nndet_run_preprocessing script

Run nnDetection pre-processing, data analysis, and image data unpacking. The CL scripts called are nndet_prep and nndet_unpack, with the arguments extracted from the given configuration file.

usage: nndet_run_preprocessing [-h] --config-file CONFIG_FILE
                               [--n-workers N_WORKERS] [-v | -q]

Named Arguments

--config-file

File path for the configuration dictionary, used to retrieve experiment variables (Task_ID, results_folder, …)

--n-workers

Number of parallel processes used when pre-processing and unpacking the image data (Default: N_THREADS)

-v, --verbose

Enable verbose output in terminal. Add multiple times to increase verbosity.

-q, --silent

Suppress most log outputs in terminal.

Example call:

nndet_run_preprocessing --config-file /PATH/TO/CONFIG_FILE.json