| 57 | |
| 58 | |
| 59 | void setupParser(mitkCommandLineParser& parser) |
| 60 | { |
| 61 | // set general information about your MiniApp |
| 62 | parser.setCategory("Dynamic Data Analysis Tools"); |
| 63 | parser.setTitle("Generic Fitting"); |
| 64 | parser.setDescription("MiniApp that allows to make a pixel based fitting on the intensity signal over time for a given model function."); |
| 65 | parser.setContributor("DKFZ MIC"); |
| 66 | //! [create parser] |
| 67 | |
| 68 | //! [add arguments] |
| 69 | // how should arguments be prefixed |
| 70 | parser.setArgumentPrefix("--", "-"); |
| 71 | // add each argument, unless specified otherwise each argument is optional |
| 72 | // see mitkCommandLineParser::addArgument for more information |
| 73 | parser.beginGroup("Model parameters"); |
| 74 | parser.addArgument( |
| 75 | "function", "f", mitkCommandLineParser::String, "Model function", "Function that should be used to fit the intensity signals. Options are: \"Linear\" or \"<Parameter Number>\" (for generic formulas).", us::Any(std::string("Linear"))); |
| 76 | parser.addArgument( |
| 77 | "formular", "y", mitkCommandLineParser::String, "Generic model function formular", "Formular of a generic model (if selected) that will be parsed and fitted.", us::Any()); |
| 78 | parser.endGroup(); |
| 79 | parser.beginGroup("Required I/O parameters"); |
| 80 | parser.addArgument( |
| 81 | "input", "i", mitkCommandLineParser::File, "Input file", "input 3D+t image file", us::Any(), false, false, false, mitkCommandLineParser::Input); |
| 82 | parser.addArgument("output", |
| 83 | "o", |
| 84 | mitkCommandLineParser::File, |
| 85 | "Output file template", |
| 86 | "where to save the output parameter images. The specified path will be used as template to determine the format (via extension) and the name \"root\". For each parameter a suffix will be added to the name.", |
| 87 | us::Any(), |
| 88 | false, false, false, mitkCommandLineParser::Output); |
| 89 | parser.endGroup(); |
| 90 | |
| 91 | parser.beginGroup("Optional parameters"); |
| 92 | parser.addArgument( |
| 93 | "mask", "m", mitkCommandLineParser::File, "Mask file", "Mask that defines the spatial image region that should be fitted. Must have the same geometry as the input image!", us::Any(), true, false, false, mitkCommandLineParser::Input); |
| 94 | parser.addArgument( |
| 95 | "verbose", "v", mitkCommandLineParser::Bool, "Verbose Output", "Whether to produce verbose output"); |
| 96 | parser.addArgument( |
| 97 | "roibased", "r", mitkCommandLineParser::Bool, "Roi based fitting", "Will compute a mean intensity signal over the ROI before fitting it. If this mode is used a mask must be specified."); |
| 98 | parser.addArgument("help", "h", mitkCommandLineParser::Bool, "Help:", "Show this help text"); |
| 99 | parser.endGroup(); |
| 100 | //! [add arguments] |
| 101 | } |
| 102 | |
| 103 | bool configureApplicationSettings(std::map<std::string, us::Any> parsedArgs) |
| 104 | { |
no test coverage detected