exaSPIM pipeline utils

Code repository to be installed in exaSPIM processing capsules.

Features

• Wrapper code for ImageJ automation.
• n5 to zarr converter to be run in a Code Ocean capsule.

ImageJ wrapper module

The ImageJ wrapper module contains Fiji macro templates and wrapper code to automatically run interest point detection and interest point based registration in the Code Ocean capsule. This functionality is set as the main entry point of the package if the whole package is invoked on the command line or the aind_exaspim_pipeline command is run.

#!/usr/bin/env bash
set -ex
cd ~/capsule
imagej_wrapper "$@"

N5 to Zarr converter

The N5 to zarr converter sets up a local dask cluster with multiple python processes as workers to read in an N5 dataset and write it out in a multiscale Zarr dataset. Both datasets may be local or directly on S3. AWS credentials must be available in the environment (Code Ocean credential assignment to environment variables).

This implementation is based on dask.array (da).

This command takes a manifest json file as the only command line argument or looks it up at the hard-wired data/manifest/exaspim_manifest.json location if not specified.

To set up a code ocean capsule, use the following run.sh script:

#!/usr/bin/env bash
set -ex
cd ~/capsule
n5tozarr_da_converter "$@"

Installation

To use the software, in the root directory, run

pip install -e .

To develop the code, run

pip install -e .[dev]

For n5tozarr and zarr multiscale conversion, install as

pip install -e .[n5tozarr]

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

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.