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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 "BrainModelSurfaceDistortion.h"
#include "BrainSet.h"
#include "CommandSurfaceDistortion.h"
#include "FileFilters.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "SurfaceShapeFile.h"
/**
* constructor.
*/
CommandSurfaceDistortion::CommandSurfaceDistortion()
: CommandBase("-surface-distortion",
"SURFACE DISTORTION")
{
}
/**
* destructor.
*/
CommandSurfaceDistortion::~CommandSurfaceDistortion()
{
}
/**
* get the script builder parameters.
*/
void
CommandSurfaceDistortion::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Fiducial Coordinate File Name",
FileFilters::getCoordinateFiducialFileFilter());
paramsOut.addFile("Coordinate File Name",
FileFilters::getCoordinateGenericFileFilter());
paramsOut.addFile("Topology File Name",
FileFilters::getTopologyGenericFileFilter());
paramsOut.addFile("Input Surface Shape File Name",
FileFilters::getSurfaceShapeFileFilter());
paramsOut.addFile("Output Surface Shape File Name",
FileFilters::getSurfaceShapeFileFilter());
paramsOut.addVariableListOfParameters("Distortion\nOptions");
}
/**
* get full help information.
*/
QString
CommandSurfaceDistortion::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<fiducial-coordinate-file-name>\n"
+ indent9 + "<coordinate-file-name>\n"
+ indent9 + "<closed-topology-file-name>\n"
+ indent9 + "<input-surface-shape-file-name>\n"
+ indent9 + "<output-surface-shape-file-name>\n"
+ indent9 + "[-generate-areal-distortion]\n"
+ indent9 + "[-generate-linear-distortion]\n"
+ indent9 + "[-areal-distortion-column-name name]\n"
+ indent9 + "[-linear-distortion-column-name name]\n"
+ indent9 + "\n"
+ indent9 + "Generate distortion measurements for the surfaces.\n"
+ indent9 + "\n"
+ indent9 + "The column names are optional, and, if not specified \n"
+ indent9 + "are " + SurfaceShapeFile::arealDistortionColumnName + "\n"
+ indent9 + "and " + SurfaceShapeFile::linearDistortionColumnName + " \n"
+ indent9 + "respectively.\n"
+ indent9 + "\n"
+ indent9 + "The \"input-surface-shape-file-name\" does not needs\n"
+ indent9 + "to exist.\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandSurfaceDistortion::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
const QString fiducialCoordinateFileName =
parameters->getNextParameterAsString("Fiducial Coordinate File Name");
const QString coordinateFileName =
parameters->getNextParameterAsString("Coordinate File Name");
const QString topologyFileName =
parameters->getNextParameterAsString("Topology File Name");
const QString inputSurfaceShapeFileName =
parameters->getNextParameterAsString("Input Surface Shape File Name");
const QString outputSurfaceShapeFileName =
parameters->getNextParameterAsString("Output Surface Shape File Name");
bool doArealFlag = false;
bool doLinearFlag = false;
QString arealDistortionColumnName(SurfaceShapeFile::arealDistortionColumnName);
QString linearDistortionColumnName(SurfaceShapeFile::linearDistortionColumnName);
//
// Check optional parameters
//
while (parameters->getParametersAvailable()) {
const QString paramName = parameters->getNextParameterAsString("SURFACE DISTORTION parameter");
if (paramName == "-generate-areal-distortion") {
doArealFlag = true;
}
else if (paramName == "-generate-linear-distortion") {
doLinearFlag = true;
}
else if (paramName == "-areal-distortion-column-name") {
arealDistortionColumnName =
parameters->getNextParameterAsString("Areal Distortion column name");
}
else if (paramName == "-linear-distortion-column-name") {
linearDistortionColumnName =
parameters->getNextParameterAsString("Linear Distortion column name");
}
else {
throw CommandException("unknown parameter: "
+ paramName);
}
}
//
// Check inputs
//
if ((doArealFlag == false) &&
(doLinearFlag == false)) {
throw CommandException("At least one of "
"\"-generate-areal-distortion\" or "
"\"-generate-linear-distortion\" must be provided.");
}
//
// Create a brain set
//
BrainSet brainSet(topologyFileName,
fiducialCoordinateFileName,
coordinateFileName,
true);
BrainModelSurface* fiducialBMS = brainSet.getBrainModelSurface(0);
if (fiducialBMS == NULL) {
throw CommandException("unable to find fiducial surface.");
}
TopologyFile* tf = fiducialBMS->getTopologyFile();
if (tf == NULL) {
throw CommandException("unable to find topology.");
}
const int numNodes = fiducialBMS->getNumberOfNodes();
if (numNodes == 0) {
throw CommandException("surface contains not nodes.");
}
BrainModelSurface* surfaceBMS = brainSet.getBrainModelSurface(1);
if (surfaceBMS == NULL) {
throw CommandException("unable to find second surface.");
}
//
// Read input surface shape file
//
SurfaceShapeFile surfaceShapeFile;
if (QFile::exists(inputSurfaceShapeFileName)) {
surfaceShapeFile.readFile(inputSurfaceShapeFileName);
}
//
// Set areal distortion column number
//
int arealColumnNumber = BrainModelSurfaceDistortion::DISTORTION_COLUMN_DO_NOT_GENERATE;
if (doArealFlag) {
arealColumnNumber = BrainModelSurfaceDistortion::DISTORTION_COLUMN_CREATE_NEW;
const int col = surfaceShapeFile.getColumnWithName(arealDistortionColumnName);
if (col >= 0) {
arealColumnNumber = col;
}
}
//
// Set linear distortion column number
//
int linearColumnNumber = BrainModelSurfaceDistortion::DISTORTION_COLUMN_DO_NOT_GENERATE;
if (doLinearFlag) {
linearColumnNumber = BrainModelSurfaceDistortion::DISTORTION_COLUMN_CREATE_NEW;
const int col = surfaceShapeFile.getColumnWithName(linearDistortionColumnName);
if (col >= 0) {
linearColumnNumber = col;
}
}
//
// Generate curvature
//
BrainModelSurfaceDistortion bmsd(&brainSet,
surfaceBMS,
fiducialBMS,
tf,
&surfaceShapeFile,
arealColumnNumber,
linearColumnNumber,
arealDistortionColumnName,
linearDistortionColumnName);
bmsd.execute();
//
// Write the surface shape file
//
surfaceShapeFile.writeFile(outputSurfaceShapeFileName);
}
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