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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 "AreaColorFile.h"
#include "BrainModelSurface.h"
#include "BrainModelSurfaceSulcalIdentificationProbabilistic.h"
#include "BrainSet.h"
#include "CommandSurfaceSulcalIdentificationProbabilistic.h"
#include "FileFilters.h"
#include "PaintFile.h"
#include "ProgramParameters.h"
#include "SpecFile.h"
#include "SurfaceShapeFile.h"
/**
* constructor.
*/
CommandSurfaceSulcalIdentificationProbabilistic::CommandSurfaceSulcalIdentificationProbabilistic()
: CommandBase("-surface-sulcal-identification-probabilistic",
"SURFACE SULCAL IDENTIFICATION PROBABILISTIC")
{
}
/**
* destructor.
*/
CommandSurfaceSulcalIdentificationProbabilistic::~CommandSurfaceSulcalIdentificationProbabilistic()
{
}
/**
* get the script builder parameters.
*/
void
CommandSurfaceSulcalIdentificationProbabilistic::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
paramsOut.addFile("Input Fiducial Coord File Name",
FileFilters::getCoordinateFiducialFileFilter());
paramsOut.addFile("Input Inflated Coord File Name",
FileFilters::getCoordinateInflatedFileFilter());
paramsOut.addFile("Input Very Inflated Coord File Name",
FileFilters::getCoordinateVeryInflatedFileFilter());
paramsOut.addFile("Input Closed Topology File Name",
FileFilters::getTopologyClosedFileFilter());
paramsOut.addFile("Input Paint File Name",
FileFilters::getPaintFileFilter());
paramsOut.addFile("Output Paint File Name",
FileFilters::getPaintFileFilter());
paramsOut.addFile("Input Area Color File Name",
FileFilters::getAreaColorFileFilter());
paramsOut.addFile("Output Area Color File Name",
FileFilters::getAreaColorFileFilter());
paramsOut.addString("Input Paint Geography Column");
paramsOut.addFile("Input Surface Shape File Name",
FileFilters::getSurfaceShapeFileFilter());
paramsOut.addString("Input Surface Shape Depth Column");
paramsOut.addFile("Probabilistic Sulcus Volume list",
"*.csv");
paramsOut.addFloat("Post Central Sulcus Offset", 25.0);
paramsOut.addFloat("Post Central Sulcus Std Dev Squared", 100.0);
paramsOut.addFloat("Post Central Sulcus Split", 5.0);
}
/**
* get full help information.
*/
QString
CommandSurfaceSulcalIdentificationProbabilistic::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<input-fiducial-coord-file-name> \n"
+ indent9 + "<input-inflated-coord-file-name> \n"
+ indent9 + "<input-very-inflated-coord-file-name> \n"
+ indent9 + "<input-closed-topo-file-name> \n"
+ indent9 + "<input-paint-file-name> \n"
+ indent9 + "<output-paint-file-name> \n"
+ indent9 + "<input-paint-file-geography-column-name-or-number> \n"
+ indent9 + "<input-area-color-file-name> \n"
+ indent9 + "<output-area-color-file-name> \n"
+ indent9 + "<input-surface-shape-file-name> \n"
+ indent9 + "<input-surface-shape-file-depth-column-name-or-number> \n"
+ indent9 + "<input-probabilistic-suclus-volume-list-file.csv> \n"
+ indent9 + "<input-post-central-sulcus-offset> \n"
+ indent9 + "<input-post-central-sulcus-std-dev-squared> \n"
+ indent9 + "<input-post-central-sulcus-split> \n"
+ indent9 + "\n"
+ indent9 + "Identify sulci on a surface by mapping a probabilistic volume. \n"
+ indent9 + "\n"
+ indent9 + "Note: Paint and Surface Shape file column numbers start at one. \n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandSurfaceSulcalIdentificationProbabilistic::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
//
// Get the parameters from those passed to base class
//
const QString fiducialCoordFileName =
parameters->getNextParameterAsString("Input Fiducial Coord File Name");
const QString inflatedCoordFileName =
parameters->getNextParameterAsString("Input Inflated Coord File Name");
const QString veryInflatedCoordFileName =
parameters->getNextParameterAsString("Input Very Inflated Coord File Name");
const QString inputTopoFileName =
parameters->getNextParameterAsString("Input Closed Topology File Name");
const QString paintFileName =
parameters->getNextParameterAsString("Input Paint File Name");
const QString outputPaintFileName =
parameters->getNextParameterAsString("Output Paint File Name");
const QString paintFileGeographyColumnNameOrNumber =
parameters->getNextParameterAsString("Paint File Geography Column Name or Number");
const QString inputAreaColorFileName =
parameters->getNextParameterAsString("Input Area Color File Name");
const QString outputAreaColorFileName =
parameters->getNextParameterAsString("Output Area Color File Name");
const QString surfaceShapeFileName =
parameters->getNextParameterAsString("Surface Shape File Name");
const QString surfaceShapeFileDepthColumnNameOrNumber =
parameters->getNextParameterAsString("Surface Shape File Depth Column Name or Number");
const QString probabilisticSulcusVolumeListFileName =
parameters->getNextParameterAsString("Probabilistic Sulcus/Volume List File (CSV)");
const float postCentralSulcusOffset =
parameters->getNextParameterAsFloat("Post Central Sulcus Offset");
const float postCentralSulcusStdDevSquared =
parameters->getNextParameterAsFloat("Post Central Sulcus Std Dev Squared");
const float postCentralSulcusSplit =
parameters->getNextParameterAsFloat("Post Central Sulcus Split");
//
// Make sure that are no more parameters
//
checkForExcessiveParameters();
//
// Create a spec file
//
SpecFile specFile;
specFile.setAllFileSelections(SpecFile::SPEC_FALSE);
specFile.addToSpecFile(SpecFile::getFiducialCoordFileTag(),
fiducialCoordFileName,
"",
SpecFile::SPEC_FALSE);
specFile.addToSpecFile(SpecFile::getInflatedCoordFileTag(),
inflatedCoordFileName,
"",
SpecFile::SPEC_FALSE);
specFile.addToSpecFile(SpecFile::getVeryInflatedCoordFileTag(),
veryInflatedCoordFileName,
"",
SpecFile::SPEC_FALSE);
specFile.addToSpecFile(SpecFile::getClosedTopoFileTag(),
inputTopoFileName,
"",
SpecFile::SPEC_FALSE);
specFile.addToSpecFile(SpecFile::getPaintFileTag(),
paintFileName,
"",
SpecFile::SPEC_FALSE);
if (inputAreaColorFileName.isEmpty() == false) {
if (QFile::exists(inputAreaColorFileName)) {
specFile.addToSpecFile(SpecFile::getAreaColorFileTag(),
inputAreaColorFileName,
"",
SpecFile::SPEC_FALSE);
}
}
specFile.addToSpecFile(SpecFile::getSurfaceShapeFileTag(),
surfaceShapeFileName,
"",
SpecFile::SPEC_FALSE);
//
// Read the spec file into a brain set
//
QString errorMessage;
BrainSet brainSet(true);
if (brainSet.readSpecFile(specFile, "temp", errorMessage)) {
const QString msg("ERROR: Reading spec file data files: \n"
+ errorMessage);
throw CommandException(msg);
}
//
// Find the fiducial and very inflated surfaces
//
BrainModelSurface* fiducialSurface = NULL;
BrainModelSurface* inflatedSurface = NULL;
BrainModelSurface* veryInflatedSurface = NULL;
for (int i = 0; i < brainSet.getNumberOfBrainModels(); i++) {
BrainModelSurface* bms = brainSet.getBrainModelSurface(i);
if (bms != NULL) {
if (bms->getSurfaceType() == BrainModelSurface::SURFACE_TYPE_FIDUCIAL) {
fiducialSurface = bms;
}
else if (bms->getSurfaceType() == BrainModelSurface::SURFACE_TYPE_INFLATED) {
inflatedSurface = bms;
}
else if (bms->getSurfaceType() == BrainModelSurface::SURFACE_TYPE_VERY_INFLATED) {
veryInflatedSurface = bms;
}
}
}
if (fiducialSurface == NULL) {
throw CommandException("Unable to find fiducial surface.");
}
if (veryInflatedSurface == NULL) {
throw CommandException("Unable to find very inflated surface.");
}
//
// Get the paint and shape column numbers
//
const int paintFileGeographyColumnNumber =
brainSet.getPaintFile()->getColumnFromNameOrNumber(paintFileGeographyColumnNameOrNumber, false);
const int surfaceShapeFileDepthColumnNumber =
brainSet.getSurfaceShapeFile()->getColumnFromNameOrNumber(surfaceShapeFileDepthColumnNameOrNumber, false);
//
// Identify the sulci
//
BrainModelSurfaceSulcalIdentificationProbabilistic bmssi(&brainSet,
fiducialSurface,
inflatedSurface,
veryInflatedSurface,
brainSet.getPaintFile(),
paintFileGeographyColumnNumber,
brainSet.getSurfaceShapeFile(),
surfaceShapeFileDepthColumnNumber,
probabilisticSulcusVolumeListFileName,
postCentralSulcusOffset,
postCentralSulcusStdDevSquared,
postCentralSulcusSplit);
try {
bmssi.execute();
if (bmssi.getOutputPaintFile() == NULL) {
throw CommandException("output paint file with Identified sulci is NULL.");
}
try {
PaintFile outputPaintFile(*bmssi.getOutputPaintFile());
outputPaintFile.writeFile(outputPaintFileName);
}
catch (FileException& e) {
const QString msg("identifying sulci writing output paint file: "
+ e.whatQString());
throw CommandException(msg);
}
if (outputAreaColorFileName.isEmpty() == false) {
const AreaColorFile* acf = bmssi.getOutputAreaColorFile();
if (acf != NULL) {
brainSet.getAreaColorFile()->append(*acf);
try {
brainSet.getAreaColorFile()->writeFile(outputAreaColorFileName);
}
catch (FileException&) {
std::cout << "WARNING: Unable to write "
<< outputAreaColorFileName.toAscii().constData()
<< std::endl;
}
}
}
}
catch (BrainModelAlgorithmException& e) {
throw CommandException("identifying sulci: "
+ e.whatQString());
}
}
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