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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 <iostream>
#include "CommandSurfaceFociStudyValidate.h"
#include "FileFilters.h"
#include "FociFile.h"
#include "FociProjectionFile.h"
#include "ProgramParameters.h"
#include "ScriptBuilderParameters.h"
#include "StudyMetaDataFile.h"
#include "TextFile.h"
/**
* constructor.
*/
CommandSurfaceFociStudyValidate::CommandSurfaceFociStudyValidate()
: CommandBase("-surface-foci-study-validate",
"SURFACE FOCI STUDY VALIDATE")
{
}
/**
* destructor.
*/
CommandSurfaceFociStudyValidate::~CommandSurfaceFociStudyValidate()
{
}
/**
* get the script builder parameters.
*/
void
CommandSurfaceFociStudyValidate::getScriptBuilderParameters(ScriptBuilderParameters& paramsOut) const
{
paramsOut.clear();
QStringList fileFilters;
fileFilters << FileFilters::getFociFileFilter();
fileFilters << FileFilters::getFociProjectionFileFilter();
paramsOut.addFile("Foci or Foci Projection File", fileFilters);
paramsOut.addFile("Study Metadata File", FileFilters::getStudyMetaDataFileFilter());
paramsOut.addVariableListOfParameters("Output Text File Name");
}
/**
* get full help information.
*/
QString
CommandSurfaceFociStudyValidate::getHelpInformation() const
{
QString helpInfo =
(indent3 + getShortDescription() + "\n"
+ indent6 + parameters->getProgramNameWithoutPath() + " " + getOperationSwitch() + " \n"
+ indent9 + "<innput-foci-or-foci-projection-file>\n"
+ indent9 + "<input-study-metatdata-file>\n"
+ indent9 + "[-output output-text-file]\n"
+ indent9 + "\n"
+ indent9 + "Verify that all foci have valid study metadata links.\n"
+ indent9 + "Errors include links to invalid studies, foci names \n"
+ indent9 + "that do not match the study name, or links to invalid\n"
+ indent9 + "tables, table subheaders, figures, figure panels, \n"
+ indent9 + "page numbers, and page subheaders.\n"
+ indent9 + "\n"
+ indent9 + "If there are any errors, they are written to the output\n"
+ indent9 + "text file if it is provided. Otherwise, results are \n"
+ indent9 + "written to the terminal.\n");
return helpInfo;
}
/**
* execute the command.
*/
void
CommandSurfaceFociStudyValidate::executeCommand() throw (BrainModelAlgorithmException,
CommandException,
FileException,
ProgramParametersException,
StatisticException)
{
const QString fociFileName =
parameters->getNextParameterAsString("Input Foci or Foci Projection File");
const QString studyFileName =
parameters->getNextParameterAsString("Input Study Metadata File");
QString textFileName;
while (parameters->getParametersAvailable()) {
QString paramName = parameters->getNextParameterAsString("Opt Param");
if (paramName == "-output") {
textFileName = parameters->getNextParameterAsString("Text File Name");
}
else {
throw CommandException("Unexpected Parameter: " + paramName);
}
}
FociFile ff;
FociProjectionFile fpf;
if (fociFileName.endsWith(SpecFile::getFociFileExtension()) ||
fociFileName.endsWith(SpecFile::getFociFileExtension() + ".csv")) {
ff.readFile(fociFileName);
}
else if (fociFileName.endsWith(SpecFile::getFociProjectionFileExtension())) {
fpf.readFile(fociFileName);
}
else {
throw CommandException("The foci or foci projection file must end with "
+ SpecFile::getFociFileExtension()
+ " or "
+ SpecFile::getFociProjectionFileExtension());
}
StudyMetaDataFile smdf;
smdf.readFile(studyFileName);
QString msg;
if (ff.getNumberOfCells() > 0) {
const int num = ff.getNumberOfCells();
for (int i = 0; i < num; i++) {
CellData* cd = ff.getCell(i);
QStringList sl = cd->validateStudyMetaDataLink(&smdf);
for (int m = 0; m < sl.count(); m++) {
msg += "Focus " + QString::number(i)
+ " " + cd->getName() + ": "
+ sl.at(m) + "\n";
}
}
}
if (fpf.getNumberOfCellProjections() > 0) {
const int num = fpf.getNumberOfCellProjections();
for (int i = 0; i < num; i++) {
CellProjection* cd = fpf.getCellProjection(i);
QStringList sl = cd->validateStudyMetaDataLink(&smdf);
for (int m = 0; m < sl.count(); m++) {
msg += "Focus " + QString::number(i)
+ " " + cd->getName() + ": "
+ sl.at(m) + "\n";
}
}
}
if (msg.isEmpty()) {
std::cout << "No foci/study problems were found." << std::endl;
}
else {
if (textFileName.isEmpty() == false) {
TextFile tf;
tf.setText(msg);
tf.writeFile(textFileName);
}
else {
std::cout << msg.toAscii().constData() << std::endl;
}
}
}
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