aind-dynamic-foraging-data-utils

Scope

Purpose: Ingests NWB and spits out dataframes with the relevant information. Focused on dynamic foraging. Other tasks can branch and build task-specific utils. Inputs are nwbs, outputs are dataframes (tidy and not) Dependencies: xarray (includes numpy and pandas), scikit-learn (includes scipy), matplotlib

Installation

To use the software, in the root directory, run

pip install -e .

To develop the code, run

pip install -e .[dev]

Usage

Accessing data from an NWB file

To load an NWB file

import aind_dynamic_foraging_data_utils.nwb_utils as nwb_utils
nwb = nwb_utils.load_nwb_from_filename(<filepath>)

To extract a pandas dataframe of trials

df_trials = nwb_utils.create_df_trials(nwb)

To extract a pandas dataframe of events

df_events = nwb_utils.create_events_df(nwb)

To extract a pandas dataframe of photometry data

fip_df = nwb_utils.create_fib_df(nwb)

By default, all of these functions adjust timestamps such that t(0) is the time of the first go cue. If you wish to disable this feature, use adjust_time=False

Time alignment tools

To align a data variable to a set of timepoints and create an event triggered response use the alignment module. For example to align FIP data to each go cue:

import aind_dynamic_foraging_data_utils.alignment as alignment

etr = alignment.event_triggered_response(
    fip_df.query('event == "<FIP channel>"'),
    "timestamps",
    "data",
    df_trials['goCue_start_time_in_session'].values,
    t_start = 0,
    t_end = 1,
    output_sampling_rate=40
    )

Contributing

Linters and testing

There are several libraries used to run linters, check documentation, and run tests.

• Please test your changes using the coverage library, which will run the tests and log a coverage report:

coverage run -m unittest discover && coverage report

• Use interrogate to check that modules, methods, etc. have been documented thoroughly:

interrogate .

• Use flake8 to check that code is up to standards (no unused imports, etc.):

  flake8 .

• Use black to automatically format the code into PEP standards:

  black .

• Use isort to automatically sort import statements:

  isort .

Pull requests

For internal members, please create a branch. For external members, please fork the repository and open a pull request from the fork. We'll primarily use Angular style for commit messages. Roughly, they should follow the pattern:

<type>(<scope>): <short summary>

where scope (optional) describes the packages affected by the code changes and type (mandatory) is one of:

• build: Changes that affect build tools or external dependencies (example scopes: pyproject.toml, setup.py)
• ci: Changes to our CI configuration files and scripts (examples: .github/workflows/ci.yml)
• docs: Documentation only changes
• feat: A new feature
• fix: A bugfix
• perf: A code change that improves performance
• refactor: A code change that neither fixes a bug nor adds a feature
• test: Adding missing tests or correcting existing tests

Semantic Release

The table below, from semantic release, shows which commit message gets you which release type when semantic-release runs (using the default configuration):

Documentation

To generate the rst files source files for documentation, run

sphinx-apidoc -o doc_template/source/ src 

Then to create the documentation HTML files, run

sphinx-build -b html doc_template/source/ doc_template/build/html

More info on sphinx installation can be found here.