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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 <iostream>
#include <fstream>
#include "CommandSurfaceAffineRegression.h"
#include "FileFilters.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "BrainModelSurfaceAffineRegression.h"
#include "BrainSet.h"
#include "StringUtilities.h"
#include "FileUtilities.h"
/**
* constructor.
*/
CommandSurfaceAffineRegression::CommandSurfaceAffineRegression()
: CommandBase("-surface-affine-regression",
"SURFACE TO SURFACE LINEAR REGRESSION AFFINE REGISTRATION")
{
}
/**
* destructor.
*/
CommandSurfaceAffineRegression::~CommandSurfaceAffineRegression()
{
}
/**
* get the script builder parameters.
*/
void
CommandSurfaceAffineRegression::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Input Target Coordinate File", FileFilters::getCoordinateGenericFileFilter());
paramsOut.addFile("Input Source Coordinate File", FileFilters::getCoordinateGenericFileFilter());
}
/**
* get full help information.
*/
QString
CommandSurfaceAffineRegression::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<target-coord>\n"
+ indent9 + "<source-coord-1>\n"
+ indent9 + "[<source-coord-2>...]\n"
+ indent9 + "\n"
+ indent9 + "Use linear regression to compute and execute an affine transormation,\n"
+ indent9 + "attempting to minimize the variability from source to target.\n"
+ indent9 + "File names will be automatically generated by adding \".afftrans.\"\n"
+ indent9 + "as the third section of the filename, eg, \"test.case5.73730.coord\"\n"
+ indent9 + "will be output as \"test.case5.afftrans.73730.coord\", in the same\n"
+ indent9 + "directory.\n"
+ indent9 + "\n"
+ indent9 + " target-coord the target to minimize the variability to\n"
+ indent9 + "\n"
+ indent9 + " source-coord-1 a source coordinate file to transform\n"
+ indent9 + "\n"
+ indent9 + " [source-coord-2...] same as above, but optional. You may\n"
+ indent9 + " specify as many sources as you wish.\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandSurfaceAffineRegression::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
const QString target =
parameters->getNextParameterAsString("Target Coordinate File");
BrainSet brainSet;
CoordinateFile targetCoord, sourceCoord, outCoord;
targetCoord.readFile(target);
QString source, out, sourceFile, sourcePath, outMat;
int i = 1, index;
BrainModelSurfaceAffineRegression* affineObject;
while (parameters->getParametersAvailable())
{
try
{
source = parameters->getNextParameterAsString("Source Coordinate File " + StringUtilities::fromNumber(i));
sourceFile = FileUtilities::basename(source);
sourcePath = FileUtilities::dirname(source);
//
// Add .afftrans. as 2nd field before extension
//
index = sourceFile.lastIndexOf('.');
index = sourceFile.lastIndexOf('.', index - 1) + 1;
if (index == -1)
{
index = 0;
}
outMat = source + ".mat";
out = sourceFile;
out.insert(index, "afftrans.");
if (sourcePath.right(1) == FileUtilities::directorySeparator() || sourcePath == "")
{
out = sourcePath + out;
} else {
out = sourcePath + FileUtilities::directorySeparator() + out;
}
sourceCoord.readFile(source);
outCoord = sourceCoord;
//
// Create the affine object
//
affineObject = new BrainModelSurfaceAffineRegression(&brainSet,
&sourceCoord,
&targetCoord,
&outCoord,
out);
//
// Execute regression
//
affineObject->execute();
outCoord.writeFile(out);
QFile affineFile(outMat);
if (!affineFile.open(QIODevice::WriteOnly))
{
std::cerr << "Error opening output file \"" << outMat.toAscii().constData() << '"' << std::endl;
} else {
for (short j = 0; j < 3; ++j)
{
for (short k = 0; k < 4; ++k, affineFile.write(" ", 2))
{
affineFile.write(StringUtilities::fromNumber(affineObject->getAffine(j, k)).toAscii());
}
affineFile.write("\n", 1);
//affineFile.write(StringUtilities::fromStdString(std::endl).toAscii());
}
affineFile.write("0 0 0 1 \n", 13);
affineFile.close();
//affineFile.write(StringUtilities::fromStdString(std::endl).toAscii());
const QString warningMessages = affineObject->getWarningMessages();
if (warningMessages.isEmpty() == false) {
std::cout << "Transformation Warnings: " << warningMessages.toAscii().constData() << std::endl;
}
}
++i;
delete affineObject;
} catch(FileException e) {
std::cerr << e.whatQString().toAscii().constData() << std::endl;
} catch(BrainModelAlgorithmException e) {
std::cerr << e.whatQString().toAscii().constData() << std::endl;
}
}
}
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