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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 "BrainModelSurfaceSulcalDepthWithNormals.h"
#include "BrainSet.h"
#include "CommandSurfaceSulcalDepth.h"
#include "FileFilters.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "SurfaceShapeFile.h"
/**
* constructor.
*/
CommandSurfaceSulcalDepth::CommandSurfaceSulcalDepth()
: CommandBase("-surface-sulcal-depth",
"SURFACE SULCAL DEPTH")
{
}
/**
* destructor.
*/
CommandSurfaceSulcalDepth::~CommandSurfaceSulcalDepth()
{
}
/**
* get the script builder parameters.
*/
void
CommandSurfaceSulcalDepth::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Fiducial Coordinate File", FileFilters::getCoordinateFiducialFileFilter());
paramsOut.addFile("Closed Topology File", FileFilters::getTopologyClosedFileFilter());
paramsOut.addFile("Hull VTK File", FileFilters::getTopologyClosedFileFilter());
paramsOut.addFile("Input Surface Shape File", FileFilters::getTopologyClosedFileFilter());
paramsOut.addFile("Output Surface Shape File", FileFilters::getTopologyClosedFileFilter());
paramsOut.addFile("Output Hull Coordinate File", FileFilters::getTopologyClosedFileFilter());
paramsOut.addVariableListOfParameters("Surface Sulcal Depth Options");
}
/**
* get full help information.
*/
QString
CommandSurfaceSulcalDepth::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<fiducial-coordinate-file-name>\n"
+ indent9 + "<closed-topology-file-name>\n"
+ indent9 + "<hull-vtk-file-name>\n"
+ indent9 + "<input-surface-shape-file-name>\n"
+ indent9 + "<output-surface-shape-file-name>\n"
+ indent9 + "<output-hull-coordinate-file-name>\n"
+ indent9 + "[-depth-column-name name]\n"
+ indent9 + "[-smoothed-depth-column-name name]\n"
+ indent9 + "[-no-depth]\n"
+ indent9 + "[-no-smoothed-depth]\n"
+ indent9 + "\n"
+ indent9 + "Generate sulcal depth for a surface.\n"
+ indent9 + "\n"
+ indent9 + "\"" + getDefaultDepthColumnName() + "\" is the default name for the depth column.\n"
+ indent9 + "\"" + getDefaultSmoothedDepthColumnName() + "\" is the default name for the depth column.\n"
+ indent9 + "\n"
+ indent9 + "Note: The input surface shape file does not need to exist.\n"
+ indent9 + "If a column exists in the input surface shape file with the\n"
+ indent9 + "name of the depth or smoothed depth column name, the column\n"
+ indent9 + "is overwritten.\n"
+ "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandSurfaceSulcalDepth::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
//
// Get required parameters
//
const QString fiducialCoordinateFileName =
parameters->getNextParameterAsString("Fiducial Coordinate File Name");
const QString closedTopologyFileName =
parameters->getNextParameterAsString("Closed Topology File Name");
const QString hullVtkFileName =
parameters->getNextParameterAsString("Hull VTK File Name");
const QString inputSurfaceShapeFileName =
parameters->getNextParameterAsString("Input Surface Shape File Name");
const QString outputSurfaceShapeFileName =
parameters->getNextParameterAsString("Output Surface Shape File Name");
const QString outputHullCoordinateFileName =
parameters->getNextParameterAsString("Output Hull Coordinate File Name");
//
// Depth columns
//
int depthColumn = BrainModelSurfaceSulcalDepthWithNormals::DEPTH_COLUMN_CREATE_NEW;
int smoothedDepthColumn = BrainModelSurfaceSulcalDepthWithNormals::DEPTH_COLUMN_CREATE_NEW;
QString depthColumnName = getDefaultDepthColumnName();
QString smoothedDepthColumnName = getDefaultSmoothedDepthColumnName();
//
// Check optional parameters
//
while (parameters->getParametersAvailable()) {
const QString paramName = parameters->getNextParameterAsString("Sulcal Depth Param");
if (paramName == "-depth-column-name") {
depthColumnName = parameters->getNextParameterAsString("Depth Column Name");
}
else if (paramName == "-no-depth") {
depthColumn = BrainModelSurfaceSulcalDepthWithNormals::DEPTH_COLUMN_DO_NOT_GENERATE;
}
else if (paramName == "-no-smoothed-depth") {
smoothedDepthColumn = BrainModelSurfaceSulcalDepthWithNormals::DEPTH_COLUMN_DO_NOT_GENERATE;
}
else if (paramName == "-smoothed-depth-column-name") {
smoothedDepthColumnName = parameters->getNextParameterAsString("Depth Column Name");
}
else {
throw CommandException("unknown parameter: "
+ paramName);
}
}
// Create a brain set
//
BrainSet brainSet(closedTopologyFileName,
fiducialCoordinateFileName,
"",
true);
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.");
}
//
// Surface Shape File
//
SurfaceShapeFile surfaceShapeFile;
if (inputSurfaceShapeFileName.isEmpty() == false) {
if (QFile::exists(inputSurfaceShapeFileName)) {
surfaceShapeFile.readFile(inputSurfaceShapeFileName);
//
// Does depth column exist, if so, reuse it
//
if (depthColumn != BrainModelSurfaceSulcalDepthWithNormals::DEPTH_COLUMN_DO_NOT_GENERATE) {
const int depCol = surfaceShapeFile.getColumnWithName(depthColumnName);
if (depCol >= 0) {
depthColumn = depCol;
}
}
//
// Does smoothed depth column exist, if so, reuse it
//
if (smoothedDepthColumn != BrainModelSurfaceSulcalDepthWithNormals::DEPTH_COLUMN_DO_NOT_GENERATE) {
const int depCol = surfaceShapeFile.getColumnWithName(smoothedDepthColumnName);
if (depCol >= 0) {
smoothedDepthColumn = depCol;
}
}
}
}
//
// Do sulcal depth
//
CoordinateFile hullCoordinateFile;
BrainModelSurfaceSulcalDepthWithNormals sd(&brainSet,
bms,
hullVtkFileName,
&surfaceShapeFile,
5,
100,
depthColumn,
smoothedDepthColumn,
depthColumnName,
smoothedDepthColumnName,
&hullCoordinateFile);
sd.execute();
//
// Write the output files
//
surfaceShapeFile.writeFile(outputSurfaceShapeFileName);
hullCoordinateFile.writeFile(outputHullCoordinateFileName);
}
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