Running the PyFibre CLI

Once installed, enter the PyFibre deployment environment using:

python -m ci shell

Calling the executable PyFibre from the command line will initiate the terminal based version of PyFibre:

    Usage: PyFibre [OPTIONS] [FILE_PATHS]

Options:
  --version             Show the version and exit.
  --debug               Prints extra debug information in
                        pyfibre.log
  --profile             Run GUI under cProfile, creating .prof and
                        .pstats files in the current directory.
  --ow_metric           Toggles overwrite analytic metrics
  --ow_segment          Toggles overwrite image segmentation
  --ow_network          Toggles overwrite network extraction
  --save_figures        Toggles saving of figures
  --test                Perform run on test image
  --key TEXT            Keywords to filter file names
  --sigma FLOAT         Gaussian smoothing standard deviation
  --alpha FLOAT         Alpha network coefficient
  --database_name TEXT  Output database filename
  --log_name TEXT       Pyfibre log filename
  --help                Show this message and exit.

Multiple file paths can be included as arguments, including directories. The user may also include also use wildcard assignments, for example:

PyFibre some-images/ other-images/some-file-path.tif more-images/other-files*