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Command-Line Arguments

This document provides an overview of command-line arguments featured in the provided example scripts (in scripts/) for running the EKS.

The following is the general syntax for running an example script in bash:

python scripts/<your_script> --csv-dir <csv-directory> --<optional-arg1> <params1> --<optional-arg2> <params2> ...

The script is run as a python executable. Arguments are parsed using the argparse Python module, as seen in each of the example scripts.

Arguments are either general or script-specific.

General Arguments

These arguments are present in all example scripts.

  • --input-dir <input_data_directory> String specifying read-in directory containing data.
  • --save-dir <save_directory> String specifying write-to directory (csv-dir by default).
  • --save-filename <save_filename> String specifying output file name ({'smoother_type}_{last_keypoint_smooth_param}' by default).
  • --data-type <data_type> String specifying input data file type. Accepts DeepLabCut (dlc), Lightning Pose (lp), and SLEAP (slp) file types. LP by default.
  • --s-frames <s-frame_int> or <list of tuples (e.g. [(1, 300), (1000, None)] Specifies frames to be considered for smoothing. If the input is an integer, selects that many frames starting from frame 1. Selects the first 10,000 frames by default.

Script-specific Arguments

These arguments are specific to the example script (e.g. eks/singleview_smoother.py) being used, which is smoother-dependent. The following are the arguments found in the provided examples in scripts/.

Single-Camera

  • --bodypart-list <bodypart_1> <bodypart_2> ... List of body parts to be tracked by the EKS. Names must have corresponding csv column names in the input data.
  • --s <smooth_param> Float specifying the extent of smoothing to be done. Smoothing increases as param decreases (range 0.01-20, 10 by default)

Multi-Camera

  • --bodypart-list <bodypart_1> <bodypart_2> ... List of body parts to be tracked by the EKS. Names must have corresponding csv column names in the input data.
  • --camera-names <camera_1> <camera_2> ... List of camera views.
  • --s <smooth_param> Float specifying the extent of smoothing to be done. Smoothing increases as param decreases (range 0.01-20, 0.01 by default)
  • --quantile_keep_pca <min_variance%> Float specifying the percentage of points kept for multi-view PCA. Selectivity increases as param increases (range 0-100, 25 by default)

IBL Pupil

  • --diameter-s <smooth_param> Float specifying the extent of smoothing to be done for diameter. Smoothing increases as param increases (range 0-1 exclusive, 0.9999 by default)
  • --com-s <smooth_param> Float specifying the extent of smoothing to be done for center of mass. Smoothing increases as param increases (range 0-1 exclusive, 0.999 by default)

IBL Paw (multiple asynchronous view)

  • --s <smooth_param> Float specifying the extent of smoothing to be done. Smoothing increases as param decreases (range 0.01-20, 0.01 by default)
  • --quantile_keep_pca <min_variance%> Float specifying the percentage of points kept for multi-view PCA. Selectivity increases as param increases (range 0-100, 25 by default)

The following table summarizes the script-specific arguments featured in each of the example scripts.

Argument\Script Single-Camera Multi-Camera IBL Pupil IBL Paw
--bodypart-list ✓ ✓
--camera-names ✓
--s ✓ ✓ ✓
--quantile_keep_pca ✓ ✓
--diameter-s ✓
--com-s ✓

TODO & Takeaways

  • Script-specific args are somewhat overlapping, suggesting refactoring will be useful.
  • Probably good to keep the smoothing param consistent as far as positive/negative correlation to smoothing amount (for IBL Pupil)