aind-registration-utils


Usage

• To use this template, click the green Use this template button and Create new repository.
• After github initially creates the new repository, please wait an extra minute for the initialization scripts to finish organizing the repo.
• To enable the automatic semantic version increments: in the repository go to Settings and Collaborators and teams. Click the green Add people button. Add svc-aindscicomp as an admin. Modify the file in .github/workflows/tag_and_publish.yml and remove the if statement in line 65. The semantic version will now be incremented every time a code is committed into the main branch.
• To publish to PyPI, enable semantic versioning and uncomment the publish block in .github/workflows/tag_and_publish.yml. The code will now be published to PyPI every time the code is committed into the main branch.
• The .github/workflows/test_and_lint.yml file will run automated tests and style checks every time a Pull Request is opened. If the checks are undesired, the test_and_lint.yml can be deleted. The strictness of the code coverage level, etc., can be modified by altering the configurations in the pyproject.toml file and the .flake8 file.

Installation

To use the software, in the root directory, run

pip install -e .

To develop the code, run

pip install -e .[dev]

Registration with the ANTs binaries

aind_registration_utils.ants_cli runs antsRegistration itself, through commandants, with every setting stated on the command line. ANTs is not a Python dependency: install it with commandants install-ants, a release archive or conda-forge ants, and put its bin directory on PATH or in $ANTSPATH.

from aind_registration_utils.ants_cli import (
    RegistrationConfig,
    build_registration,
    run_syn_registration,
)
from aind_registration_utils.chains import SynTransform, transform_points

config = RegistrationConfig.lightsheet_25um()
reg = build_registration(template, brain, out_dir / "reg_", config,
                         fixed_mask=template_mask, moving_mask=brain_mask)
result = run_syn_registration(reg, threads=1, config=config)

run_syn_registration checks the ANTs version, rejects headers in µm, and writes transform_information.json (the sidecar) and registration_provenance.json (the command, ANTs version, threads and config) beside the transforms.

aind_registration_utils.chains applies the result with SimpleITK, so consumers need no ANTs install. Directions name where points go, and hops chain registrations:

brain_reg = SynTransform.from_sidecar(result.sidecar)
tpl_to_ccf = SynTransform.from_sidecar("template_to_ccf/transform_information.json")
pts_ccf = transform_points(
    pts_brain, [(brain_reg, "moving_to_fixed"), (tpl_to_ccf, "moving_to_fixed")]
)

Points that land outside a warp field, where ANTs silently applies only the affine, raise unless outside="warn" or "ignore" is given. Integration tests run when ANTs is found and are skipped otherwise.

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.