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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 "BrainSet.h"
#include "CommandSurfaceFociProjectionPals.h"
#include "FileFilters.h"
#include "FociFile.h"
#include "FociFileToPalsProjector.h"
#include "FociProjectionFile.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "StudyMetaDataFile.h"
/**
* constructor.
*/
CommandSurfaceFociProjectionPals::CommandSurfaceFociProjectionPals()
: CommandBase("-surface-foci-projection-pals",
"SURFACE FOCI PROJECTION TO PALS ATLAS")
{
}
/**
* destructor.
*/
CommandSurfaceFociProjectionPals::~CommandSurfaceFociProjectionPals()
{
}
/**
* get the script builder parameters.
*/
void
CommandSurfaceFociProjectionPals::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
QStringList inputFilters;
inputFilters << FileFilters::getFociFileFilter();
inputFilters << FileFilters::getFociProjectionFileFilter();
paramsOut.clear();
paramsOut.addFile("Input Foci or Foci Projection File",
inputFilters);
paramsOut.addFile("Output Foci Projection File",
FileFilters::getFociProjectionFileFilter());
paramsOut.addFile("Study Metadata File",
FileFilters::getStudyMetaDataFileFilter());
paramsOut.addVariableListOfParameters("");
}
/**
* get full help information.
*/
QString
CommandSurfaceFociProjectionPals::getHelpInformation() const
{
const QString cerebralCutoffValue(
QString::number(FociFileToPalsProjector::getDefaultCerebralCutoffDistance(), 'f', 2));
const QString cerebellumCutoffValue(
QString::number(FociFileToPalsProjector::getDefaultCerebellumCutoffDistance(), 'f', 2));
QString s = "cell";
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<input-foci-or-foci-projection-file-name>\n"
+ indent9 + "<output-foci-projection-file-name>\n"
+ indent9 + "<input-study-metadata-file-name>\n"
+ indent9 + "[-cutoffs cerebral-cutoff cerebellum-cutoff]\n"
+ indent9 + "[-no-cerebellum]\n"
+ indent9 + "[-project-onto-surface onto-surface-above-distance]\n"
+ indent9 + "\n"
+ indent9 + "Project foci to the PALS Atlas.\n"
+ indent9 + "\n"
+ indent9 + "The input file may be either a foci file or a foci\n"
+ indent9 + "projection file. If the input file is a foci file, its\n"
+ indent9 + "name must end with \"" + SpecFile::getFociFileExtension() + "\".\n"
+ indent9 + "\n"
+ indent9 + "Add the \"-no-cerebellum\" option if you DO NOT want foci\n"
+ indent9 + "projected using the cerebellum.\n"
+ indent9 + "\n"
+ indent9 + "Use the \"-project-onto-surface\" option to project the\n"
+ indent9 + "foci so that they are a specified distance on or above\n"
+ indent9 + "the surfaces.\n"
+ indent9 + "\n"
+ indent9 + "Use the \"-cutoffs\" to control how foci are projected \n"
+ indent9 + "using a cerebral hemisphere and/or the cerebellum.\n"
+ indent9 + " A ratio of the distance to the cerebral cortex relative\n"
+ indent9 + " to the distance to the cerebellum is computed.\n"
+ indent9 + " If this ratio is less than the \"cerebral-cutoff\", \n"
+ indent9 + " the focus is assigned to the cerebral cortex. If this\n"
+ indent9 + " ratio is greater than \"cerebellum-cutoff\", the focus\n"
+ indent9 + " is assigned to the cerebellum. If the ratio is between\n"
+ indent9 + " the two cutoffs, the focus is assigned to both a \n"
+ indent9 + " cerebral hemisphere and the cerebellum.\n"
+ indent9 + "\n"
+ indent9 + " Default \"cerebral-cutoff\": " + cerebralCutoffValue + "\n"
+ indent9 + " Default \"cerebellum-cutoff\": " + cerebellumCutoffValue + "\n"
+ indent9 + "\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandSurfaceFociProjectionPals::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
const QString inputFociProjectionFileName =
parameters->getNextParameterAsString("Input Foci or Foci Projection File Name");
const QString outputFociProjectionFileName =
parameters->getNextParameterAsString("Output Foci Projection File Name");
const QString inputStudyMetaDataFileName =
parameters->getNextParameterAsString("Input Study Metadata File Name");
//
// Process optional parameters
//
float cerebralCutoffDistance =
FociFileToPalsProjector::getDefaultCerebralCutoffDistance();
float cerebellumCutoffDistance =
FociFileToPalsProjector::getDefaultCerebellumCutoffDistance();
bool projectToCerebellumFlag = true;
bool projectToSurfaceFlag = false;
float surfaceAboveDistance = 0.0;
while (parameters->getParametersAvailable()) {
const QString paramName =
parameters->getNextParameterAsString("Foci Projection Parameter");
if (paramName == "-cutoffs") {
cerebralCutoffDistance =
parameters->getNextParameterAsFloat("Cerebral Cutoff Distance");
cerebellumCutoffDistance =
parameters->getNextParameterAsFloat("Cerebellum Cutoff Distance");
}
else if (paramName == "-no-cerebellum") {
projectToCerebellumFlag = false;
}
else if (paramName == "-project-onto-surface") {
projectToSurfaceFlag = true;
surfaceAboveDistance =
parameters->getNextParameterAsFloat("Foci Projection Parameter: Above surface distance");
}
else {
throw CommandException("unrecognized option");
}
}
//
// Create a brain set
//
BrainSet brainSet;
//
// Read the foci projection file
//
FociProjectionFile fociProjectionFile;
if (inputFociProjectionFileName.endsWith(SpecFile::getFociFileExtension())) {
FociFile ff;
ff.readFile(inputFociProjectionFileName);
fociProjectionFile.appendFiducialCellFile(ff);
}
else {
fociProjectionFile.readFile(inputFociProjectionFileName);
}
//
// Read the study metadata file
//
StudyMetaDataFile studyMetaDataFile;
studyMetaDataFile.readFile(inputStudyMetaDataFileName);
//
// Project the foci file to the PALS atlas
//
FociFileToPalsProjector palsProjector(&brainSet,
&fociProjectionFile,
&studyMetaDataFile,
0,
fociProjectionFile.getNumberOfCellProjections() - 1,
surfaceAboveDistance,
projectToSurfaceFlag,
projectToCerebellumFlag,
cerebralCutoffDistance,
cerebellumCutoffDistance);
palsProjector.execute();
//
// Write the foci projection file
//
fociProjectionFile.writeFile(outputFociProjectionFileName);
}
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