diff --git a/apps/BioModelCalc/BioModelCalcApplicationData.cpp b/apps/BioModelCalc/BioModelCalcApplicationData.cpp
index 5474684..cc9a343 100644
--- a/apps/BioModelCalc/BioModelCalcApplicationData.cpp
+++ b/apps/BioModelCalc/BioModelCalcApplicationData.cpp
@@ -1,72 +1,66 @@
// -----------------------------------------------------------------------
// RTToolbox - DKFZ radiotherapy quantitative evaluation library
//
// Copyright (c) German Cancer Research Center (DKFZ),
// Software development for Integrated Diagnostics and Therapy (SIDT).
// ALL RIGHTS RESERVED.
// See rttbCopyright.txt or
// http://www.dkfz.de/en/sidt/projects/rttb/copyright.html
//
// This software is distributed WITHOUT ANY WARRANTY; without even
// the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
// PURPOSE. See the above copyright notices for more information.
//
//------------------------------------------------------------------------
-/*!
-// @file
-// @version $Revision: 1233 $ (last changed revision)
-// @date $Date: 2016-01-20 15:47:47 +0100 (Mi, 20 Jan 2016) $ (last change date)
-// @author $Author: hentsch $ (last changed by)
-*/
#include "BioModelCalcApplicationData.h"
#include "BioModelCmdLineParser.h"
namespace rttb
{
namespace apps
{
namespace bioModelCalc
{
ApplicationData::
ApplicationData()
{
this->reset();
}
void
ApplicationData::
reset()
{
_doseFileName = "";
_outputFileName = "";
_doseScaling = 1.0;
_nFractions = 1;
_modelParameters.clear();
_modelParameterMapsFilename.clear();
_modelParameterMaps.clear();
}
void populateAppData(boost::shared_ptr<BioModelCmdLineParser> argParser, ApplicationData& appData)
{
appData._doseFileName = argParser->get<std::string>(argParser->OPTION_DOSE_FILE);
- appData._doseLoadStyle = argParser->get<std::vector<std::string> >(argParser->OPTION_LOAD_STYLE);
+ appData._doseLoadStyle = argParser->get<std::string>(argParser->OPTION_LOAD_STYLE);
appData._doseScaling = argParser->get<double>(argParser->OPTION_DOSE_SCALING);
appData._outputFileName = argParser->get<std::string>(argParser->OPTION_OUTPUT_FILE);
appData._model = argParser->get<std::string>(argParser->OPTION_MODEL);
if (argParser->isSet(argParser->OPTION_MODEL_PARAMETERS)){
appData._modelParameters = argParser->get<std::vector<double> >(argParser->OPTION_MODEL_PARAMETERS);
}
else {
appData._modelParameterMapsFilename = argParser->get<std::vector<std::string> >(argParser->OPTION_MODEL_PARAMETER_MAPS);
- appData._parameterMapsLoadStyle = argParser->get<std::vector<std::string> >(argParser->OPTION_LOAD_STYLE_PARAMETER_MAPS);
+ appData._parameterMapsLoadStyle = argParser->get<std::string>(argParser->OPTION_LOAD_STYLE_PARAMETER_MAPS);
}
if (argParser->isSet(argParser->OPTION_N_FRACTIONS)){
appData._nFractions = argParser->get<unsigned int>(argParser->OPTION_N_FRACTIONS);
}
}
}
}
}
diff --git a/apps/BioModelCalc/BioModelCalcApplicationData.h b/apps/BioModelCalc/BioModelCalcApplicationData.h
index 165e3e9..9a27136 100644
--- a/apps/BioModelCalc/BioModelCalcApplicationData.h
+++ b/apps/BioModelCalc/BioModelCalcApplicationData.h
@@ -1,74 +1,62 @@
// -----------------------------------------------------------------------
// RTToolbox - DKFZ radiotherapy quantitative evaluation library
//
// Copyright (c) German Cancer Research Center (DKFZ),
// Software development for Integrated Diagnostics and Therapy (SIDT).
// ALL RIGHTS RESERVED.
// See rttbCopyright.txt or
// http://www.dkfz.de/en/sidt/projects/rttb/copyright.html
//
// This software is distributed WITHOUT ANY WARRANTY; without even
// the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
// PURPOSE. See the above copyright notices for more information.
//
//------------------------------------------------------------------------
-/*!
-// @file
-// @version $Revision: 1210 $ (last changed revision)
-// @date $Date: 2015-11-24 15:52:45 +0100 (Di, 24 Nov 2015) $ (last change date)
-// @author $Author: hentsch $ (last changed by)
-*/
-
#ifndef __BIO_MODEL_CALC_APPLICATION_DATA_H
#define __BIO_MODEL_CALC_APPLICATION_DATA_H
#include <deque>
#include <boost/shared_ptr.hpp>
#include "rttbDoseAccessorInterface.h"
namespace rttb
{
namespace apps
{
namespace bioModelCalc
{
class BioModelCmdLineParser;
/*! @class ApplicationData
@brief Class for storing all relevant variables needed in BioModelCalc
*/
class ApplicationData
{
public:
- /**Vector of arguments used to specify the loading style (always the first argument)
- * and, if needed, additional arguments for the specified loading style.
- */
- typedef std::vector<std::string> LoadingStyleArgType;
-
core::DoseAccessorInterface::DoseAccessorPointer _dose;
std::deque<core::AccessorInterface::AccessorPointer> _modelParameterMaps;
std::string _doseFileName;
- LoadingStyleArgType _doseLoadStyle;
- LoadingStyleArgType _parameterMapsLoadStyle;
+ std::string _doseLoadStyle;
+ std::string _parameterMapsLoadStyle;
double _doseScaling;
unsigned int _nFractions;
std::string _outputFileName;
std::string _model;
std::vector<double> _modelParameters;
std::vector<std::string> _modelParameterMapsFilename;
void reset();
ApplicationData();
};
/*! @brief Reads the necessary arguments from the BioModelCmdLineParser and writes them in the respective variables of ApplicationData
*/
void populateAppData(boost::shared_ptr<BioModelCmdLineParser> argParser, ApplicationData& appData);
}
}
}
#endif
diff --git a/apps/BioModelCalc/BioModelCmdLineParser.cpp b/apps/BioModelCalc/BioModelCmdLineParser.cpp
index 6738c9a..35d4fb8 100644
--- a/apps/BioModelCalc/BioModelCmdLineParser.cpp
+++ b/apps/BioModelCalc/BioModelCmdLineParser.cpp
@@ -1,125 +1,141 @@
+// -----------------------------------------------------------------------
+// RTToolbox - DKFZ radiotherapy quantitative evaluation library
+//
+// Copyright (c) German Cancer Research Center (DKFZ),
+// Software development for Integrated Diagnostics and Therapy (SIDT).
+// ALL RIGHTS RESERVED.
+// See rttbCopyright.txt or
+// http://www.dkfz.de/en/sidt/projects/rttb/copyright.html
+//
+// This software is distributed WITHOUT ANY WARRANTY; without even
+// the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+// PURPOSE. See the above copyright notices for more information.
+//
+//------------------------------------------------------------------------
+
#include "BioModelCmdLineParser.h"
namespace rttb
{
namespace apps
{
namespace bioModelCalc
{
BioModelCmdLineParser::BioModelCmdLineParser(int argc, const char** argv, const std::string& name, const std::string& version,
const std::string& description, const std::string& contributor, const std::string& category) :
CmdLineParserBase(name, version, description, contributor, category)
{
//REQUIRED
addOption<std::string>(OPTION_DOSE_FILE, OPTION_GROUP_REQUIRED,
"The name of the dose file. Can be omitted if used as "
"positional argument (see above).", 'd', true);
addInformationForXML(OPTION_DOSE_FILE, cmdlineparsing::XMLGenerator::paramType::INPUT, { "*" });
addOption<std::string>(OPTION_OUTPUT_FILE, OPTION_GROUP_REQUIRED,
"The name of the output file. Can be omitted if used as "
"positional argument (see above).", 'o', true);
addInformationForXML(OPTION_OUTPUT_FILE, cmdlineparsing::XMLGenerator::paramType::OUTPUT, { "*" });
addPositionalOption(OPTION_DOSE_FILE, 1);
addPositionalOption(OPTION_OUTPUT_FILE, 1);
addOptionWithDefaultValue<std::string>(OPTION_MODEL, OPTION_GROUP_REQUIRED,
"The used radiobiological model the dose should be analyzed with. Available models are:\n \"LQ\", Formula: exp(-(alpha * D + beta * D^2/n))",
"LQ", "LQ", 'm');
addInformationForXML(OPTION_MODEL, cmdlineparsing::XMLGenerator::paramType::STRINGENUMERATION, { "LQ" });
addOptionWithDefaultValue<double>(OPTION_DOSE_SCALING, OPTION_GROUP_REQUIRED,
"Dose scaling that should be applied.", 1.0, "1.0", 'e');
addInformationForXML(OPTION_DOSE_SCALING, cmdlineparsing::XMLGenerator::paramType::DOUBLE);
- std::vector<std::string> defaultLoadingStyle;
- defaultLoadingStyle.push_back("itk");
+ std::string defaultLoadingStyle;
+ defaultLoadingStyle = "itk";
- std::string doseLoadStyleDescription = "The loading style for the dose. Available styles are:\n"
- "\"dicom\": normal dicom dose\n"
- "\"itk\": use itk image loading\n"
- "\"helax\": load a helax dose (choosing this style, the dose path should only be a directory).";
+ std::string doseLoadStyleDescription = "The loading style for the dose. Available styles are:"
+ "\ndicom: normal dicom dose"
+ "\nitk: use itk image loading"
+ "\nitkDicom: use itk dicom image loading"
+ "\nhelax: load a helax dose (choosing this style, the dose path should only be a directory).";
- addOptionWithDefaultValue<std::vector<std::string> >(OPTION_LOAD_STYLE, OPTION_GROUP_REQUIRED, doseLoadStyleDescription,
- defaultLoadingStyle, defaultLoadingStyle.at(0),
+ addOptionWithDefaultValue<std::string>(OPTION_LOAD_STYLE, OPTION_GROUP_REQUIRED, doseLoadStyleDescription,
+ defaultLoadingStyle, defaultLoadingStyle,
't', true, true);
- addInformationForXML(OPTION_LOAD_STYLE, cmdlineparsing::XMLGenerator::paramType::STRINGENUMERATION, { "itk", "dicom", "helax" });
+ addInformationForXML(OPTION_LOAD_STYLE, cmdlineparsing::XMLGenerator::paramType::STRING);
//OPTIONAL
addOption<std::vector<double> >(OPTION_MODEL_PARAMETERS, OPTION_GROUP_OPTIONAL,
"The parameters for the radiobiological model.", 'p', false, true);
addInformationForXML(OPTION_MODEL_PARAMETERS, cmdlineparsing::XMLGenerator::paramType::STRING);
addOption<std::vector<std::string> >(OPTION_MODEL_PARAMETER_MAPS, OPTION_GROUP_OPTIONAL,
"The parameters maps as itk readable image files for the radiobiological model.", 'a', false, true);
addInformationForXML(OPTION_MODEL_PARAMETER_MAPS, cmdlineparsing::XMLGenerator::paramType::INPUT, { "*" });
addOption<unsigned int>(OPTION_N_FRACTIONS, OPTION_GROUP_OPTIONAL,
"The number of fractions (n in the formula).", 'f');
addInformationForXML(OPTION_N_FRACTIONS, cmdlineparsing::XMLGenerator::paramType::INTEGER);
- addOptionWithDefaultValue<std::vector<std::string> >(OPTION_LOAD_STYLE_PARAMETER_MAPS, OPTION_GROUP_OPTIONAL, doseLoadStyleDescription,
- defaultLoadingStyle, defaultLoadingStyle.at(0),
+ addOptionWithDefaultValue<std::string>(OPTION_LOAD_STYLE_PARAMETER_MAPS, OPTION_GROUP_OPTIONAL, doseLoadStyleDescription,
+ defaultLoadingStyle, defaultLoadingStyle,
'u', true, true);
- addInformationForXML(OPTION_LOAD_STYLE_PARAMETER_MAPS, cmdlineparsing::XMLGenerator::paramType::STRINGENUMERATION, { "itk", "dicom", "helax" });
+ addInformationForXML(OPTION_LOAD_STYLE_PARAMETER_MAPS, cmdlineparsing::XMLGenerator::paramType::STRING);
parse(argc, argv);
}
void BioModelCmdLineParser::validateInput() const
{
std::string model = get<std::string>(OPTION_MODEL);
if (model != "LQ")
{
throw cmdlineparsing::InvalidConstraintException("Unknown model: " + model +
".\nPlease refer to the help for valid models.");
}
else
{
if (!isSet(OPTION_MODEL_PARAMETERS) && !isSet(OPTION_MODEL_PARAMETER_MAPS)){
throw cmdlineparsing::InvalidConstraintException("Either the model parameters or model parameter maps must be specified!");
}
if ((isSet(OPTION_MODEL_PARAMETERS) && get<std::vector<double> >(OPTION_MODEL_PARAMETERS).size() != 2) || (isSet(OPTION_MODEL_PARAMETER_MAPS) && get<std::vector<std::string> >(OPTION_MODEL_PARAMETER_MAPS).size() != 2))
{
throw cmdlineparsing::InvalidConstraintException("The LQ Model requires two parameters or parameter maps!");
}
}
- std::vector<std::string> loadStyle = get<std::vector<std::string> >(OPTION_LOAD_STYLE);
- std::string loadStyleAbbreviation = loadStyle.at(0);
+ std::string loadStyle = get<std::string>(OPTION_LOAD_STYLE);
- if (loadStyleAbbreviation != "dicom"
- && loadStyleAbbreviation != "itk"
- && loadStyleAbbreviation != "helax")
+ if (loadStyle != "dicom"
+ && loadStyle != "itk"
+ && loadStyle != "itkDicom"
+ && loadStyle != "helax")
{
- throw cmdlineparsing::InvalidConstraintException("Unknown load style: " + loadStyleAbbreviation +
+ throw cmdlineparsing::InvalidConstraintException("Unknown load style: " + loadStyle +
".\nPlease refer to the help for valid loading style settings.");
}
double doseScaling = get<double>(OPTION_DOSE_SCALING);
if (doseScaling <= 0)
{
throw cmdlineparsing::InvalidConstraintException("Negative dose scaling is not allowed. Dose scaling has to be >0.");
}
}
void BioModelCmdLineParser::printHelp() const
{
cmdlineparsing::CmdLineParserBase::printHelp();
std::cout << "Example:" << std::endl << std::endl;
std::cout << m_programName <<
" dose.mhd result.mhd -m LQ -p 0.2 0.02" <<
std::endl << std::endl;
std::cout <<
"This will calculate the Linear quadratic (LQ) BioModel from \"dose.mhd\" and will write the result to \"result.mhd\". "
"The alpha and beta parameters for the LQ model are 0.2 and 0.02, respectively."
<< std::endl;
}
}
}
}