PyOPIA 2.16.4

A Python Ocean Particle Image Analysis toolbox.

PyOPIA

A Python Ocean Particle Image Analysis toolbox

Quick tryout of PyOPIA

1. Install uv
2. Initialize PyOPIA project with a small example image dataset and run processing

uvx --python 3.12 --from pyopia[classification] pyopia init-project pyopiatest --example-data

cd pyopiatest

uvx --python 3.12 --from pyopia[classification] pyopia process config.toml

3. Inspect the processed particle statistics in the processed/ folder
4. Merge the individual processed image STATS files into a single STATS.nc file, then create a montage of the processed STATS.nc

uvx --python 3.12 --from pyopia[classification] pyopia merge-mfdata processed

uvx --python 3.12 --from pyopia[classification] pyopia make-montage processed\pyopiatest-STATS.nc

5. Visualise the monatge of all processed singular particle images in one

montage.png

Will show you a montage of all the processed particle images in one.

See the documentation for more information on how to install and use PyOPIA.

Running with Docker

A prebuilt container image is published to GitHub Container Registry on every release, for users who prefer not to install PyOPIA's dependencies directly.

One-off invocation

From any directory that contains a config.toml:

docker run --rm \
    --user $(id -u):$(id -g) \
    -v "$PWD:$PWD" -w "$PWD" \
    ghcr.io/sintef/pyopia:latest \
    process config.toml

The 1:1 volume mount (-v "$PWD:$PWD") makes the container see your current directory at the same path as the host, so an existing config.toml with absolute paths under $PWD works unchanged.

If your config references paths outside $PWD — most commonly a classifier weights file — add a matching bind mount for each of them. The target (right of the colon) must equal the source (left) so the path in the config resolves unchanged. For a config like

[steps.classifier]
pipeline_class = "pyopia.classify_torch.Classify"
model_path = "/home/you/models/classifier.pt"

the invocation becomes

docker run --rm \
    --user $(id -u):$(id -g) \
    -v "$PWD:$PWD" -w "$PWD" \
    -v /home/you/models:/home/you/models:ro \
    ghcr.io/sintef/pyopia:latest \
    process config.toml

Any PyOPIA CLI command works, e.g. docker run --rm ghcr.io/sintef/pyopia:latest --help.

Using docker compose

Each GitHub release attaches a compose.yaml as an asset. Download it once per project:

curl -LO https://github.com/SINTEF/pyopia/releases/latest/download/compose.yaml
docker compose run --rm pyopia                       # runs `pyopia process config.toml`
docker compose run --rm pyopia --help                # or any other CLI argument

The compose file has commented-out stubs for paths that live outside $PWD — in particular the classifier weights file. Edit compose.yaml to uncomment the line and point it at your actual host path, e.g.

    volumes:
      - ${PWD}:${PWD}
      - /home/you/models:/home/you/models:ro    # classifier weights

The target must match the source so the config-referenced path resolves unchanged. Override the default config filename with PYOPIA_CONFIG:

PYOPIA_CONFIG=my_run.toml docker compose run --rm pyopia

Documentation:

pyopia.readthedocs.io

Current status:

• Under development. See/regester issues, here

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Development targets for PyOpia:

1. Allow nonfamiliar users to install and use PyOpia, and to contribute & commit code changes
2. Not hardware specific
3. Smaller dependency list than PySilCam -Eventual optional dependencies (e.g. for classification)
4. Can be imported by pysilcam or other hardware-specific tools
5. Work on a single-image basis (...primarily, with options for multiprocess to be considered later)
6. No use of settings/config files within the core code - pass arguments directly. Eventual use of settings/config files should be handled by high-level wrappers that provide arguments to functions.
7. Github workflows
8. Tests

Normal functions within PyOpia should:

1. take inputs
2. return new outputs
3. don't modify state of input
4. minimum possible disc IO during processing

Contributions

We welcome additions and improvements to the code! We request that you follow a few guidelines. These are in place to make sure the code improves over time.

1. All code changes must be submitted as pull requests, either from a branch or a fork.
2. Good documentation of the code is needed for PyOpia to succeed and so please include up-to-date docstrings as you make changes, so that the auto-build on readthedocs is complete and useful for users. (A version of the new docs will complie when you make a pull request and a link to this can be found in the pull request checks)
3. All pull requests are required to pass all tests before merging. Please do not disable or remove tests just to make your branch pass the pull request.
4. All pull requests must be reviewed by a person. The benefits from code review are plenty, but we like to emphasise that code reviews help spreading the awarenes of code changes. Please note that code reviews should be a pleasant experience, so be plesant, polite and remember that there is a human being with good intentions on the other side of the screen.
5. All contributions are linted with flake8. We recommend that you run flake8 on your code while developing to fix any issues as you go. We recommend using autopep8 to autoformat your Python code (but please check the code behaviour is not affected by autoformatting before pushing). This makes flake8 happy, and makes it easier for us all to maintain a consistent and readable code base.

Docstrings

Use the NumPy style in docstrings. See style guide here

Installing

For users

Users are expected to be familiar with Python. Please refer to the recommended installation instructions provided on the documentation pages, here

For developers from source

Install (uv)[https://docs.astral.sh/uv/getting-started/installation/]

1. Navigate to the folder where you want to install pyopia using the 'cd' command.

If you use git: Download repository from github, and move into the new directory:

git clone https://github.com/SINTEF/pyopia.git
cd pyopia

For the next steps, you need to be located in the PyOPIA root directory that contains the file 'pyproject.toml'.

2. Install all requirements with

uv sync --all-extras

3. (optional) Run local tests:

uv run pytest

Version numbering

The version number of PyOPIA is split into three sections: MAJOR.MINOR.PATCH

• MAJOR: Changes in high-level pipeline use and/or data output that are not backwards-compatible.
• MINOR: New features that are backwards-compatible.
• PATCH: Backwards-compatible bug fixes or enhancements to existing functionality

Build docs locally

sphinx-apidoc -f -o docs/source docs/build --separate

sphinx-build -b html ./docs/ ./docs/build

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License

PyOpia is licensed under the BSD3 license. See LICENSE. All contributors should be recognised & aknowledged.