat("Blue Color Component");
}
else {
throw CommandException("Unrecognized parameter: " + param);
}
}
//
// Read the input files
//
TransformationMatrixFile transformMatrixFile;
transformMatrixFile.readFile(fslTransformationMatrixFileName);
TransformationMatrix* fslMatrix = transformMatrixFile.getTransformationMatrix(0);
if (fslMatrix == NULL) {
throw CommandException("Unable to find a matrix in FSL Matrix File.");
}
std::vector<VolumeFile*> xyzVolumes;
VolumeFile::setVolumeSpace(VolumeFile::VOLUME_SPACE_VOXEL_NATIVE); // DO NOT make LPI
VolumeFile::readFile(inputXYZVolumeFileName,
-1,
xyzVolumes);
if (xyzVolumes.size() != 3) {
throw CommandException(inputXYZVolumeFileName +
" must contain exactly three subvolumes.");
}
VolumeFile magnitudeVolume;
VolumeFile::setVolumeSpace(VolumeFile::VOLUME_SPACE_VOXEL_NATIVE); // DO NOT make LPI
magnitudeVolume.readFile(inputMagnitudeVolumeFileName);
VolumeFile outputSpaceVolumeFile;
outputSpaceVolumeFile.readFile(outputSpaceVolumeFileName);
TransformationMatrix outputTransformationMatrix;
VectorFile* vf = VectorFile::createVectorFileFromFSLVectorVolumes(
*(xyzVolumes[0]),
*(xyzVolumes[1]),
*(xyzVolumes[2]),
magnitudeVolume,
outputSpaceVolumeFile,
*fslMatrix,
outputTransformationMatrix,
rgba);
vf->writeFile(outputVectorFileName);
if (outputMatrixFileName.isEmpty() == false) {
TransformationMatrixFile tm;
tm.addTransformationMatrix(outputTransformationMatrix);
tm.writeFile(outputMatrixFileName);
}
delete vf;
}
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