Allow inference on multiple individual videos via `sleap-track`

[emdavis02]

Discussed in https://github.com/talmolab/sleap/discussions/1439

Problem Description

^{Originally posted by **roomrys** August 4, 2023} Currently, to run inference on multiple videos via the `sleap-track` command, users need to call this command many times either manually or in a script. It might be a nice feature to allow multiple videos/inputs.

Feature Proposal

• Add an option for a folder of files in the cli instead of only an individual file path
• Later expand this to also include a csv of file paths

Implementation Details

Currently, sleap_track takes in an argument data_path from the command line that is the file path to a .slp file, this means that the user must run this function once for every video they wish to run an inference on either manually or through a script. We would like to allow the argument data_path to also take in a path to a folder of .slp files and run an inference on each of these files. This will all be acomplished in sleap/nn/inference.py

1. Create an optional flag to the cli to specify if data_path is a folder

• [ ] Add this component to the _make_cli_parser() function
• [ ] Also add a description to help docs https://github.com/talmolab/sleap/blob/43a4f13ab28d2726af4a9c1858e8e2cde06d53cc/sleap/nn/inference.py#L5051-L5068

2. Make data_path a list to enable iteration

• [ ] Check if the flag was called in args to communicate that args.data_path is a folder
• [ ] If it is, enter the folder and add all compatible files to data_path
• [ ] Else, data_path = [args.data_path]

Note: The "labels" cli argument has been deprecated and will not need to be edited to accomodate this new function. https://github.com/talmolab/sleap/blob/43a4f13ab28d2726af4a9c1858e8e2cde06d53cc/sleap/nn/inference.py#L5292-L5296

3. Add a loop to file loading lines

• [ ] Iterate through data_path. The loop will encompass the entire code section shown below.
• [ ] Change provider to a list to store a value for each item in data_path https://github.com/talmolab/sleap/blob/43a4f13ab28d2726af4a9c1858e8e2cde06d53cc/sleap/nn/inference.py#L5304-L5328

4. Add a loop to main() for running inference and tracking

• [ ] Iterate through data_path in the section of main shown below. The loop will start at line 5476, before we run the inference but after the predictor.tracker is set. https://github.com/talmolab/sleap/blob/43a4f13ab28d2726af4a9c1858e8e2cde06d53cc/sleap/nn/inference.py#L5473-L5485

• [ ] transplate the following lines of code into the above loop. This will need to be run for each item in data_path https://github.com/talmolab/sleap/blob/43a4f13ab28d2726af4a9c1858e8e2cde06d53cc/sleap/nn/inference.py#L5510-L5541

5. Add an aditional loop to main() for just running tracking

• [ ] Iterate through data_path for the following code. The loop will start after the elif and contain the rest of the attatched lines. https://github.com/talmolab/sleap/blob/43a4f13ab28d2726af4a9c1858e8e2cde06d53cc/sleap/nn/inference.py#L5487-L5500

• [ ] Again, we will have to transplant the following lines of code into the loop. https://github.com/talmolab/sleap/blob/43a4f13ab28d2726af4a9c1858e8e2cde06d53cc/sleap/nn/inference.py#L5510-L5541

Documentation Changes

Changes will be made to the sleap-track section of the documentation

positional arguments: data_path Path to data to predict on. This can be one of the following:

• A .slp file containing labeled data.
• A folder containing multiple video files in supported formats.
• An individual video file in a supported format.

optional arguments: ... -o OUTPUT, --output OUTPUT The output filename or directory path to use for the predicted data. If not provided, defaults to '[data_path].predictions.slp'.

[eberrigan]

Great job @emdavis02!

• We could try it with and without the additional argument to determine if the input is a directory. It might be sufficient to use Path.isdir() and Path.isfile() documented here.
• There is either inference alone, or inference with tracking.
• Make sure our current implementation of the CLI works so that these changes are backwards-compatible.
• Please add examples of intended use cases and test that the new implementation behaves as expected. These examples will be added to the CLI documentation.
• Add necessary tests for inference.py to make sure changes are covered.

[talmo]

• We could try it with and without the additional argument to determine if the input is a directory. It might be sufficient to use os.path.isdir() and os.path.isfile()` documented here.

Just jumping in to say: please use pathlib instead of os.path APIs!

[eberrigan]

Thanks! Here is the correspondence between os.path and Path: correspondence to tools in the os module