spec for YAML files to configure label prediction

This document specifies the structure of HVC config files written in YAML.

structure

Every predict.config.yml file should be written in YAML as a dictionary with (key, value) pairs In other words, any YAML file that contains a configuration for feature extraction should define a dictionary named ‘predict` with keys as outlined below.

required key: todo_list

Every predict.config.yml file has exactly one required key at the top level:
todo_list: list of dicts
list where each element is a dict. each dict sets parameters for a ‘job’, typically data associated with one set of vocalizations.

specification for dictionaries in todo_list

required keys

Every dict in a todo_list has the following required keys:

  • bird_ID : str for example, bl26lb16

  • file_format: str {‘evtaf’,’koumura’}

  • data_dirs: list of str directories containing data each str must be a valid directory that can be found on the path for example

    - C:\DATA\bl26lb16\pre_surgery_baseline\041912
- C:\DATA\bl26lb16\pre_surgery_baseline\042012

  • model_file: str filename of machine learning model / neural network that will be used to predict labels for syllables example: somedir/select_output_170814_005430/knn/knn_100samples_replicate0

  • output_dir: str directory in which to save output if it doesn’t exist, HVC will create it for example, C:\DATA\bl26lb16\

  • predict_proba : bool If True, calculate probabilities for predicted labels.

example predict_config.yml

These are some of the predict.config.yml files used for testing, found in hybrid-vocal-classifier/tests/data_for_tests/config.yml/: