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Other Useful Features

Other Useful Scripts

These scripts ship inside the package, as libcuflynx.scripts.* (in a checkout, src/libcuflynx/scripts/). Most are examples or utilities and may need adjustments for your specific model. Run one with python -m libcuflynx.scripts.<script_name>, or copy it out of the package and edit your copy.

Prerequisites

  • pip install libcuflynx (or an editable install of a checkout).
  • A configured user_inputs.yaml and relevant resource files.

generate_modules_files.py

Converts a generic CellML file into the modular format used by Circulatory_Autogen.

  • Currently works for models made from a single module.
  • Generates [file_prefix]_modules.cellml and [file_prefix]_module_config.json in module_config_user/.

generate_obs_json.py

Example script for automating creation of an obs_data.json file from input data.

  • Use this as a template if you do not want to hand-edit JSON.
  • Note: it uses legacy fields such as sample_rate; update to obs_dt for series entries.
  • For a more structured helper, see example_format_obs_data_json_file.py.

example_format_obs_data_json_file.py

Example script showing how to build an obs_data.json using the helper class libcuflynx.utilities.obs_data_helpers.ObsDataCreator. Copy it and change it for your own task.

read_and_insert_parameters.py

Updates a parameters.csv file with values from a JSON input file.

convert_0d_to_1d.py

Utility for converting a 0D vessel array into a 1D representation (useful when preparing 1D-0D coupled models).

run_multiple_param_id.py

Runs multiple parameter identification experiments over a list of observation files.

Expected outcome

You should be able to locate and run auxiliary scripts for module conversion, data preparation, and batch workflows.