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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 "BrainModelSurfaceROIAssignMetricNodeArea.h"
#include "BrainModelSurfaceROINodeSelection.h"
#include "BrainSet.h"
#include "CommandSurfaceRoiNodeAreas.h"
#include "FileFilters.h"
#include "MetricFile.h"
#include "NodeRegionOfInterestFile.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "TextFile.h"
/**
* constructor.
*/
CommandSurfaceRoiNodeAreas::CommandSurfaceRoiNodeAreas()
: CommandBase("-surface-roi-node-areas",
"SURFACE ROI NODE AREAS")
{
}
/**
* destructor.
*/
CommandSurfaceRoiNodeAreas::~CommandSurfaceRoiNodeAreas()
{
}
/**
* get the script builder parameters.
*/
void
CommandSurfaceRoiNodeAreas::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Input Coordinate File", FileFilters::getCoordinateGenericFileFilter());
paramsOut.addFile("Input Topology File", FileFilters::getTopologyGenericFileFilter());
paramsOut.addFile("Input Metric/Shape File", FileFilters::getMetricShapeFileFilter());
paramsOut.addFile("Output Metric/Shape File", FileFilters::getMetricShapeFileFilter());
paramsOut.addVariableListOfParameters("Options");
}
/**
* get full help information.
*/
QString
CommandSurfaceRoiNodeAreas::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<coordinate-file-name>\n"
+ indent9 + "<topology-file-name>\n"
+ indent9 + "<input-metric-or-shape-file-name>\n"
+ indent9 + "<output-metric-or-shape-file-name>\n"
+ indent9 + "[-roi region-of-interest-file-name]\n"
+ indent9 + "[-percentage]\n"
+ indent9 + "\n"
+ indent9 + "Generate a new metric or shape file column containing\n"
+ indent9 + "the surface area for each node. While nodes technically\n"
+ indent9 + "do not have area, triangles do. Since a triangle is made\n"
+ indent9 + "from three nodes, assign one-third of the triangle's\n"
+ indent9 + "surface area to each node and sum these amounts for each\n"
+ indent9 + "node.\n"
+ indent9 + "\n"
+ indent9 + "If an ROI is provided, the area measurements are limited\n"
+ indent9 + "to that region of the surface and nodes not in the ROI are\n"
+ indent9 + "assigned a value of zero.\n"
+ indent9 + "\n"
+ indent9 + "If the \"-percentage\" option is specified, the value \n"
+ indent9 + "assigned to each node is the percentage of total surface \n"
+ indent9 + "area contributed by that node.\n"
+ indent9 + " Value = ((node-surface-area / total-surface-area) * 100.0)\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandSurfaceRoiNodeAreas::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
//
// Get the parameters
//
const QString coordinateFileName =
parameters->getNextParameterAsString("Coordinate File Name");
const QString topoFileName =
parameters->getNextParameterAsString("Topology File Name");
const QString inputMetricShapeFileName =
parameters->getNextParameterAsString("Input Metric/Surface Shape File Name");
const QString outputMetricShapeFileName =
parameters->getNextParameterAsString("Output Metric/Surface Shape File Name");
QString roiFileName;
bool percentageFlag = false;
while (parameters->getParametersAvailable()) {
const QString paramName =
parameters->getNextParameterAsString("Optional parameter");
if (paramName == "-roi") {
roiFileName =
parameters->getNextParameterAsString("Region of Interest File Name");
if (roiFileName.isEmpty()) {
throw CommandException("Region of Interest File Name is missing.");
}
}
else if (paramName == "-percentage") {
percentageFlag = true;
}
else {
throw CommandException("Unrecognized parameter \""
+ paramName
+ "\".");
}
}
//
// Create a brain set
//
BrainSet brainSet(topoFileName,
coordinateFileName,
"");
//
// Find the surface
//
BrainModelSurface* bms = brainSet.getBrainModelSurface(0);
if (bms == NULL) {
throw CommandException("Unable to find surface after reading files.");
}
if (bms->getTopologyFile() == NULL) {
throw CommandException("Unable to find topology after reading files.");
}
//
// Read input metric/shape file
//
MetricFile mf;
if (inputMetricShapeFileName.isEmpty() == false) {
mf.readFile(inputMetricShapeFileName);
}
//
// Get the ROI
//
BrainModelSurfaceROINodeSelection* surfaceROI =
brainSet.getBrainModelSurfaceRegionOfInterestNodeSelection();
if (roiFileName.isEmpty() == false) {
NodeRegionOfInterestFile nroi;
nroi.readFile(roiFileName);
surfaceROI->getRegionOfInterestFromFile(nroi);
}
else {
surfaceROI->selectAllNodes(bms);
}
QString columnName = "Node Area";
if (percentageFlag) {
columnName += " Percentage";
}
//
// Get the areas
//
BrainModelSurfaceROIAssignMetricNodeArea
roiOp(&brainSet,
bms,
surfaceROI,
&mf,
-1,
"Node Area Percentage",
percentageFlag);
roiOp.execute();
//
// Write the metric file
//
mf.writeFile(outputMetricShapeFileName);
}
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