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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 "CommandPaintAssignNodes.h"
#include "FileFilters.h"
#include "NodeRegionOfInterestFile.h"
#include "PaintFile.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
/**
* constructor.
*/
CommandPaintAssignNodes::CommandPaintAssignNodes()
: CommandBase("-paint-assign-to-nodes",
"PAINT ASSIGN TO NODES")
{
}
/**
* destructor.
*/
CommandPaintAssignNodes::~CommandPaintAssignNodes()
{
}
/**
* get the script builder parameters.
*/
void
CommandPaintAssignNodes::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Input Paint File Name",
FileFilters::getPaintFileFilter());
paramsOut.addFile("Output Paint File Name",
FileFilters::getPaintFileFilter());
paramsOut.addString("Paint Column");
paramsOut.addString("Paint Name");
paramsOut.addVariableListOfParameters("Options");
}
/**
* get full help information.
*/
QString
CommandPaintAssignNodes::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + " <input-paint-file-name>\n"
+ indent9 + " <output-paint-file-name>\n"
+ indent9 + " <paint-column>\n"
+ indent9 + " <paint-name>\n"
+ indent9 + "[-assign-from-roi-file roi-file-name]\n"
+ indent9 + "[-set-column-name name]\n"
+ indent9 + "\n"
+ indent9 + "Assign paint values to nodes. The input paint file must\n"
+ indent9 + "exist. If the input paint column is not found and its\n"
+ indent9 + "name is non-numeric, a new column will be added to the paint\n"
+ indent9 + "file if the paint file contains nodes.\n"
+ indent9 + "\n"
+ indent9 + " \"column\" is either the number of the column, which\n"
+ indent9 + " starts at one, or the name of the column. If a\n"
+ indent9 + " a name contains spaces, it must be enclosed in double \n"
+ indent9 + " quotes. Name has priority over number.\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandPaintAssignNodes::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
//
// Get the parameters
//
const QString inputPaintFileName =
parameters->getNextParameterAsString("Input Paint File Name");
const QString outputPaintFileName =
parameters->getNextParameterAsString("Output Paint File Name");
const QString paintColumn =
parameters->getNextParameterAsString("Paint Column");
const QString paintName =
parameters->getNextParameterAsString("Paint Name");
//
// Read the paint file
//
PaintFile paintFile;
paintFile.readFile(inputPaintFileName);
//
// Get the column number
//
const int paintColumnNumber = paintFile.getColumnFromNameOrNumber(paintColumn, true);
//
// Get index of paint name
//
const int paintNameIndex = paintFile.addPaintName(paintName);
while (parameters->getParametersAvailable()) {
const QString paramName =
parameters->getNextParameterAsString("Paint Parameter");
if (paramName == "-assign-from-roi-file") {
const QString roiFileName =
parameters->getNextParameterAsString("ROI File Name");
//
// Read the ROI file
//
NodeRegionOfInterestFile nodeRoiFile;
nodeRoiFile.readFile(roiFileName);
//
// Assign paints
//
const int numNodes = std::max(paintFile.getNumberOfNodes(),
nodeRoiFile.getNumberOfNodes());
for (int i = 0; i < numNodes; i++) {
if (nodeRoiFile.getNodeSelected(i) != 0) {
paintFile.setPaint(i, paintColumnNumber, paintNameIndex);
}
}
}
else if (paramName == "-set-column-name") {
const QString columnName =
parameters->getNextParameterAsString("Set Column Name");
paintFile.setColumnName(paintColumnNumber, columnName);
}
}
//
// Write the paint file
//
paintFile.writeFile(outputPaintFileName);
}
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