2. Command line interfaces

2.1. Data organization

It is assumed that there will be one directory per experiment. This directory contains the acquired data, but will also contain the result data as depicted below.

$ /path/to/experiment/
├── RAWDATA/
│  └── ...
├── FUSE
│  └── ...
├── SEG
│  └── ...
└── POST
   └── ...

2.2. Principle

2.3. Command line interfaces common options

-h, --help

prints a help message

-p file, --parameters file

set the parameter file to be parsed

-e path, --embryo-rep path

set the path to the directory where the RAWDATA/ directory is located. Can also be given in the parameter file by the variable PATH_EMBRYO.

-k, --keep-temporary-files

allows to keep the temporary files. Not to be routinely used.

-f, --force

forces execution, even if (temporary) result files are already existing

-v, --verbose

increases verboseness (both at console and in the log file)

-nv, --no-verbose

no verboseness

-d, --debug

increases debug information (in the log file)

-nd, --no-debug

no debug information

-pp, --print-param

print parameters in console and exit. A parameter file has to be provided (-p option). Allows to check the parameters that will be used before any processing; it is also a means to have access to the whole parameter list.