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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 "BrainSet.h"
#include "CommandSurfaceApplyTransformationMatrix.h"
#include "FileFilters.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "TransformationMatrixFile.h"
/**
* constructor.
*/
CommandSurfaceApplyTransformationMatrix::CommandSurfaceApplyTransformationMatrix()
: CommandBase("-surface-apply-transformation-matrix",
"SURFACE APPLY TRANSFORMATION MATRIX")
{
}
/**
* destructor.
*/
CommandSurfaceApplyTransformationMatrix::~CommandSurfaceApplyTransformationMatrix()
{
}
/**
* get the script builder parameters.
*/
void
CommandSurfaceApplyTransformationMatrix::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Input Coordinate File Name", FileFilters::getCoordinateGenericFileFilter());
paramsOut.addFile("Topology File Name", FileFilters::getTopologyGenericFileFilter());
paramsOut.addFile("Output Coordinate File Name", FileFilters::getCoordinateGenericFileFilter());
paramsOut.addVariableListOfParameters("Matrix Options");
}
/**
* get full help information.
*/
QString
CommandSurfaceApplyTransformationMatrix::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<input-coordinate-file-name>\n"
+ indent9 + "<topology-file-name>\n"
+ indent9 + "<output-coordinate-file-name>\n"
+ indent9 + "[-matrix-file matrix-file-name matrix-name]\n"
+ indent9 + "[-matrix matrix-values-left-to-right-and-top-to-bottom]\n"
+ indent9 + "\n"
+ indent9 + "Apply a transformation matrix to a surface.\n"
+ indent9 + "\n"
+ indent9 + "The matrix may be within a specified file or the matrix\n"
+ indent9 + "may be specified on the command line.\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandSurfaceApplyTransformationMatrix::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
//
// Get the parameters
//
const QString inputCoordinateFileName =
parameters->getNextParameterAsString("Input Coordinate File Name");
const QString inputTopologyFileName =
parameters->getNextParameterAsString("Input Topology File Name");
const QString outputCoordinateFileName =
parameters->getNextParameterAsString("Output Coordinate File Name");
//
// Get optional parameters
//
enum MATRIX_SOURCE {
MATRIX_SOURCE_NONE,
MATRIX_SOURCE_FROM_FILE,
MATRIX_SOURCE_VALUES
};
MATRIX_SOURCE matrixSource = MATRIX_SOURCE_NONE;
QString matrixFileName;
QString matrixName;
float matrixValues[4][4];
while (parameters->getParametersAvailable()) {
const QString paramName = parameters->getNextParameterAsString("Apply Transform Parameter");
if (paramName == "-matrix-file") {
matrixFileName = parameters->getNextParameterAsString("Matrix File Name");
matrixName = parameters->getNextParameterAsString("Matrix Name");
matrixSource = MATRIX_SOURCE_FROM_FILE;
}
else if (paramName == "-matrix") {
int counter = 1;
for (int i = 0; i < 4; i++) {
for (int j = 0; j < 4; j++) {
const QString text("Matrix value " + QString::number(counter));
matrixValues[i][j] = parameters->getNextParameterAsFloat(text);
}
counter++;
}
matrixSource = MATRIX_SOURCE_VALUES;
}
else {
throw CommandException("unrecognized parameter: "
+ paramName);
}
}
//
// Did user forget to supply a matrix
//
if (matrixSource == MATRIX_SOURCE_NONE) {
throw CommandException("A matrix must be supplied "
"with either \"-matrix-file\" or \"-matrix\".");
}
//
// Create a brain set
//
BrainSet brainSet(inputTopologyFileName,
inputCoordinateFileName,
"",
true);
BrainModelSurface* surface = brainSet.getBrainModelSurface(0);
if (surface == NULL) {
throw CommandException("unable to find fiducial surface.");
}
const TopologyFile* tf = surface->getTopologyFile();
if (tf == NULL) {
throw CommandException("unable to find topology.");
}
const int numNodes = surface->getNumberOfNodes();
if (numNodes == 0) {
throw CommandException("surface contains no nodes.");
}
//
// Apply the transformation matrix
//
switch (matrixSource) {
case MATRIX_SOURCE_NONE:
break;
case MATRIX_SOURCE_FROM_FILE:
{
TransformationMatrixFile tmf;
tmf.readFile(matrixFileName);
TransformationMatrix* matrix = tmf.getTransformationMatrixWithName(matrixName);
if (matrix == NULL)
{
throw CommandException("matrix file does not contain a matrix with that name.");
}
surface->applyTransformationMatrix(*matrix);
}
break;
case MATRIX_SOURCE_VALUES:
{
TransformationMatrix matrix;
matrix.setMatrix(matrixValues);
surface->applyTransformationMatrix(matrix);
}
break;
}
//
// Write the coordinate file
//
CoordinateFile* cf = surface->getCoordinateFile();
cf->writeFile(outputCoordinateFileName);
}
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