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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 "CellFile.h"
#include "CellFileProjector.h"
#include "CellProjectionFile.h"
#include "CommandSurfaceCellProjection.h"
#include "FileFilters.h"
#include "FociFile.h"
#include "FociProjectionFile.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
/**
* constructor.
*/
CommandSurfaceCellProjection::CommandSurfaceCellProjection(const QString& operationSwitchIn,
const QString& shortDescriptionIn,
const bool fociFlagIn)
: CommandBase(operationSwitchIn,
shortDescriptionIn)
{
fociFlag = fociFlagIn;
}
/**
* destructor.
*/
CommandSurfaceCellProjection::~CommandSurfaceCellProjection()
{
}
/**
* get the script builder parameters.
*/
void
CommandSurfaceCellProjection::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Coordinate File Name",
FileFilters::getCoordinateGenericFileFilter());
paramsOut.addFile("Topology File Name",
FileFilters::getTopologyGenericFileFilter());
if (fociFlag) {
paramsOut.addFile("Input Foci File",
FileFilters::getFociFileFilter());
paramsOut.addFile("Output Foci Projection File",
FileFilters::getFociProjectionFileFilter());
}
else {
paramsOut.addFile("Input Cell File",
FileFilters::getCellFileFilter());
paramsOut.addFile("Output Cell Projection File",
FileFilters::getCellProjectionFileFilter());
}
}
/**
* get full help information.
*/
QString
CommandSurfaceCellProjection::getHelpInformation() const
{
QString s = "cell";
if (fociFlag) s = "foci";
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<coordinate-file-name>\n"
+ indent9 + "<topology-file-name>\n"
+ indent9 + "<input-" + s + "-file-name>\n"
+ indent9 + "<output-" + s + "-projection-file-name>\n"
+ indent9 + "[-project-onto-surface onto-surface-above-distance]\n"
+ indent9 + "\n"
+ indent9 + "Project the " + s + " to the surface and save into the " + s + "\n"
+ indent9 + "projection file.\n"
+ indent9 + "\n"
+ indent9 + "\"-project-onto-surface\" is used to project the " + s + " so that\n"
+ indent9 + "they are a specified distance above the surface.\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandSurfaceCellProjection::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
QString s = "Cell";
if (fociFlag) s = "Foci";
const QString coordinateFileName =
parameters->getNextParameterAsString("Coordinate File Name");
const QString topologyFileName =
parameters->getNextParameterAsString("Topology File Name");
const QString cellFileName =
parameters->getNextParameterAsString(s + " File Name");
const QString cellProjectionFileName =
parameters->getNextParameterAsString(s + " Projection File Name");
//
// Process optional parameters
//
bool projectToSurfaceFlag = false;
float surfaceAboveDistance = 0.0;
while (parameters->getParametersAvailable()) {
const QString paramName =
parameters->getNextParameterAsString(s + " Projection Parameter");
if (paramName == "-project-onto-surface") {
projectToSurfaceFlag = true;
surfaceAboveDistance =
parameters->getNextParameterAsFloat(s + " Projection Parameter: Above surface distance");
}
else {
throw CommandException("unrecognized option");
}
}
//
// Create a brain set
//
BrainSet brainSet(topologyFileName,
coordinateFileName,
"",
true);
const BrainModelSurface* bms = brainSet.getBrainModelSurface(0);
if (bms == NULL) {
throw CommandException("unable to find surface.");
}
const TopologyFile* tf = bms->getTopologyFile();
if (tf == NULL) {
throw CommandException("unable to find topology.");
}
const int numNodes = bms->getNumberOfNodes();
if (numNodes == 0) {
throw CommandException("surface contains no nodes.");
}
//
// Read the cell file
//
CellFile* cellFile = NULL;
if (fociFlag) {
cellFile = new FociFile;
}
else {
cellFile = new CellFile;
}
cellFile->readFile(cellFileName);
//
// Project the cell file
//
CellProjectionFile* cellProjectionFile = NULL;
if (fociFlag) {
cellProjectionFile = new FociProjectionFile;
}
else {
cellProjectionFile = new CellProjectionFile;
}
cellProjectionFile->appendFiducialCellFile(*cellFile);
CellFileProjector projector(bms);
projector.projectFile(cellProjectionFile,
0,
CellFileProjector::PROJECTION_TYPE_ALL,
surfaceAboveDistance,
projectToSurfaceFlag,
NULL);
//
// Write the cell projection file
//
cellProjectionFile->writeFile(cellProjectionFileName);
}
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