diff --git a/.github/ISSUE_TEMPLATE/issue.yml b/.github/ISSUE_TEMPLATE/issue.yml new file mode 100644 index 0000000..1b9876f --- /dev/null +++ b/.github/ISSUE_TEMPLATE/issue.yml @@ -0,0 +1,49 @@ +# GitHub Issue template for bug reports +name: Open a GitHub issue +description: > + Please use this form to send along new ideas for content or + changes that might be helpful! + +body: + - type: checkboxes + attributes: + label: Is this a duplicate of an existing idea for this project? + description: > + Please make sure to search in the + [issues](https://github.com/WayScience/nViz/issues) first + to see whether the same issue was reported already. + If you find an existing issue, please don't hesitate to comment + on it or add a reaction to existing content! + options: + - label: > + I found no existing + [issues](https://github.com/WayScience/nViz/issues) + covering this topic. + required: true + + - type: textarea + id: description + attributes: + label: What is your idea? + description: > + Please provide a specific description of what you'd like to see + including the context and what the result might look like. + placeholder: > + For example: "When x happens I see y. + The following might be a good way to address this ..." + validations: + required: true + + - type: checkboxes + attributes: + label: Would you like to work on a solution for this? + description: > + This is a community-driven project and we + love new contributors (including through opening or adding to issues)! + This is an optional check to help us understand your interest to be + involved (especially if you already have a good understanding + of how to implement it). + We are happy to guide you in the contribution process and please + don't hesitate to reach out for help along the way. + options: + - label: Yes I am willing to submit a PR for this! diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md new file mode 100644 index 0000000..d8f6cfa --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -0,0 +1,37 @@ + + +# Description + + + +## What kind of change(s) are included? + +- [ ] Documentation (changes docs or other related content) +- [ ] Bug fix (fixes an issue). +- [ ] Enhancement (adds functionality). +- [ ] Breaking change (these changes would cause existing functionality to not work as expected). + +# Checklist + +Please ensure that all boxes are checked before indicating that this pull request is ready for review. + +- [ ] I have read and followed the [CONTRIBUTING.md](CONTRIBUTING.md) guidelines. +- [ ] I have searched for existing content to ensure this is not a duplicate. +- [ ] I have performed a self-review of these additions (including spelling, grammar, and related). +- [ ] These changes pass all pre-commit checks. +- [ ] I have added comments to my code to help provide understanding +- [ ] I have added a test which covers the code changes found within this PR +- [ ] I have deleted all non-relevant text in this pull request template. diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 0000000..b9c048a --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,27 @@ +# GitHub Dependabot configuration +# Note: there is no interaction between this +# configuration and dependabot security updates. +# See here for more information: +# https://docs.github.com/en/code-security/dependabot/dependabot-security-updates/about-dependabot-security-updates#about-dependabot-security-updates + +version: 2 +updates: + # GitHub Actions checks + # See here for more information: + # https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuring-dependabot-version-updates + - package-ecosystem: "github-actions" + directory: "/" + schedule: + # Check for updates to GitHub Actions every week + interval: "weekly" + + # Perform checks and updates for python uv environment. + # This depends on changes to dependabot via: + # https://github.com/dependabot/dependabot-core/pull/10040 + # See here for more information: + # https://docs.github.com/en/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file#pip-and-pip-compile + - package-ecosystem: "pip" + directory: "/" + schedule: + # Check for updates to uv environment files every week + interval: "weekly" diff --git a/.github/release-drafter.yml b/.github/release-drafter.yml new file mode 100644 index 0000000..3d8f4ed --- /dev/null +++ b/.github/release-drafter.yml @@ -0,0 +1,21 @@ +--- +# template configuration for release-drafter +# see: https://github.com/release-drafter/release-drafter +name-template: 'v$RESOLVED_VERSION' +tag-template: 'v$RESOLVED_VERSION' +version-resolver: + major: + labels: + - 'release-major' + minor: + labels: + - 'release-minor' + patch: + labels: + - 'release-patch' + default: patch +change-template: '- $TITLE (@$AUTHOR via #$NUMBER)' +template: | + ## Changes + + $CHANGES diff --git a/.github/workflows/draft-release.yml b/.github/workflows/draft-release.yml new file mode 100644 index 0000000..4847e3e --- /dev/null +++ b/.github/workflows/draft-release.yml @@ -0,0 +1,23 @@ +--- +# workflow for drafting releases on GitHub +# see: https://github.com/release-drafter/release-drafter +name: release drafter + +on: + push: + branches: + - main + +jobs: + draft_release: + permissions: + # write permission is required to create a github release + contents: write + # write permission is required for autolabeler + # otherwise, read permission is required at least + pull-requests: write + runs-on: ubuntu-latest + steps: + - uses: release-drafter/release-drafter@v6 + env: + GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/publish-docs.yml b/.github/workflows/publish-docs.yml new file mode 100644 index 0000000..fd867f2 --- /dev/null +++ b/.github/workflows/publish-docs.yml @@ -0,0 +1,41 @@ +--- +# used for publishing documentation on push to main or published release +name: publish docs + +on: + push: + branches: + - main + release: + types: + - published + +jobs: + build: + # only build and deploy docs if the actor is not dependabot + if: ${{ github.actor != 'dependabot[bot]' }} + runs-on: ubuntu-22.04 + steps: + - name: Checkout + uses: actions/checkout@v4 + with: + fetch-depth: 0 + - uses: actions/setup-python@v5 + with: + python-version: "3.11" + - name: Install the latest version of uv + uses: astral-sh/setup-uv@v5 + - name: Build documentation + run: | + mkdir pages + touch pages/.nojekyll + cd docs + uv run sphinx-build src build + # remove any doctrees dirs which aren't needed for publishing + find ./build -type d -name '.doctrees' -exec rm -rf {} + + cp -r build/* ../pages/ + - name: Deploy documentation + uses: JamesIves/github-pages-deploy-action@v4 + with: + branch: pages + folder: pages diff --git a/.github/workflows/publish-pypi.yml b/.github/workflows/publish-pypi.yml new file mode 100644 index 0000000..c6473da --- /dev/null +++ b/.github/workflows/publish-pypi.yml @@ -0,0 +1,33 @@ +--- +# used for publishing packages to pypi on release +name: publish pypi release + +on: + release: + types: + - published + +jobs: + publish_pypi: + runs-on: ubuntu-latest + environment: release + permissions: + # IMPORTANT: this permission is mandatory for trusted publishing + id-token: write + steps: + - name: Checkout + uses: actions/checkout@v4 + with: + fetch-depth: 0 + - name: Fetch tags + run: git fetch --all --tags + - name: Python setup + uses: actions/setup-python@v5 + with: + python-version: "3.11" + - name: Install the latest version of uv + uses: astral-sh/setup-uv@v5 + - name: uv build distribution content + run: uv build + - name: Publish package distributions to PyPI + uses: pypa/gh-action-pypi-publish@release/v1 diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml new file mode 100644 index 0000000..8517b6a --- /dev/null +++ b/.github/workflows/run-tests.yml @@ -0,0 +1,41 @@ +--- +# used for running tests +name: tests + +on: + push: + branches: [main] + pull_request: + branches: [main] + +jobs: + pre_commit_checks: + runs-on: ubuntu-22.04 + steps: + # checks out the repo + - uses: actions/checkout@v4 + # run pre-commit + - name: Python setup + uses: actions/setup-python@v5 + with: + python-version: "3.11" + - uses: pre-commit/action@v3.0.1 + run_tests: + strategy: + matrix: + python_version: ["3.11", "3.12"] + os: [ubuntu-22.04, macos-13] + runs-on: ${{ matrix.os }} + env: + OS: ${{ matrix.os }} + steps: + - name: Checkout + uses: actions/checkout@v4 + - name: Python setup + uses: actions/setup-python@v5 + with: + python-version: ${{ matrix.python_version }} + - name: Install the latest version of uv + uses: astral-sh/setup-uv@v5 + - name: Run pytest + run: uv run pytest diff --git a/.gitignore b/.gitignore index 15201ac..023c7ad 100644 --- a/.gitignore +++ b/.gitignore @@ -44,7 +44,6 @@ htmlcov/ .coverage.* .cache nosetests.xml -coverage.xml *.cover *.py,cover .hypothesis/ @@ -169,3 +168,10 @@ cython_debug/ # PyPI configuration file .pypirc + +# custom ignores +*.zarr +src/raw_organoid_images_to_omezarr/data/GFF-data +*.tiff +*.tif +_version.py diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..498bbda --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,77 @@ +# See https://pre-commit.com for more information +# See https://pre-commit.com/hooks.html for more hooks +default_language_version: + python: python3.11 +repos: +- repo: https://github.com/pre-commit/pre-commit-hooks + rev: v5.0.0 + hooks: + - id: trailing-whitespace + - id: end-of-file-fixer + exclude: | + (?x)^( + .*\.svg + )$ + - id: check-yaml + - id: detect-private-key +- repo: https://github.com/tox-dev/pyproject-fmt + rev: "v2.5.0" + hooks: + - id: pyproject-fmt +- repo: https://github.com/citation-file-format/cffconvert + rev: 5295f87c0e261da61a7b919fc754e3a77edd98a7 + hooks: + - id: validate-cff +- repo: https://github.com/codespell-project/codespell + rev: v2.4.0 + hooks: + - id: codespell + exclude: | + (?x)^( + .*\.lock | + .*\.csv | + .*\.cff + )$ +- repo: https://github.com/executablebooks/mdformat + rev: 0.7.21 + hooks: + - id: mdformat + additional_dependencies: + - mdformat-gfm +- repo: https://github.com/adrienverge/yamllint + rev: v1.35.1 + hooks: + - id: yamllint + exclude: pre-commit-config.yaml +- repo: https://github.com/astral-sh/ruff-pre-commit + rev: "v0.9.3" + hooks: + - id: ruff-format + - id: ruff +- repo: https://github.com/rhysd/actionlint + rev: v1.7.7 + hooks: + - id: actionlint +- repo: https://gitlab.com/vojko.pribudic.foss/pre-commit-update + rev: v0.6.0 + hooks: + - id: pre-commit-update + args: ["--keep", "mdformat", "--keep", "pre-commit-update", "--keep", "cffconvert"] +- repo: https://github.com/jendrikseipp/vulture + rev: 'v2.14' + hooks: + - id: vulture +- repo: local + hooks: + - id: code-cov-gen + name: Generate code coverage + language: system + entry: uv run coverage run -m pytest + pass_filenames: false + always_run: true +- repo: https://github.com/Weird-Sheep-Labs/coverage-pre-commit + rev: 0.1.1 + hooks: + - id: coverage-xml + - id: coverage-badge + args: ["-o", "docs/src/_static/coverage-badge.svg"] diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..7bf6fc4 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,555 @@ +# This CITATION.cff file was generated with cffinit. +# Visit https://bit.ly/cffinit to generate yours today! +--- +cff-version: 1.2.0 +title: nViz +message: >- + If you use this software, please cite it using the + metadata from this file. +type: software +authors: + - given-names: Dave + family-names: Bunten + orcid: 'https://orcid.org/0000-0001-6041-3665' + - given-names: Michael + family-names: Lippincott + orcid: 'https://orcid.org/0000-0002-8637-1448' + - given-names: Jenna + family-names: Tomkinson + orcid: 'https://orcid.org/0000-0003-2676-5813' + - given-names: Cameron + family-names: Mattson + orcid: 'https://orcid.org/0009-0008-4969-779X' + - given-names: Gregory + family-names: Way + orcid: 'https://orcid.org/0000-0002-0503-9348' +repository-code: 'https://github.com/WayScience/nViz' +abstract: >- + A tool for creating and visualizing n-dimensional microscopy images. +keywords: + - python + - microscopy + - profiling + - organoids + - data + - ome-zarr + - napari + - n-dimensional + - way-lab +license: BSD-3-Clause +references: + - title: >- + OME-Zarr: a cloud-optimized bioimaging file format with international community support + type: article + database: Bioinformatics + url: http://biorxiv.org/lookup/doi/10.1101/2023.02.17.528834 + authors: + - family-names: Moore + given-names: Josh + - family-names: Basurto-Lozada + given-names: Daniela + - family-names: Besson + given-names: Sébastien + - family-names: Bogovic + given-names: John + - family-names: Bragantini + given-names: Jordão + - family-names: Brown + given-names: Eva M. + - family-names: Burel + given-names: Jean-Marie + - family-names: Casas Moreno + given-names: Xavier + - family-names: De Medeiros + given-names: Gustavo + - family-names: Diel + given-names: Erin E. + - family-names: Gault + given-names: David + - family-names: Ghosh + given-names: Satrajit S. + - family-names: Gold + given-names: Ilan + - family-names: Halchenko + given-names: Yaroslav O. + - family-names: Hartley + given-names: Matthew + - family-names: Horsfall + given-names: Dave + - family-names: Keller + given-names: Mark S. + - family-names: Kittisopikul + given-names: Mark + - family-names: Kovacs + given-names: Gabor + - family-names: Küpcü Yoldaş + given-names: Aybüke + - family-names: Kyoda + given-names: Koji + - family-names: Le Tournoulx De La Villegeorges + given-names: Albane + - family-names: Li + given-names: Tong + - family-names: Liberali + given-names: Prisca + - family-names: Lindner + given-names: Dominik + - family-names: Linkert + given-names: Melissa + - family-names: Lüthi + given-names: Joel + - family-names: Maitin-Shepard + given-names: Jeremy + - family-names: Manz + given-names: Trevor + - family-names: Marconato + given-names: Luca + - family-names: McCormick + given-names: Matthew + - family-names: Lange + given-names: Merlin + - family-names: Mohamed + given-names: Khaled + - family-names: Moore + given-names: William + - family-names: Norlin + given-names: Nils + - family-names: Ouyang + given-names: Wei + - family-names: Özdemir + given-names: Bugra + - family-names: Palla + given-names: Giovanni + - family-names: Pape + given-names: Constantin + - family-names: Pelkmans + given-names: Lucas + - family-names: Pietzsch + given-names: Tobias + - family-names: Preibisch + given-names: Stephan + - family-names: Prete + given-names: Martin + - family-names: Rzepka + given-names: Norman + - family-names: Samee + given-names: Sameeul + - family-names: Schaub + given-names: Nicholas + - family-names: Sidky + given-names: Hythem + - family-names: Solak + given-names: Ahmet Can + - family-names: Stirling + given-names: David R. + - family-names: Striebel + given-names: Jonathan + - family-names: Tischer + given-names: Christian + - family-names: Toloudis + given-names: Daniel + - family-names: Virshup + given-names: Isaac + - family-names: Walczysko + given-names: Petr + - family-names: Watson + given-names: Alan M. + - family-names: Weisbart + given-names: Erin + - family-names: Wong + given-names: Frances + - family-names: Yamauchi + given-names: Kevin A. + - family-names: Bayraktar + given-names: Omer + - family-names: Cimini + given-names: Beth A. + - family-names: Gehlenborg + given-names: Nils + - family-names: Haniffa + given-names: Muzlifah + - family-names: Hotaling + given-names: Nathan + - family-names: Onami + given-names: Shuichi + - family-names: Royer + given-names: Loic A. + - family-names: Saalfeld + given-names: Stephan + - family-names: Stegle + given-names: Oliver + - family-names: Theis + given-names: Fabian J. + - family-names: Swedlow + given-names: Jason R. + date-published: 2023-02-21 + identifiers: + - type: doi + value: 10.1101/2023.02.17.528834 + - title: Napari + type: software + identifiers: + - type: doi + value: 10.5281/zenodo.3555620 + authors: + - given-names: Nicholas + family-names: Sofroniew + affiliation: Chan Zuckerberg Initiative + orcid: https://orcid.org/0000-0002-3426-0914 + alias: sofroniewn + - given-names: Talley + family-names: Lambert + affiliation: Harvard Medical School + orcid: https://orcid.org/0000-0002-2409-0181 + alias: tlambert03 + - given-names: Grzegorz + family-names: Bokota + affiliation: University of Warsaw, Faculty of Mathematics, Informatics, and Mechanics + orcid: https://orcid.org/0000-0002-5470-1676 + alias: Czaki + - given-names: Juan + family-names: Nunez-Iglesias + affiliation: Monash eResearch Centre, Monash University + orcid: https://orcid.org/0000-0002-7239-5828 + alias: jni + - given-names: Peter + family-names: Sobolewski + affiliation: The Jackson Laboratory + orcid: https://orcid.org/0000-0002-2097-0990 + alias: psobolewskiPhD + - given-names: Andrew + family-names: Sweet + affiliation: Chan Zuckerberg Initiative + alias: andy-sweet + - given-names: Lorenzo + family-names: Gaifas + affiliation: Gutsche Lab - University of Grenoble + orcid: https://orcid.org/0000-0003-4875-9422 + alias: brisvag + - given-names: Kira + family-names: Evans + affiliation: Chan Zuckerberg Initiative + alias: kne42 + - given-names: Alister + family-names: Burt + affiliation: MRC-LMB + alias: alisterburt + - given-names: Draga + family-names: Doncila Pop + affiliation: Monash University + alias: DragaDoncila + - given-names: Kevin + family-names: Yamauchi + affiliation: Iber Lab - ETH Zürich + alias: kevinyamauchi + - given-names: Melissa + family-names: Weber Mendonça + affiliation: Quansight + orcid: https://orcid.org/0000-0002-3212-402X + alias: melissawm + - given-names: Genevieve + family-names: Buckley + affiliation: Monash University + orcid: https://orcid.org/0000-0003-2763-492X + alias: GenevieveBuckley + - given-names: Wouter-Michiel + family-names: Vierdag + affiliation: European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, + Germany + orcid: https://orcid.org/0000-0003-1666-5421 + alias: melonora + - given-names: Loic + family-names: Royer + affiliation: Chan Zuckerberg Biohub + alias: royerloic + - given-names: Ahmet + family-names: Can Solak + affiliation: Chan Zuckerberg Biohub + alias: AhmetCanSolak + - given-names: Kyle I. S. + family-names: Harrington + affiliation: Chan Zuckerberg Initiative + orcid: https://orcid.org/0000-0002-7237-1973 + alias: kephale + - given-names: Jannis + family-names: Ahlers + affiliation: Monash University + orcid: https://orcid.org/0000-0003-0630-1819 + alias: jnahlers + - given-names: Daniel + family-names: Althviz Moré + affiliation: Quansight + orcid: https://orcid.org/0000-0003-1759-4194 + alias: dalthviz + - given-names: Oren + family-names: Amsalem + affiliation: Harvard Medical School, BIDMC + orcid: https://orcid.org/0000-0002-8070-0378 + alias: orena1 + - given-names: Ashley + family-names: Anderson + affiliation: Chan Zuckerberg Initiative + orcid: https://orcid.org/0000-0002-3841-8344 + alias: aganders3 + - given-names: Andrew + family-names: Annex + affiliation: SETI Institute/NASA ARC + orcid: https://orcid.org/0000-0002-0253-2313 + alias: AndrewAnnex + - given-names: Peter + family-names: Boone + alias: boonepeter + - given-names: Jordão + family-names: Bragantini + affiliation: Chan Zuckerberg Biohub + alias: JoOkuma + - given-names: Matthias + family-names: Bussonnier + affiliation: Quansight Labs + orcid: https://orcid.org/0000-0002-7636-8632 + alias: Carreau + - given-names: Clément + family-names: Caporal + affiliation: Laboratory for Optics and Biosciences, Ecole Polytechnique, INSERM, + CNRS, Palaiseau, France + orcid: https://orcid.org/0000-0002-9441-9173 + alias: ClementCaporal + - given-names: Jan + family-names: Eglinger + affiliation: Friedrich Miescher Institute for Biomedical Research (FMI), Basel (Switzerland) + orcid: https://orcid.org/0000-0001-7234-1435 + alias: imagejan + - given-names: Andreas + family-names: Eisenbarth + affiliation: EMBL Heidelberg, Germany + orcid: https://orcid.org/0000-0002-1113-9556 + alias: aeisenbarth + - given-names: Jeremy + family-names: Freeman + affiliation: Chan Zuckerberg Initiative + alias: freeman-lab + - given-names: Christoph + family-names: Gohlke + affiliation: University of California, Irvine + alias: cgohlke + - given-names: Kabilar + family-names: Gunalan + alias: kabilar + - given-names: Hagai + family-names: Har-Gil + affiliation: Tel Aviv University, Israel + alias: HagaiHargil + - given-names: Mark + family-names: Harfouche + affiliation: Ramona Optics Inc, Durham, North Carolina, USA + orcid: https://orcid.org/0000-0002-4657-4603 + alias: hmaarrfk + - given-names: Volker + family-names: Hilsenstein + affiliation: EMBL Heidelberg, Germany + orcid: https://orcid.org/0000-0002-2255-2960 + alias: VolkerH + - given-names: Katherine + family-names: Hutchings + affiliation: University College London + alias: katherine-hutchings + - given-names: Jessy + family-names: Lauer + affiliation: Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland + orcid: https://orcid.org/0000-0002-3656-2449 + alias: jeylau + - given-names: Gregor + family-names: Lichtner + affiliation: Universitätsmedizin Greifswald + orcid: https://orcid.org/0000-0002-5890-1958 + alias: glichtner + - given-names: Ziyang + family-names: Liu + affiliation: Chan Zuckerberg Initiative Foundation + alias: liu-ziyang + - given-names: Lucy + family-names: Liu + affiliation: Quansight + alias: lucyleeow + - given-names: Alan + family-names: Lowe + affiliation: UCL & The Alan Turing Institute + alias: quantumjot + - given-names: Luca + family-names: Marconato + affiliation: EMBL Heidelberg + orcid: https://orcid.org/0000-0003-3198-1326 + alias: LucaMarconato + - given-names: Sean + family-names: Martin + affiliation: MetaCell + orcid: https://orcid.org/0000-0001-7600-0291 + alias: seankmartin + - given-names: Abigail + family-names: McGovern + affiliation: Monash University + alias: AbigailMcGovern + - given-names: Lukasz + family-names: Migas + affiliation: Delft University of Technology + alias: lukasz-migas + - given-names: Nadalyn + family-names: Miller + affiliation: Apex Systems + orcid: https://orcid.org/0009-0007-6993-1267 + alias: Nadalyn-CZI + - given-names: Hector + family-names: Muñoz + affiliation: University of California, Los Angeles + orcid: https://orcid.org/0000-0001-7851-2549 + alias: hectormz + - given-names: Jan-Hendrik + family-names: Müller + affiliation: Georg-August-Universität Göttingen + orcid: https://orcid.org/0009-0007-3670-9969 + alias: kolibril13 + - given-names: Christopher + family-names: Nauroth-Kreß + affiliation: University Hospital Würzburg - Institute of Neuroradiology + alias: Chris-N-K + - given-names: David + family-names: Palecek + affiliation: Algarve Centre of Marine Sciences (CCMAR) + orcid: https://orcid.org/0009-0003-9328-8540 + alias: palec87 + - given-names: Constantin + family-names: Pape + affiliation: Georg-August-Universität Göttingen + orcid: https://orcid.org/0000-0001-6562-7187 + alias: constantinpape + - given-names: Eric + family-names: Perlman + affiliation: Yikes LLC + orcid: https://orcid.org/0000-0001-5542-1302 + alias: perlman + - given-names: Kim + family-names: Pevey + alias: kcpevey + - given-names: Gonzalo + family-names: Peña-Castellanos + affiliation: Quansight + orcid: https://orcid.org/0000-0002-1214-4680 + alias: goanpeca + - given-names: Andrea + family-names: Pierré + affiliation: Brown University + orcid: https://orcid.org/0000-0003-4501-5428 + alias: kir0ul + - given-names: David + family-names: Pinto + alias: MarchisLost + - given-names: Jaime + family-names: Rodríguez-Guerra + affiliation: Quansight Labs + orcid: https://orcid.org/0000-0001-8974-1566 + alias: jaimergp + - given-names: David + family-names: Ross + affiliation: NanoString Technologies, Inc. + orcid: https://orcid.org/0000-0001-9998-3817 + alias: davidpross + - given-names: Craig T. + family-names: Russell + affiliation: European Bioinformatics Institute - European Molecular Biology Laboratory + orcid: https://orcid.org/0000-0002-2447-5911 + alias: ctr26 + - given-names: James + family-names: Ryan + alias: jamesyan-git + - given-names: Gabriel + family-names: Selzer + affiliation: University of Wisconsin-Madison + orcid: https://orcid.org/0009-0002-2400-1940 + alias: gselzer + - given-names: MB + family-names: Smith + affiliation: AI lab for Living Technologies, University Medical Centre Utrecht (The Netherlands) + orcid: https://orcid.org/0000-0002-1405-0100 + alias: odinsbane + - given-names: Paul + family-names: Smith + affiliation: University College London + orcid: https://orcid.org/0000-0002-3676-5318 + alias: p-j-smith + - given-names: Konstantin + family-names: Sofiiuk + alias: ksofiyuk + - given-names: Johannes + family-names: Soltwedel + affiliation: DFG cluster of excellence 'Physics of Life', TU Dresden + orcid: https://orcid.org/0000-0003-1273-2412 + alias: jo-mueller + - given-names: David + family-names: Stansby + affiliation: University College London + orcid: https://orcid.org/0000-0002-1365-1908 + alias: dstansby + - given-names: Jules + family-names: Vanaret + affiliation: Aix Marseille University, CNRS, Fresnel, I2M, IBDM, Turing Centre for Living systems + orcid: https://orcid.org/0009-0004-6070-2263 + alias: jules-vanaret + - given-names: Pam + family-names: Wadhwa + affiliation: Quansight Labs + alias: ppwadhwa + - given-names: Martin + family-names: Weigert + affiliation: TU-Dresden / EPFL + orcid: https://orcid.org/0000-0002-7780-9057 + alias: maweigert + - given-names: Jonas + family-names: Windhager + affiliation: ETH Zurich / University of Zurich + orcid: https://orcid.org/0000-0002-2111-5291 + alias: jwindhager + - given-names: Philip + family-names: Winston + affiliation: Tobeva Software + alias: pwinston + - given-names: Rubin + family-names: Zhao + affiliation: Chinese Academy of Sciences - SIAT, Shenzhen, China + orcid: https://orcid.org/0009-0005-8264-5682 + alias: BeanLi + repository-code: https://github.com/napari/napari + license: BSD-3-Clause + - title: >- + The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging + type: article + issn: 1474-760X + issue: 5 + journal: Genome Biol + pages: R47 + volume: 6 + url: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2005-6-5-r47 + authors: + - family-names: Goldberg + given-names: Ilya G + - family-names: Allan + given-names: Chris + - family-names: Burel + given-names: Jean-Marie + - family-names: Creager + given-names: Doug + - family-names: Falconi + given-names: Andrea + - family-names: Hochheiser + given-names: Harry + - family-names: Johnston + given-names: Josiah + - family-names: Mellen + given-names: Jeff + - family-names: Sorger + given-names: Peter K + - family-names: Swedlow + given-names: Jason R + date-published: 2005-05-03 + identifiers: + - type: doi + value: 10.1186/gb-2005-6-5-r47 diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 0000000..bde3cb7 --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,132 @@ +# Contributor Covenant Code of Conduct + +## Our Pledge + +We as members, contributors, and leaders pledge to make participation in our +community a harassment-free experience for everyone, regardless of age, body +size, visible or invisible disability, ethnicity, sex characteristics, gender +identity and expression, level of experience, education, socioeconomic status, +nationality, personal appearance, race, caste, color, religion, or sexual +identity and orientation. + +We pledge to act and interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. + +## Our Standards + +Examples of behavior that contributes to a positive environment for our +community include: + +- Demonstrating empathy and kindness toward other people +- Being respectful of differing opinions, viewpoints, and experiences +- Giving and gracefully accepting constructive feedback +- Accepting responsibility and apologizing to those affected by our mistakes, + and learning from the experience +- Focusing on what is best not just for us as individuals, but for the overall + community + +Examples of unacceptable behavior include: + +- The use of sexualized language or imagery, and sexual attention or advances of + any kind +- Trolling, insulting or derogatory comments, and personal or political attacks +- Public or private harassment +- Publishing others' private information, such as a physical or email address, + without their explicit permission +- Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Enforcement Responsibilities + +Community leaders are responsible for clarifying and enforcing our standards of +acceptable behavior and will take appropriate and fair corrective action in +response to any behavior that they deem inappropriate, threatening, offensive, +or harmful. + +Community leaders have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, and will communicate reasons for moderation +decisions when appropriate. + +## Scope + +This Code of Conduct applies within all community spaces, and also applies when +an individual is officially representing the community in public spaces. +Examples of representing our community include using an official email address, +posting via an official social media account, or acting as an appointed +representative at an online or offline event. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to community leaders responsible for enforcement. +Please reach out to the maintainers of this repository by using their GitHub profile email address contact information to privately notify us of any incidents of this nature. +All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +## Enforcement Guidelines + +Community leaders will follow these Community Impact Guidelines in determining +the consequences for any action they deem in violation of this Code of Conduct: + +### 1. Correction + +**Community Impact**: Use of inappropriate language or other behavior deemed +unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing +clarity around the nature of the violation and an explanation of why the +behavior was inappropriate. A public apology may be requested. + +### 2. Warning + +**Community Impact**: A violation through a single incident or series of +actions. + +**Consequence**: A warning with consequences for continued behavior. No +interaction with the people involved, including unsolicited interaction with +those enforcing the Code of Conduct, for a specified period of time. This +includes avoiding interactions in community spaces as well as external channels +like social media. Violating these terms may lead to a temporary or permanent +ban. + +### 3. Temporary Ban + +**Community Impact**: A serious violation of community standards, including +sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public +communication with the community for a specified period of time. No public or +private interaction with the people involved, including unsolicited interaction +with those enforcing the Code of Conduct, is allowed during this period. +Violating these terms may lead to a permanent ban. + +### 4. Permanent Ban + +**Community Impact**: Demonstrating a pattern of violation of community +standards, including sustained inappropriate behavior, harassment of an +individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within the +community. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], +version 2.1, available at +[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1]. + +Community Impact Guidelines were inspired by +[Mozilla's code of conduct enforcement ladder][mozilla coc]. + +For answers to common questions about this code of conduct, see the FAQ at +[https://www.contributor-covenant.org/faq][faq]. Translations are available at +[https://www.contributor-covenant.org/translations][translations]. + +[faq]: https://www.contributor-covenant.org/faq +[homepage]: https://www.contributor-covenant.org +[mozilla coc]: https://github.com/mozilla/diversity +[translations]: https://www.contributor-covenant.org/translations +[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 0000000..7c278bc --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,3 @@ +# Contributing + +Please see our [contributing](https://WayScience.github.io/nViz/main/contributing) documentation for more details on contributions, development, and testing. diff --git a/README.md b/README.md index 1355844..45d2b09 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,32 @@ -# nVis -A tool for creating and visualizing n-dimensional microscopy images +# nViz + +[![Build Status](https://github.com/WayScience/nViz/actions/workflows/run-tests.yml/badge.svg?branch=main)](https://github.com/WayScience/nViz/actions/workflows/run-tests.yml?query=branch%3Amain) +![Coverage Status](https://raw.githubusercontent.com/WayScience/nViz/main/docs/src/_static/coverage-badge.svg) +[![Ruff](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json)](https://github.com/astral-sh/ruff) +[![uv](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/uv/main/assets/badge/v0.json)](https://github.com/astral-sh/uv) + +This project focuses on ingesting a set of [TIFF](https://en.wikipedia.org/wiki/TIFF) images as [OME-Zarr](https://pmc.ncbi.nlm.nih.gov/articles/PMC9980008/) or [OME-TIFF](https://genomebiology.biomedcentral.com/articles/10.1186/gb-2005-6-5-r47). +Each input image set[^[1]^](#image_set_ref) are organized by channel and z-slices which form four dimensional (4D) microscopy data. +These 4D microscopy data contain information for biological objects (such as organoids). + +We read the output with [Napari](https://napari.org/dev/index.html), which provides a way to analyze and understand the 3D image data. + +> 1. __Image set__ is loosely defined and changes depending on the context of the data. +> Here it represents a set of images in multiple dimensions that contain information regarding the same sample. +> Each image in an imageset is paired data and must be related as such. + +## Installation + +Install nViz from [PyPI](https://pypi.org/project/nViz/) or from source: + +```shell +# install from pypi +pip install nviz + +# install directly from source +pip install git+https://github.com/WayScience/nViz.git +``` + +## Contributing, Development, and Testing + +Please see our [contributing](https://WayScience.github.io/coSMicQC/main/contributing) documentation for more details on contributions, development, and testing. diff --git a/docs/src/_static/coverage-badge.svg b/docs/src/_static/coverage-badge.svg new file mode 100644 index 0000000..c8bc401 --- /dev/null +++ b/docs/src/_static/coverage-badge.svg @@ -0,0 +1 @@ +coverage: 97.31%coverage97.31% \ No newline at end of file diff --git a/docs/src/code_of_conduct.md b/docs/src/code_of_conduct.md new file mode 100644 index 0000000..51bed04 --- /dev/null +++ b/docs/src/code_of_conduct.md @@ -0,0 +1,132 @@ +# Code of Conduct + +## Our Pledge + +We as members, contributors, and leaders pledge to make participation in our +community a harassment-free experience for everyone, regardless of age, body +size, visible or invisible disability, ethnicity, sex characteristics, gender +identity and expression, level of experience, education, socioeconomic status, +nationality, personal appearance, race, caste, color, religion, or sexual +identity and orientation. + +We pledge to act and interact in ways that contribute to an open, welcoming, +diverse, inclusive, and healthy community. + +## Our Standards + +Examples of behavior that contributes to a positive environment for our +community include: + +- Demonstrating empathy and kindness toward other people +- Being respectful of differing opinions, viewpoints, and experiences +- Giving and gracefully accepting constructive feedback +- Accepting responsibility and apologizing to those affected by our mistakes, + and learning from the experience +- Focusing on what is best not just for us as individuals, but for the overall + community + +Examples of unacceptable behavior include: + +- The use of sexualized language or imagery, and sexual attention or advances of + any kind +- Trolling, insulting or derogatory comments, and personal or political attacks +- Public or private harassment +- Publishing others' private information, such as a physical or email address, + without their explicit permission +- Other conduct which could reasonably be considered inappropriate in a + professional setting + +## Enforcement Responsibilities + +Community leaders are responsible for clarifying and enforcing our standards of +acceptable behavior and will take appropriate and fair corrective action in +response to any behavior that they deem inappropriate, threatening, offensive, +or harmful. + +Community leaders have the right and responsibility to remove, edit, or reject +comments, commits, code, wiki edits, issues, and other contributions that are +not aligned to this Code of Conduct, and will communicate reasons for moderation +decisions when appropriate. + +## Scope + +This Code of Conduct applies within all community spaces, and also applies when +an individual is officially representing the community in public spaces. +Examples of representing our community include using an official email address, +posting via an official social media account, or acting as an appointed +representative at an online or offline event. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to community leaders responsible for enforcement. +Please open a [new security advisory notice](https://github.com/WayScience/nviz/security/advisories/new) (using defaults or "n/a" where unable to fill in the form) to privately notify us of any incidents of this nature. +All complaints will be reviewed and investigated promptly and fairly. + +All community leaders are obligated to respect the privacy and security of the +reporter of any incident. + +## Enforcement Guidelines + +Community leaders will follow these Community Impact Guidelines in determining +the consequences for any action they deem in violation of this Code of Conduct: + +### 1. Correction + +**Community Impact**: Use of inappropriate language or other behavior deemed +unprofessional or unwelcome in the community. + +**Consequence**: A private, written warning from community leaders, providing +clarity around the nature of the violation and an explanation of why the +behavior was inappropriate. A public apology may be requested. + +### 2. Warning + +**Community Impact**: A violation through a single incident or series of +actions. + +**Consequence**: A warning with consequences for continued behavior. No +interaction with the people involved, including unsolicited interaction with +those enforcing the Code of Conduct, for a specified period of time. This +includes avoiding interactions in community spaces as well as external channels +like social media. Violating these terms may lead to a temporary or permanent +ban. + +### 3. Temporary Ban + +**Community Impact**: A serious violation of community standards, including +sustained inappropriate behavior. + +**Consequence**: A temporary ban from any sort of interaction or public +communication with the community for a specified period of time. No public or +private interaction with the people involved, including unsolicited interaction +with those enforcing the Code of Conduct, is allowed during this period. +Violating these terms may lead to a permanent ban. + +### 4. Permanent Ban + +**Community Impact**: Demonstrating a pattern of violation of community +standards, including sustained inappropriate behavior, harassment of an +individual, or aggression toward or disparagement of classes of individuals. + +**Consequence**: A permanent ban from any sort of public interaction within the +community. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], +version 2.1, available at +[https://www.contributor-covenant.org/version/2/1/code_of_conduct.html][v2.1]. + +Community Impact Guidelines were inspired by +[Mozilla's code of conduct enforcement ladder][mozilla coc]. + +For answers to common questions about this code of conduct, see the FAQ at +[https://www.contributor-covenant.org/faq][faq]. Translations are available at +[https://www.contributor-covenant.org/translations][translations]. + +[faq]: https://www.contributor-covenant.org/faq +[homepage]: https://www.contributor-covenant.org +[mozilla coc]: https://github.com/mozilla/diversity +[translations]: https://www.contributor-covenant.org/translations +[v2.1]: https://www.contributor-covenant.org/version/2/1/code_of_conduct.html diff --git a/docs/src/conf.py b/docs/src/conf.py new file mode 100644 index 0000000..6afb7ae --- /dev/null +++ b/docs/src/conf.py @@ -0,0 +1,82 @@ +# Configuration file for the Sphinx documentation builder. +# +# This file only contains a selection of the most common options. For a full +# list see the documentation: +# https://www.sphinx-doc.org/en/master/usage/configuration.html + +# -- Path setup -------------------------------------------------------------- + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +# +import pathlib +import sys + +basedir = str(pathlib.Path(__file__).parent.parent.parent.resolve()) + +sys.path.insert(0, basedir) + +# -- Project information ----------------------------------------------------- + +project = "nViz" +# is used here due to sphinx decision-making: https://github.com/sphinx-doc/sphinx/issues/8132 +copyright = "2024, WayScience Community" # noqa: A001 +author = "WayScience Community" + +# -- General configuration --------------------------------------------------- + +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom +# ones. +extensions = [ + "myst_parser", + "sphinx.ext.autodoc", + "sphinx.ext.napoleon", + "sphinx.ext.viewcode", + "pydata_sphinx_theme", +] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ["_templates"] + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +# This pattern also affects html_static_path and html_extra_path. +exclude_patterns = [] # type: ignore + +# -- Options for HTML output ------------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +html_theme = "pydata_sphinx_theme" + +html_theme_options = { + "header_links_before_dropdown": 5, + "icon_links": [ + { + "name": "GitHub", + "url": "https://github.com/WayScience/nViz", + "icon": "fa-brands fa-github", + }, + ], + "logo": {"text": "nViz"}, + "use_edit_page_button": False, + "show_toc_level": 1, + "navbar_align": "left", + "navbar_center": ["navbar-nav"], + "footer_start": ["copyright"], + "footer_center": ["sphinx-version"], + "secondary_sidebar_items": { + "**/*": ["page-toc", "edit-this-page", "sourcelink"], + }, +} + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ["_static"] +html_css_files = ["custom.css"] + +# set option to avoid rendering default variables +autodoc_preserve_defaults = True diff --git a/docs/src/contributing.md b/docs/src/contributing.md new file mode 100644 index 0000000..1870ee4 --- /dev/null +++ b/docs/src/contributing.md @@ -0,0 +1,131 @@ +# Contributing + +First of all, thank you so much for contributing! 🎉 💯 + +This document contains guidelines on how to most effectively contribute within this repository. + +If you are stuck, please feel free to ask any questions or ask for help. + +## Code of conduct + +This project is governed by our [code of conduct](code_of_conduct.md). By participating, you are expected to uphold this code. +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported to community leaders responsible for enforcement. +Please open a [new security advisory notice](https://github.com/WayScience/nviz/security/advisories/new) (using defaults or "n/a" where unable to fill in the form) to privately notify us of any incidents of this nature. + +## Development + +This project leverages development environments managed by [uv](https://docs.astral.sh/uv/). +We use [pytest](https://docs.pytest.org/) for testing and [GitHub actions](https://docs.github.com/en/actions) for automated tests. + +### Development setup + +Perform the following steps to setup a Python development environment. + +1. [Install Python](https://www.python.org/downloads/) (we recommend using [`pyenv`](https://github.com/pyenv/pyenv) or similar) +1. [Install uv](https://docs.astral.sh/uv/getting-started/installation/) + +### Linting + +Work added to this project is automatically checked using [pre-commit](https://pre-commit.com/) via [GitHub Actions](https://docs.github.com/en/actions). +Pre-commit can work alongside your local [git with git-hooks](https://pre-commit.com/index.html#3-install-the-git-hook-scripts) + +After [installing pre-commit](https://pre-commit.com/#installation) within your development environment, the following command also can perform the same checks within your local development environment: + +```sh +% pre-commit run --all-files +``` + +We use these same checks within our automated tests which are managed by [GitHub Actions workflows](https://docs.github.com/en/actions/using-workflows). +These automated tests generally must pass in order to merge work into this repository. + +### Testing + +Work added to this project is automatically tested using [pytest](https://docs.pytest.org/) via [GitHub Actions](https://docs.github.com/en/actions). +Pytest is installed through the uv environment for this project. +We recommend testing your work before opening pull requests with proposed changes. + +You can run pytest on your work using the following example: + +```sh +% uv run pytest +``` + +## Making changes to this repository + +We welcome anyone to use [GitHub issues](https://docs.github.com/en/issues/tracking-your-work-with-issues/about-issues) (requires a GitHub login) or create [pull requests](https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests) (to directly make changes within this repository) to modify content found within this repository. + +Specifically, there are several ways to suggest or make changes to this repository: + +1. Open a GitHub issue: https://github.com/WayScience/nviz/issues +1. Create a pull request from a forked branch of the repository + +### Creating a pull request + +### Pull requests + +After you’ve decided to contribute code and have written it up, please file a pull request. +We specifically follow a [forked pull request model](https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/creating-a-pull-request-from-a-fork). +Please create a fork of this repository, clone the fork, and then create a new, feature-specific branch. +Once you make the necessary changes on this branch, you should file a pull request to incorporate your changes into this (fork upstream) repository. + +The content and description of your pull request are directly related to the speed at which we are able to review, approve, and merge your contribution. +To ensure an efficient review process please perform the following steps: + +1. Follow all instructions in the [pull request template](https://github.com/WayScience/nviz/blob/main/.github/PULL_REQUEST_TEMPLATE.md) +1. Triple check that your pull request is adding _one_ specific feature or additional group of content. + Small, bite-sized pull requests move so much faster than large pull requests. +1. After submitting your pull request, ensure that your contribution passes all status checks (e.g. passes all tests) + +Pull request review and approval is required by at least one project maintainer to merge. +We will do our best to review the code addition in a timely fashion. +Ensuring that you follow all steps above will increase our speed and ability to review. +We will check for accuracy, style, code coverage, and scope. + +## Versioning + +We use [`setuptools-scm`](https://github.com/pypa/setuptools-scm) to help version this software through [`PEP 440`](https://peps.python.org/pep-0440/) standards and [semver.org](https://semver.org/) standards. +Configuration for versioning is found within the `pyproject.toml` file. +All builds for packages include dynamic version data to help label distinct versions of the software. +`setuptools-scm` uses `git` tags to help distinguish version data. +We also use the `_version.py` file as a place to persist the version data for occaissions where the `git` history is unavailable or unwanted (this file is only present in package builds). +Versioning for the project is intended to align with GitHub Releases which provide `git` tag capabilities. + +### Releases + +We publish source code by using [GitHub Releases](https://docs.github.com/en/repositories/releasing-projects-on-github/about-releases) available [here](https://github.com/wayscience/nviz/releases). +We publish a related Python package through the [Python Packaging Index (PyPI)](https://pypi.org/) available [here](https://pypi.org/project/nviz/). + +#### Release Publishing Process + +Several manual and automated steps are involved with publishing nviz releases. +See below for an overview of how this works. + +Notes about [semantic version](https://en.wikipedia.org/wiki/Software_versioning#Semantic_versioning) (semver) specifications: +nviz version specifications are controlled through [`setuptools-scm`](https://github.com/pypa/setuptools-scm) to create version data based on [git tags](https://git-scm.com/book/en/v2/Git-Basics-Tagging) and commits. +nviz release git tags are automatically applied through [GitHub Releases](https://docs.github.com/en/repositories/releasing-projects-on-github/about-releases) and related inferred changes from [`release-drafter`](https://github.com/release-drafter/release-drafter). + +1. Open a pull request and use a repository label for `release-` to label the pull request for visibility with [`release-drafter`](https://github.com/release-drafter/release-drafter) (for example, see [nviz#24](https://github.com/wayscience/nviz/pull/24) as a reference of a semver patch update). +1. On merging the pull request for the release, a [GitHub Actions workflow](https://docs.github.com/en/actions/using-workflows) defined in `draft-release.yml` leveraging [`release-drafter`](https://github.com/release-drafter/release-drafter) will draft a release for maintainers. +1. The draft GitHub release will include a version tag based on the GitHub PR label applied and `release-drafter`. +1. Make modifications as necessary to the draft GitHub release, then publish the release (the draft release does not normally need additional modifications). +1. On publishing the release, another GitHub Actions workflow defined in `publish-pypi.yml` will run to build and deploy the Python package to PyPI (utilizing the earlier modified `pyproject.toml` semantic version reference for labeling the release). + +## Documentation + +Documentation for this project is published using [Sphinx](https://www.sphinx-doc.org) with markdown and Jupyter notebook file compatibility provided by [myst-parser](https://myst-parser.readthedocs.io/en/latest/) and [myst-nb](https://myst-nb.readthedocs.io/en/latest/) to create a "documentation website" (also known as "docsite"). +The docsite is hosted through [GitHub Pages](https://pages.github.com/) and deployed through automated [GitHub Actions](https://docs.github.com/en/actions) jobs which trigger on pushes to the main branch or the publishing of a new release on GitHub. +Documentation is versioned as outlined earlier sections covering versioning details to help ensure users are able to understand each release independently of one another. + +It can sometimes be useful to test documentation builds locally before proposing changes within a pull request. +See below for some examples of how to build documentation locally. + +```shell +# build single-version sphinx documentation +# (useful for troubleshooting potential issues) +uv run sphinx-build docs/src docs/build + +# build multi-version sphinx documentation +# (used in production) +uv run sphinx-multiversion docs/src docs/build +``` diff --git a/docs/src/index.md b/docs/src/index.md new file mode 100644 index 0000000..a73d3d1 --- /dev/null +++ b/docs/src/index.md @@ -0,0 +1,18 @@ + + +```{include} ../../README.md +--- +relative-docs: docs/src/ +relative-images: +--- +``` + +```{toctree} +--- +caption: 'Contents:' +maxdepth: 3 +--- +python-api +contributing +code_of_conduct +``` diff --git a/docs/src/python-api.md b/docs/src/python-api.md new file mode 100644 index 0000000..0108834 --- /dev/null +++ b/docs/src/python-api.md @@ -0,0 +1,30 @@ +# Python API + +```{eval-rst} +nviz.image +------------------- + +.. automodule:: src.nviz.image + :members: + :private-members: + :undoc-members: + :show-inheritance: + +nviz.image_meta +------------------- + +.. automodule:: src.nviz.image_meta + :members: + :private-members: + :undoc-members: + :show-inheritance: + +nviz.view +------------------- + +.. automodule:: src.nviz.view + :members: + :private-members: + :undoc-members: + :show-inheritance: +``` diff --git a/justfile b/justfile new file mode 100644 index 0000000..c0d0156 --- /dev/null +++ b/justfile @@ -0,0 +1,58 @@ +# justfile for common project commands +# see here for more information: https://github.com/casey/just + +# find system default shell +hashbang := if os() == 'macos' { + '/usr/bin/env zsh' +} else { + '/usr/bin/env bash' +} + +# show a list of just commands for this project +default: + @just --list + +# install the project for development purposes +@setup: + #!{{hashbang}} + uv pip install '.' + +# run testing on development source +@test: + #!{{hashbang}} + uv run pre-commit run -a + uv run pytest + +# run tiff to omezarr example with real data +@tiff_to_zarr: + #!{{hashbang}} + uv run python src/raw_organoid_images_to_omezarr/tiff_to_omezarr.py + +@tiff_to_ometiff: + #!{{hashbang}} + uv run python src/raw_organoid_images_to_omezarr/tiff_to_ometiff.py + +@tiff_to_ometiff_to_napari: + #!{{hashbang}} + uv run python src/raw_organoid_images_to_omezarr/tiff_to_ometiff.py + uv run python src/raw_organoid_images_to_omezarr/ometiff_to_napari.py + +@tiff_to_ometiff_to_avivator: + #!{{hashbang}} + uv run python src/raw_organoid_images_to_omezarr/tiff_to_ometiff.py + uv run python src/raw_organoid_images_to_omezarr/ometiff_to_avivator.py + +@tiff_to_zarr_napari: + #!{{hashbang}} + uv run python src/raw_organoid_images_to_omezarr/tiff_to_omezarr.py + uv run python src/raw_organoid_images_to_omezarr/zarr_to_napari.py + +@tiff_to_zarr_neuroglancer: + #!{{hashbang}} + uv run python src/raw_organoid_images_to_omezarr/tiff_to_omezarr.py + uv run python src/raw_organoid_images_to_omezarr/zarr_to_neuroglancer.py + +# run tiff to omezarr example with randomized data +@randomized_to_omezarr: + #!{{hashbang}} + uv run python src/raw_organoid_images_to_omezarr/randomized_to_omezarr.py diff --git a/pyproject.toml b/pyproject.toml new file mode 100644 index 0000000..b25784f --- /dev/null +++ b/pyproject.toml @@ -0,0 +1,84 @@ +[build-system] +build-backend = "setuptools.build_meta" +requires = [ "setuptools>=64", "setuptools-scm>=8" ] + +[project] +name = "nviz" +description = "A tool for creating and visualizing n-dimensional microscopy images." +readme = "README.md" +requires-python = ">=3.11" +classifiers = [ + "Programming Language :: Python :: 3 :: Only", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", +] +dynamic = [ "version" ] +dependencies = [ + "napari[all]>=0.5.5", + "napari-ome-zarr>=0.6.1", + "numpy<2.1", + "ome-zarr>=0.10.2", + "tifffile>=2024.12.12", + "xmltodict>=0.14.2", + "zarr>=2.18.4", +] + +[dependency-groups] +# dependency groups for uv +dev = [ + "coverage>=7.6.10", + "myst-parser>=4", + "pre-commit>=4.0.1", + "pydata-sphinx-theme>=0.16.1", + "pytest>=8.3.4", + "setuptools-scm>=8.1", + "sphinx>=8.1.3", +] + +[tool.setuptools_scm] +root = "." +version_scheme = "no-guess-dev" +version_file = "src/nviz/_version.py" + +[tool.ruff] +target-version = "py38" +line-length = 88 +fix = true +lint.select = [ + # flake8-builtins + "A", + # flake8-annotations + "ANN", + # flake8-comprehensions + "C4", + # mccabe + "C90", + # pycodestyle + "E", + # pyflakes + "F", + # isort + "I", + # pylint + "PL", + # ruff + "RUF", + # flake8-simplify + "SIM", + "W", +] +# Ignore `E402` and `F401` (unused imports) in all `__init__.py` files +lint.per-file-ignores."__init__.py" = [ "F401" ] +# ignore typing rules for tests +lint.per-file-ignores."tests/*" = [ "ANN201", "PLR0913", "PLR2004" ] + +[tool.pytest.ini_options] +pythonpath = [ "." ] + +[tool.jupytext] +formats = "ipynb,py:light" + +[tool.vulture] +min_confidence = 90 +paths = [ "src/nviz", "tests" ] diff --git a/reports/coverage/coverage.xml b/reports/coverage/coverage.xml new file mode 100644 index 0000000..8093758 --- /dev/null +++ b/reports/coverage/coverage.xml @@ -0,0 +1,280 @@ + + + + + + /Users/buntend/Documents/work/nVis + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/nviz/image.py b/src/nviz/image.py new file mode 100644 index 0000000..8cd8c29 --- /dev/null +++ b/src/nviz/image.py @@ -0,0 +1,324 @@ +""" +Experiment with GFF image stacks to OME-ZARR with display in Napari. +""" + +import os +import pathlib +from itertools import groupby +from typing import Dict, List, Optional, Tuple, Union + +import numpy as np +import tifffile as tiff +import zarr +from ome_zarr.io import parse_url as zarr_parse_url +from ome_zarr.writer import write_image as zarr_write_image + +from .image_meta import extract_z_slice_number_from_filename, generate_ome_xml + + +def image_set_to_arrays( + image_dir: str, + label_dir: Optional[str], + channel_map: Dict[str, str], + ignore: Optional[List[str]] = ["Merge"], +) -> Dict[str, Dict[str, np.ndarray]]: + """ + Read a set of images as an array of images. + We follow a convention of splitting the following + into separate nested dictionaries for use by + other functions within this project. + + - "images": original images + - "labels": images which represent objects of interest + within the original "images" + + Args: + image_dir (str): + Directory containing TIFF image files. + label_dir (Optional[str]): + Directory containing label TIFF files. + channel_map (Dict[str, str]): + Mapping from filename codes to channel names. + ignore (Optional[List[str]]): + List of filename codes to ignore. + + Returns: + Dict[str, Dict[str, np.ndarray]]: + A dictionary containing two keys: "images" and "labels". + Each key maps to another dictionary where the keys are + channel names and the values are numpy arrays of images. + """ + # build a reference to the observations + zstack_arrays = { + "images": { + channel_map.get(filename_code, f"Unknown_{filename_code}"): np.stack( + [ + tiff.imread(tiff_file.path).astype(np.uint16) + for tiff_file in sorted( + files, + key=lambda x: extract_z_slice_number_from_filename(x.name), + ) + ] + ).astype(np.uint16) + for filename_code, files in groupby( + sorted( + [ + file + for file in os.scandir(image_dir) + if (file.name.endswith(".tif") or file.name.endswith(".tiff")) + and ( + file.name.split("_")[1] not in ignore + if ignore is not None + else True + ) + ], + key=lambda x: x.name.split("_")[1], + ), + key=lambda x: x.name.split("_")[1], + ) + } + } + + if label_dir: + zstack_arrays["labels"] = { + f"{pathlib.Path(label_name).stem} (labels)": tiff.imread( + next(iter(file)).path + ).astype(np.uint16) + for label_name, file in groupby( + sorted( + [ + file + for file in os.scandir(label_dir) + if (file.name.endswith(".tif") or file.name.endswith(".tiff")) + and ( + file.name.split("_")[0] not in ignore + if ignore is not None + else True + ) + ], + key=lambda x: x.name.split("_")[0], + ), + key=lambda x: x.name.split("_")[0], + ) + } + + return zstack_arrays + + +def tiff_to_zarr( # noqa: PLR0913 + image_dir: str, + label_dir: Optional[str], + output_path: str, + channel_map: Dict[str, str], + scaling_values: Union[List[int], Tuple[int]], + ignore: Optional[List[str]], +) -> str: + """ + Convert TIFF files to OME-Zarr format. + + Args: + image_dir (str): + Directory containing TIFF image files. + label_dir (Optional[str]): + Directory containing label TIFF files. + output_path (str): + Path to save the output OME-Zarr file. + channel_map (Dict[str, str]): + Mapping from filename codes to channel names. + scaling_values (Union[List[int], Tuple[int]]): + Scaling values for the images. + ignore (Optional[List[str]]): + List of filename codes to ignore. + + Returns: + str: Path to the output OME-Zarr file. + """ + + # except on dir already existing + if pathlib.Path(output_path).is_dir(): + raise FileExistsError( + ( + f"Output path {output_path} already exists." + "Please remove before creating a new Zarr." + ) + ) + + if not pathlib.Path(image_dir).is_dir(): + raise NotADirectoryError(f"Image directory {image_dir} does not exist.") + + # build a reference to the observations + frame_zstacks = image_set_to_arrays( + image_dir=image_dir, label_dir=label_dir, channel_map=channel_map, ignore=ignore + ) + + # Parse URL and ensure store is compatible + store = zarr_parse_url(output_path, mode="w").store + # Ensure we are working with a Zarr group + root = zarr.group(store, overwrite=True) + + # create scaling metadata + scale_metadata = [ + { + "datasets": [ + { + "path": "0", # Path to the dataset + "coordinateTransformations": [ + { + "type": "scale", + "scale": list(scaling_values), + } # Apply scaling values + ], + } + ], + "axes": [ + { + "name": "z", + "unit": "micrometer", + "type": "space", + }, # Define the z-axis + { + "name": "y", + "unit": "micrometer", + "type": "space", + }, # Define the y-axis + { + "name": "x", + "unit": "micrometer", + "type": "space", + }, # Define the x-axis + ], + } + ] + + # Write each channel separately to the Zarr file with no compression + # Save images to OME-Zarr format + images_group = root.create_group("images") + for channel, stack in frame_zstacks["images"].items(): + zarr_write_image( + image=stack, + group=(group := images_group.create_group(channel)), + axes="zyx", # Specify the axes order for each channel + dtype="uint16", # Ensure the dtype is set correctly + scaler=None, # Disable scaler + ) + # Set the units attribute for the group to "micrometers" + group.attrs["units"] = "micrometers" + + # Define the multiscales metadata for the group + group.attrs["multiscales"] = scale_metadata + + if label_dir: + # Save masks to OME-Zarr format + labels_group = root.create_group("labels") + for compartment_name, stack in frame_zstacks["labels"].items(): + zarr_write_image( + image=stack, + group=(group := labels_group.create_group(compartment_name)), + axes="zyx", # Specify the axes order for each mask + dtype="uint16", # Ensure the dtype is set correctly + scaler=None, # Disable scaler + ) + # Set the units attribute for the group to "micrometers" + group.attrs["units"] = "micrometers" + + # Define the multiscales metadata for the group + group.attrs["multiscales"] = scale_metadata + + return output_path + + +def tiff_to_ometiff( # noqa: PLR0913 + image_dir: str, + label_dir: Optional[str], + output_path: str, + channel_map: Dict[str, str], + scaling_values: Union[List[int], Tuple[int]], + ignore: Optional[List[str]], +) -> str: + """ + Convert TIFF files to OME-TIFF format. + + Args: + image_dir (str): + Directory containing TIFF image files. + label_dir (Optional[str]): + Directory containing label TIFF files. + output_path (str): + Path to save the output OME-TIFF file. + channel_map (Dict[str, str]): + Mapping from filename codes to channel names. + scaling_values (Union[List[int], Tuple[int]]): + Scaling values for the images. + ignore (Optional[List[str]]): + List of filename codes to ignore. + + Returns: + str: Path to the output OME-TIFF file. + """ + + # except on dir already existing + if pathlib.Path(output_path).is_file(): + raise FileExistsError( + ( + f"Output path {output_path} already exists." + "Please remove before creating a new OME-TIFF." + ) + ) + + if not pathlib.Path(image_dir).is_dir(): + raise NotADirectoryError(f"Image directory {image_dir} does not exist.") + + frame_zstacks = image_set_to_arrays( + image_dir=image_dir, label_dir=label_dir, channel_map=channel_map, ignore=ignore + ) + + # Prepare the data for writing + images_data = [] + labels_data = [] + channel_names = [] + label_names = [] + + # Collect image data + for channel, stack in frame_zstacks["images"].items(): + images_data.append(stack) + channel_names.append(channel) + + # Collect label data + if label_dir: + for compartment_name, stack in frame_zstacks["labels"].items(): + labels_data.append(stack) + label_names.append(f"{compartment_name} (labels)") + + # Stack the images and labels along a new axis for channels + images_data = np.stack(images_data, axis=0) + if labels_data: + labels_data = np.stack(labels_data, axis=0) + combined_data = np.concatenate((images_data, labels_data), axis=0) + combined_channel_names = channel_names + label_names + else: + combined_data = images_data + combined_channel_names = channel_names + + # Generate OME-XML metadata + ome_metadata = { + "SizeC": combined_data.shape[0], + "SizeZ": combined_data.shape[1], + "SizeY": combined_data.shape[2], + "SizeX": combined_data.shape[3], + "PhysicalSizeX": scaling_values[2], + "PhysicalSizeY": scaling_values[1], + "PhysicalSizeZ": scaling_values[0], + # note: we use 7-bit ascii compatible characters below + # due to tifffile limitations + "PhysicalSizeXUnit": "um", + "PhysicalSizeYUnit": "um", + "PhysicalSizeZUnit": "um", + "Channel": [{"Name": name} for name in combined_channel_names], + } + ome_xml = generate_ome_xml(ome_metadata) + + # Write the combined data to a single OME-TIFF + with tiff.TiffWriter(output_path, bigtiff=True) as tif: + tif.write(combined_data, description=ome_xml, photometric="minisblack") + + return output_path diff --git a/src/nviz/image_meta.py b/src/nviz/image_meta.py new file mode 100644 index 0000000..48ac214 --- /dev/null +++ b/src/nviz/image_meta.py @@ -0,0 +1,117 @@ +""" +Viewing utilities for GFF 3D organoid project +""" + +import re +import xml.etree.ElementTree as ET +from typing import Dict, Optional, Tuple +from xml.etree.ElementTree import Element, SubElement, tostring + + +def extract_z_slice_number_from_filename(filename: str) -> int: + """ + Extracts a z-slice number from a filename. + Follows conventions from images which are produced + to our knowledge by ZEISS LSM 880 with Airyscan + microscope output. + + Assumes the z-slice number + is a zero-padded number in the filename + with the pattern '_ZS###_'. + + Args: + filename (str): + The name of the file from which to extract the z-slice number. + + Returns: + int: + The extracted z-slice number. Returns 0 if the pattern is not found. + """ + match = re.search(r"_ZS(\d+)_", filename) + return int(match.group(1)) if match else 0 + + +def gather_scaling_info_from_scaninfoxml( + xml_file: str, +) -> Tuple[Optional[float], Optional[float], Optional[float]]: + """ + Reads the scan information from an XML file and + returns the values of ZStackSpacingMicrons, + MicronsPerPixelY, and MicronsPerPixelX. + + This function specifically caters to a file named + ScanInfo.xml which is included to our knowledge within + ZEISS LSM 880 with Airyscan microscope output (and perhaps + others). + + Args: + xml_file (str): + Path to the XML file. + + Returns: + Tuple[Optional[float], Optional[float], Optional[float]]: + A tuple containing the values of + ZStackSpacingMicrons, MicronsPerPixelY, + and MicronsPerPixelX. If a value is not found, + it will be None. + """ + tree = ET.parse(xml_file) + root = tree.getroot() + + microns_per_pixel_y: Optional[float] = None + microns_per_pixel_x: Optional[float] = None + z_stack_spacing_microns: Optional[float] = None + + for setting in root.findall(".//Setting"): + param = setting.get("Parameter") + if param == "MicronsPerPixelY": + microns_per_pixel_y = float(setting.text) + elif param == "MicronsPerPixelX": + microns_per_pixel_x = float(setting.text) + elif param == "ZStackSpacingMicrons": + z_stack_spacing_microns = float(setting.text) + + return (z_stack_spacing_microns, microns_per_pixel_y, microns_per_pixel_x) + + +def generate_ome_xml(metadata: Dict) -> str: + """ + Generate OME-XML metadata for use within an OME-TIFF file. + + Args: + metadata (Dict): Dictionary containing metadata. + + Returns: + str: OME-XML string. + """ + ome = Element("OME", xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06") + image = SubElement(ome, "Image", ID="Image:0") + pixels = SubElement( + image, + "Pixels", + { + "ID": "Pixels:0", + "Type": "uint16", + "DimensionOrder": "CZYX", + "SizeC": str(metadata["SizeC"]), + "SizeZ": str(metadata["SizeZ"]), + "SizeY": str(metadata["SizeY"]), + "SizeX": str(metadata["SizeX"]), + "PhysicalSizeX": str(metadata["PhysicalSizeX"]), + "PhysicalSizeY": str(metadata["PhysicalSizeY"]), + "PhysicalSizeZ": str(metadata["PhysicalSizeZ"]), + "PhysicalSizeXUnit": metadata["PhysicalSizeXUnit"], + "PhysicalSizeYUnit": metadata["PhysicalSizeYUnit"], + "PhysicalSizeZUnit": metadata["PhysicalSizeZUnit"], + }, + ) + for i, channel in enumerate(metadata["Channel"]): + SubElement( + pixels, + "Channel", + { + "ID": f"Channel:0:{i}", + "Name": channel["Name"], + }, + ) + return tostring(ome, encoding="unicode") diff --git a/src/nviz/view.py b/src/nviz/view.py new file mode 100644 index 0000000..3c45ee7 --- /dev/null +++ b/src/nviz/view.py @@ -0,0 +1,137 @@ +""" +Utilities for viewing n-dimensional data +""" + +import logging +from typing import Optional + +import napari +import tifffile as tiff +import xmltodict +import zarr + +logger = logging.getLogger(__name__) + + +def view_zarr_with_napari( + zarr_dir: str, scaling_values: tuple, headless: bool = False +) -> Optional[napari.Viewer]: + """ + View a Zarr file created with nviz through napari. + + Args: + zarr_dir (str): + The path to the Zarr file. + scaling_values (tuple): + The scaling values for the image. + headless (bool): + Whether to run in headless mode + (where we don't run napari and hand + back the viewer object instead). + + Returns: + Optional[napari.Viewer]]: + The napari viewer object if not headless, + otherwise None. + """ + # Check Zarr file structure + frame_zarr = zarr.open(zarr_dir, mode="r") + + # Visualize with napari, start in 3d mode + viewer = napari.Viewer(ndisplay=3) + + # Iterate through each channel in the Zarr file + for channel_name in sorted(frame_zarr["images"].keys(), reverse=True): + viewer.add_image( + frame_zarr["images"][channel_name]["0"][:], + name=channel_name, + scale=scaling_values, + ) + + # Iterate through each compartment in the Zarr file and add labels to Napari + if "labels" in frame_zarr: + for label_name in sorted(frame_zarr["labels"].keys(), reverse=True): + viewer.add_labels( + frame_zarr["labels"][label_name]["0"][:], + name=f"{label_name} (label)", + scale=scaling_values, + ) + + if not headless: + # Start the Napari event loop + napari.run() + else: + logger.warning( + "Running view in headless mode and returning a napari viewer object." + ) + + # otherwise return the viewer + return viewer + + +def view_ometiff_with_napari( + ometiff_path: str, scaling_values: tuple, headless: bool = False +) -> Optional[napari.Viewer]: + """ + View a OME-TIFF file created with nviz through napari. + + Args: + ometiff_path (str): + The path to the OME-TIFF file. + scaling_values (tuple): + The scaling values for the image. + headless (bool): + Whether to run in headless mode + (where we don't run napari and hand + back the viewer object instead). + + Returns: + Optional[napari.Viewer]]: + The napari viewer object if not headless, + otherwise None. + """ + + # Visualize with napari, start in 3d mode + viewer = napari.Viewer(ndisplay=3) + + # Read and add layers from the combined OME-TIFF file + with tiff.TiffFile(ometiff_path) as tif: + combined_data = tif.asarray() + metadata = xmltodict.parse(tif.ome_metadata) + channel_names = [ + channel["@Name"] + for channel in metadata["OME"]["Image"]["Pixels"]["Channel"] + ] + + # First, add image layers + for i, (channel_data, channel_name) in enumerate( + zip(combined_data, channel_names) + ): + if "(labels)" not in channel_name: + viewer.add_image( + channel_data, + name=channel_name, + scale=scaling_values, + ) + + # Then, add label layers + for i, (channel_data, channel_name) in enumerate( + zip(combined_data, channel_names) + ): + if "(labels)" in channel_name: + viewer.add_labels( + channel_data, + name=channel_name, + scale=scaling_values, + ) + + if not headless: + # Start the Napari event loop + napari.run() + else: + logger.warning( + "Running view in headless mode and returning a napari viewer object." + ) + + # otherwise return the viewer + return viewer diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/data/random_tiff_z_stacks/ScanInfo.xml b/tests/data/random_tiff_z_stacks/ScanInfo.xml new file mode 100644 index 0000000..0a7c7f3 --- /dev/null +++ b/tests/data/random_tiff_z_stacks/ScanInfo.xml @@ -0,0 +1,16 @@ + + + + 0.0.0.0 + + + 0.1006 + 0.1006 + + + + + 1.000 + + + diff --git a/tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS000.tif b/tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS000.tif new file mode 100644 index 0000000..2ea5eee Binary files /dev/null and b/tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS000.tif differ diff --git a/tests/data/random_tiff_z_stacks/Z99/Z99_111_ZS001.tif 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/dev/null +++ b/tests/data/random_tiff_z_stacks/generate_data.py @@ -0,0 +1,128 @@ +""" +Generates example z-stack TIFF files with randomized data for testing. +""" + +import pathlib +from typing import Tuple + +import numpy as np +import tifffile as tiff + +# human readable channel names +channels = [ + "Channel A", + "Channel B", + "Channel C", + "Channel D", + "Channel E", +] + +# map human readable channel names to machine ones +# which simulate what is produced by the microscope +# or teams who create images. +channels_map = { + "Channel A": "111", + "Channel B": "222", + "Channel C": "333", + "Channel D": "444", + "Channel E": "555", +} + +# gather a relative path +relpath = pathlib.Path(__file__).parent + +# Set common static scaling values +scaling_values = (1.0, 0.1, 0.1) # (z, y, x) in microns + +# Generate random data for z-slices +num_z_slices = 10 +image_shape = (100, 100) # Example shape, adjust as needed + +# create random data for each channel +channels = { + channel: [ + np.random.randint(0, 65535, size=image_shape, dtype=np.uint16) + for _ in range(num_z_slices) + ] + for channel in channels +} + +# Debug: show channel keys and file counts +print(channels.keys()) +for channel, files in channels.items(): + print(f"Channel: {channel}, Slices: {len(files)}") + +# Define the output directory +output_dir = relpath / "Z99" +pathlib.Path(output_dir).mkdir(exist_ok=True) + +# Write each z-slice as a separate TIFF file +for channel, z_slices in channels.items(): + for z_index, z_slice in enumerate(z_slices): + filename = f"Z99_{channels_map[channel]}_ZS{z_index:03d}.tif" + filepath = output_dir / filename + tiff.imwrite(filepath, z_slice) + +print(f"TIFF files written to {output_dir}") + + +# Create a single multidimensional TIFF file with sphere shapes +def create_sphere_image( + shape: Tuple[int, int, int], radius: int, center: Tuple[int, int, int] +) -> np.ndarray: + """Create a 3D image with a sphere. + + Args: + shape (Tuple[int, int, int]): The shape of the 3D image (z, y, x). + radius (int): The radius of the sphere. + center (Tuple[int, int, int]): The center of the sphere (z, y, x). + + Returns: + np.ndarray: A 3D image with a sphere. + """ + z, y, x = np.indices(shape) + distance = np.sqrt( + (z - center[0]) ** 2 + (y - center[1]) ** 2 + (x - center[2]) ** 2 + ) + sphere = (distance <= radius).astype(np.uint16) * 65535 + return sphere + + +sphere_radius = 20 +sphere_center = (num_z_slices // 2, image_shape[0] // 2, image_shape[1] // 2) +sphere_image = create_sphere_image( + (num_z_slices, *image_shape), sphere_radius, sphere_center +) + +# create a path for labels +label_path = output_dir.parent / "labels" +pathlib.Path(label_path).mkdir(exist_ok=True) + +# Write the sphere image as a single multidimensional TIFF file +sphere_tiff_path = label_path / "compartment.tif" +tiff.imwrite(sphere_tiff_path, sphere_image, photometric="minisblack") + +print(f"Sphere TIFF file written to {sphere_tiff_path}") + +scaninfo_file = relpath / "ScanInfo.xml" + +with open(scaninfo_file, "w") as file: + file.write( + """ + + + 0.0.0.0 + + + 0.1006 + 0.1006 + + + + + 1.000 + + + +""" + ) diff --git a/tests/data/random_tiff_z_stacks/labels/compartment.tif b/tests/data/random_tiff_z_stacks/labels/compartment.tif new file mode 100644 index 0000000..8a5c3bd Binary files /dev/null and b/tests/data/random_tiff_z_stacks/labels/compartment.tif differ diff --git a/tests/test_image.py b/tests/test_image.py new file mode 100644 index 0000000..c13e97e --- /dev/null +++ b/tests/test_image.py @@ -0,0 +1,161 @@ +""" +Tests for the image module. +""" + +import pathlib +import xml.etree.ElementTree as ET +from pathlib import Path +from typing import Dict, List, Optional, Tuple + +import pytest +import tifffile as tiff +import zarr + +from nviz.image import image_set_to_arrays, tiff_to_ometiff, tiff_to_zarr +from tests.utils import example_data_for_image_tests + + +@pytest.mark.parametrize( + ( + "image_dir, label_dir, output_path, channel_map, " + "scaling_values, ignore, expected_labels" + ), + example_data_for_image_tests, +) +def test_image_set_to_arrays( + image_dir: str, + label_dir: Optional[str], + output_path: str, + channel_map: Dict[str, str], + scaling_values: Tuple[int, int, int], + ignore: Optional[List[str]], + expected_labels: List[str], +): + # Call the function + result = image_set_to_arrays( + image_dir=image_dir, label_dir=label_dir, channel_map=channel_map, ignore=ignore + ) + + # check that we have all keys + if ignore is None: + all(channel not in result["images"] for channel in channel_map.values()) + + # check that we ignored what we should have + elif ignore is not None: + assert all(ignored not in result["images"] for ignored in ignore) + + +@pytest.mark.parametrize( + ( + "image_dir, label_dir, output_path, channel_map, " + "scaling_values, ignore, expected_labels" + ), + example_data_for_image_tests, +) +def test_tiff_to_zarr( + image_dir: str, + label_dir: Optional[str], + output_path: str, + channel_map: Dict[str, str], + scaling_values: Tuple[int, int, int], + ignore: Optional[List[str]], + expected_labels: List[str], + tmp_path: pathlib.Path, +): + """ + Tests the tiff_to_zarr function. + """ + + output_path = tiff_to_zarr( + image_dir=image_dir, + label_dir=label_dir, + output_path=f"{tmp_path}/{output_path}", + channel_map=channel_map, + scaling_values=scaling_values, + ignore=ignore, + ) + + # Check if the output path exists + assert Path(output_path).exists() + + # Check if the Zarr structure is correct + zarr_root = zarr.open(output_path, mode="r") + assert "images" in list(zarr_root.keys()) + + # check if we have labels if we supplied them + if label_dir is not None: + assert "labels" in zarr_root + + for channel in channel_map.values(): + if ignore is not None and channel not in [ + channel_map[ignored] for ignored in ignore + ]: + assert channel in list(zarr_root["images"]) + + # check if we have labels if we supplied them + if label_dir is not None: + assert all( + expected_label in list(zarr_root["labels"].keys()) + for expected_label in expected_labels + ) + + +@pytest.mark.parametrize( + ( + "image_dir, label_dir, output_path, channel_map, " + "scaling_values, ignore, expected_labels" + ), + example_data_for_image_tests, +) +def test_tiff_to_ometiff( + image_dir: str, + label_dir: Optional[str], + output_path: str, + channel_map: Dict[str, str], + scaling_values: Tuple[int, int, int], + ignore: Optional[List[str]], + expected_labels: List[str], + tmp_path: pathlib.Path, +): + """ + Tests the tiff_to_ometiff function. + """ + + output_path = tiff_to_ometiff( + image_dir=image_dir, + label_dir=label_dir, + output_path=f"{tmp_path}/{output_path}", + channel_map=channel_map, + scaling_values=scaling_values, + ignore=ignore, + ) + + # Check if the output path exists + assert Path(output_path).exists() + + # Read the OME-TIFF file and check its contents + with tiff.TiffFile(output_path) as tif: + assert len(tif.pages) > 0 + metadata = tif.ome_metadata + assert metadata is not None + + # Parse the OME-XML metadata + root = ET.fromstring(metadata) + channels = root.find( + ".//{http://www.openmicroscopy.org/Schemas/OME/2016-06}Pixels" + ).findall("{http://www.openmicroscopy.org/Schemas/OME/2016-06}Channel") + + # Check the metadata for channels + for channel in channel_map.values(): + if ignore is not None and channel not in [ + channel_map[ignored] for ignored in ignore + ]: + assert any(channel == ch.get("Name") for ch in channels) + + # Check the metadata for physical sizes + pixels = root.find( + ".//{http://www.openmicroscopy.org/Schemas/OME/2016-06}Pixels" + ) + assert pixels.get("PhysicalSizeX") == str(scaling_values[2]) + assert pixels.get("PhysicalSizeY") == str(scaling_values[1]) + assert pixels.get("PhysicalSizeZ") == str(scaling_values[0]) diff --git a/tests/test_image_meta.py b/tests/test_image_meta.py new file mode 100644 index 0000000..990a1b4 --- /dev/null +++ b/tests/test_image_meta.py @@ -0,0 +1,183 @@ +""" +Tests for nviz/view.py +""" + +import pathlib +from typing import Dict, List, Optional, Tuple, Union +from xml.etree.ElementTree import fromstring + +import pytest + +from nviz.image_meta import ( + extract_z_slice_number_from_filename, + gather_scaling_info_from_scaninfoxml, + generate_ome_xml, +) + + +@pytest.mark.parametrize( + "filename, expected", + [ + ("C10-1_405_ZS034_FOV-1.tif", 34), + ("C10-1_405_ZS018_FOV-1.tif", 18), + ("C10-1_405_ZS039_FOV-1.tif", 39), + ("C10-1_405_ZS043_FOV-1.tif", 43), + ("C10-1_405_ZS033_FOV-1.tif", 33), + ("C10-1_405_ZS027_FOV-1.tif", 27), + ("C10-1_405_ZS006_FOV-1.tif", 6), + ("C10-1_405_FOV-1.tif", 0), # No ZS pattern + ("C10-1_405_ZS_FOV-1.tif", 0), # Incomplete ZS pattern + ], +) +def test_extract_z_slice_number_from_filename(filename: str, expected: int): + """ + Tests extract_z_slice_number_from_filename + """ + assert extract_z_slice_number_from_filename(filename) == expected + + +@pytest.mark.parametrize( + "xml_content, expected", + [ + ( + """ + + + + 0.1006 + 0.1006 + + + + + 1.000 + + + """, + (1.000, 0.1006, 0.1006), + ), + ( + """ + + + + 0.200 + 0.200 + + + + + 2.000 + + + """, + (2.000, 0.200, 0.200), + ), + ( + """ + + + + 0.300 + + + + + 3.000 + + + """, + (3.000, None, 0.300), + ), + ], +) +def test_gather_scaling_info_from_scaninfoxml( + xml_content: str, + expected: Tuple[Optional[float], Optional[float], Optional[float]], + tmp_path: pathlib.Path, +): + """ + Tests gather_scaling_info_from_scaninfoxml + """ + + # write a temp file + xml_file = tmp_path / "temp_scaninfo.xml" + xml_file.write_text(xml_content) + + # check the results + assert gather_scaling_info_from_scaninfoxml(xml_file) == expected + + +@pytest.mark.parametrize( + "metadata, expected_channels", + [ + ( + { + "SizeC": 3, + "SizeZ": 10, + "SizeY": 512, + "SizeX": 512, + "PhysicalSizeX": 0.1, + "PhysicalSizeY": 0.1, + "PhysicalSizeZ": 1.0, + "PhysicalSizeXUnit": "um", + "PhysicalSizeYUnit": "um", + "PhysicalSizeZUnit": "um", + "Channel": [ + {"Name": "Channel A"}, + {"Name": "Channel B"}, + {"Name": "Channel C"}, + ], + }, + ["Channel A", "Channel B", "Channel C"], + ), + ( + { + "SizeC": 2, + "SizeZ": 5, + "SizeY": 256, + "SizeX": 256, + "PhysicalSizeX": 0.2, + "PhysicalSizeY": 0.2, + "PhysicalSizeZ": 2.0, + "PhysicalSizeXUnit": "um", + "PhysicalSizeYUnit": "um", + "PhysicalSizeZUnit": "um", + "Channel": [ + {"Name": "Channel X"}, + {"Name": "Channel Y"}, + ], + }, + ["Channel X", "Channel Y"], + ), + ], +) +def test_generate_ome_xml( + metadata: Dict[str, Union[int, str]], expected_channels: List[str] +): + ome_xml = generate_ome_xml(metadata) + + # Parse the generated OME-XML + root = fromstring(ome_xml) + + # Verify the Pixels attributes + pixels = root.find(".//{http://www.openmicroscopy.org/Schemas/OME/2016-06}Pixels") + assert pixels is not None + assert pixels.get("SizeC") == str(metadata["SizeC"]) + assert pixels.get("SizeZ") == str(metadata["SizeZ"]) + assert pixels.get("SizeY") == str(metadata["SizeY"]) + assert pixels.get("SizeX") == str(metadata["SizeX"]) + assert pixels.get("PhysicalSizeX") == str(metadata["PhysicalSizeX"]) + assert pixels.get("PhysicalSizeY") == str(metadata["PhysicalSizeY"]) + assert pixels.get("PhysicalSizeZ") == str(metadata["PhysicalSizeZ"]) + assert pixels.get("PhysicalSizeXUnit") == metadata["PhysicalSizeXUnit"] + assert pixels.get("PhysicalSizeYUnit") == metadata["PhysicalSizeYUnit"] + assert pixels.get("PhysicalSizeZUnit") == metadata["PhysicalSizeZUnit"] + + # Verify the Channel names + channels = pixels.findall( + "{http://www.openmicroscopy.org/Schemas/OME/2016-06}Channel" + ) + assert len(channels) == len(expected_channels) + for i, channel in enumerate(channels): + assert channel.get("Name") == expected_channels[i] diff --git a/tests/test_view.py b/tests/test_view.py new file mode 100644 index 0000000..c964eab --- /dev/null +++ b/tests/test_view.py @@ -0,0 +1,86 @@ +""" +Tests for the view module +""" + +import pathlib +from typing import Dict, List, Optional, Tuple + +import pytest + +from nviz.image import tiff_to_ometiff, tiff_to_zarr +from nviz.view import view_ometiff_with_napari, view_zarr_with_napari +from tests.utils import example_data_for_image_tests + + +@pytest.mark.parametrize( + ( + "image_dir, label_dir, output_path, channel_map, " + "scaling_values, ignore, expected_labels" + ), + example_data_for_image_tests, +) +def test_view_zarr_with_napari( + image_dir: str, + label_dir: Optional[str], + output_path: str, + channel_map: Dict[str, str], + scaling_values: Tuple[int, int, int], + ignore: Optional[List[str]], + expected_labels: List[str], + tmp_path: pathlib.Path, +): + """ + Tests the view_zarr_with_napari function. + """ + + zarr_dir = tiff_to_zarr( + image_dir=image_dir, + label_dir=label_dir, + output_path=f"{tmp_path}/{output_path}", + channel_map=channel_map, + scaling_values=scaling_values, + ignore=ignore, + ) + + # Call the function + view_zarr_with_napari( + zarr_dir=zarr_dir, scaling_values=scaling_values, headless=True + ) + + +@pytest.mark.parametrize( + ( + "image_dir, label_dir, output_path, channel_map, " + "scaling_values, ignore, expected_labels" + ), + example_data_for_image_tests, +) +def test_view_ometiff_with_napari( + image_dir: str, + label_dir: Optional[str], + output_path: str, + channel_map: Dict[str, str], + scaling_values: Tuple[int, int, int], + ignore: Optional[List[str]], + expected_labels: List[str], + tmp_path: pathlib.Path, +): + """ + Tests the view_ometiff_with_napari function. + """ + + ometiff_path = tiff_to_ometiff( + image_dir=image_dir, + label_dir=label_dir, + output_path=f"{tmp_path}/{output_path}", + channel_map=channel_map, + scaling_values=scaling_values, + ignore=ignore, + ) + + # Call the function + view_ometiff_with_napari( + ometiff_path=ometiff_path, + scaling_values=scaling_values, + headless=True, + ) diff --git a/tests/utils.py b/tests/utils.py new file mode 100644 index 0000000..d760a7c --- /dev/null +++ b/tests/utils.py @@ -0,0 +1,57 @@ +""" +Utilities for testing. +""" + +# data examples for use with pytest parameterized tests +# (creating a data value here because it's simpler to use +# than a fixture inside parameterized tests). +example_data_for_image_tests = [ + # test example data without labels + ( + "tests/data/random_tiff_z_stacks/Z99", + None, + "output.zarr", + { + "111": "Channel A", + "222": "Channel B", + "333": "Channel C", + "444": "Channel D", + "555": "Channel E", + }, + (1.0, 0.1, 0.1), + None, + None, + ), + # test example data with labels + ( + "tests/data/random_tiff_z_stacks/Z99", + "tests/data/random_tiff_z_stacks/labels", + "output.zarr", + { + "111": "Channel A", + "222": "Channel B", + "333": "Channel C", + "444": "Channel D", + "555": "Channel E", + }, + (1.0, 0.1, 0.1), + None, + ["compartment (labels)"], + ), + # test example data with labels and ignore a channel + ( + "tests/data/random_tiff_z_stacks/Z99", + "tests/data/random_tiff_z_stacks/labels", + 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