aind-ophys-utils 0.1.0

Generated from aind-library-template

Welcome to aind-ophys-utils

Python utility library for processing calcium imaging (optical physiology) data. All interfaces are array-based (NumPy / h5py) with no project-specific data structures, making the modules easy to integrate into any pipeline.

Modules

Module	Description
baseline_fitting	Robust parametric baseline fitting: M-estimator norms (Tukey biweight variants), IRLS nonlinear fitting with JAX autodiff, robust LOWESS smoother, and a high-level fit_baseline orchestrator that chains bleach-trend fitting with local fluctuation estimation.
dff	ΔF/F computation from fluorescence traces. Inactive-frame masking baseline, parallelised across ROIs, with a plot_dff helper for QA visualisation.
signal_utils	Signal processing primitives: running percentile filter, nanmedian filter, robust noise standard deviation (MAD / FFT / Welch), and a fast noise estimator using GPU-accelerated FFTs via PyTorch.
summary_images	GPU-accelerated summary images for calcium imaging movies: mean, max-correlation (Cn), and peak-to-noise ratio (PNR).
array_utils	Array downsampling and subsampling utilities with flexible strategies (mean, max, median, first, last, mid) and optional NaN-skipping.
video_utils	H5 video downsampling and VP9 video encoding via imageio-ffmpeg.
motion_border_utils	Compute motion borders from frame-shift correction outputs.

Installation

pip install aind-ophys-utils

GPU / CPU note. aind-ophys-utils depends on PyTorch, which pulls in CUDA libraries by default from PyPI (~2 GB). To install a CPU-only build instead, install PyTorch first using the official CPU index, then install this package:

pip install torch --index-url https://download.pytorch.org/whl/cpu
pip install aind-ophys-utils

Alternatively, pass --extra-index-url in a single command:

pip install aind-ophys-utils --extra-index-url https://download.pytorch.org/whl/cpu

To use the software from source, clone the repository and in the root directory run

pip install -e .

To develop the code in place, run

pip install -e .[dev]

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 pytest && 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):

Commit message	Release type
fix(pencil): stop graphite breaking when too much pressure applied	Patch Fix Release, Default release
feat(pencil): add 'graphiteWidth' option	Minor Feature Release
perf(pencil): remove graphiteWidth option BREAKING CHANGE: The graphiteWidth option has been removed. The default graphite width of 10mm is always used for performance reasons.	Major Breaking Release (Note that the BREAKING CHANGE: token must be in the footer of the commit)

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.