Compare commits
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main
..
2c5e1ffa9e
| Author | SHA1 | Date | |
|---|---|---|---|
 Wim Pomp
|
2c5e1ffa9e | ||
|
Wim Pomp
|
b5e583f760 |
@@ -1,31 +1,54 @@
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name: Publish
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on: [workflow_dispatch]
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on: [push, pull_request, workflow_call]
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permissions:
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contents: read
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jobs:
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publish_pytest:
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uses: ./.github/workflows/pytest.yml
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pypi_publish:
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crates_io_publish:
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name: Publish (crates.io)
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runs-on: ubuntu-latest
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needs: [ publish_pytest ]
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timeout-minutes: 25
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steps:
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- name: Checkout
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uses: actions/checkout@v6
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- name: Build sdist
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uses: actions/setup-python@v6
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- uses: actions/checkout@v4
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- uses: dtolnay/rust-toolchain@stable
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- name: cargo-release Cache
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id: cargo_release_cache
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uses: actions/cache@v3
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with:
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python-version: "3.12"
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- name: Install build
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run: pip install build
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- name: Build a binary wheel and a source tarball
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run: python -m build
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- name: Publish to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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skip-existing: true
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password: ${{ secrets.PYPI_API_TOKEN }}
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env:
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GITHUB_WORKFLOW_REF: 1.10.1
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path: ~/.cargo/bin/cargo-release
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key: ${{ runner.os }}-cargo-release
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- run: cargo install cargo-release
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if: steps.cargo_release_cache.outputs.cache-hit != 'true'
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- name: cargo login
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run: cargo login ${{ secrets.CRATES_IO_API_TOKEN }}
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# allow-branch HEAD is because GitHub actions switches
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# to the tag while building, which is a detached head
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# Publishing is currently messy, because:
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#
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# * `peace_rt_model_core` exports `NativeError` or `WebError` depending on the target.
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# * `peace_rt_model_web` fails to build when publishing the workspace for a native target.
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# * `peace_rt_model_web` still needs its dependencies to be published before it can be
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# published.
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# * `peace_rt_model_hack` needs `peace_rt_model_web` to be published before it can be
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# published.
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#
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# We *could* pass through `--no-verify` so `cargo` doesn't build the crate before publishing,
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# which is reasonable, since this job only runs after the Linux, Windows, and WASM builds
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# have passed.
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- name: "cargo release publish"
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run: |-
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cargo release \
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publish \
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--workspace \
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--all-features \
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--allow-branch "main" \
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--no-confirm \
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--no-verify \
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--execute
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@@ -1,26 +0,0 @@
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name: PyTest
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on: [push, pull_request, workflow_call]
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permissions:
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contents: read
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jobs:
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pytest:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: [ "3.10", "3.12", "3.14" ]
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os: [ ubuntu-latest ]
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steps:
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- name: Checkout
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uses: actions/checkout@v6
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v6
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install
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run: pip install .[test]
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- name: Test with pytest
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run: pytest
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+73
-6
@@ -1,6 +1,73 @@
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/build/
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/dist/
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/parfor.egg-info/
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/.idea/
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/.pytest_cache/
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._*
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/target
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# Byte-compiled / optimized / DLL files
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__pycache__/
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.pytest_cache/
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*.py[cod]
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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.venv/
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env/
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bin/
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build/
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develop-eggs/
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dist/
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eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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||||
include/
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man/
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venv/
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||||
*.egg-info/
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.installed.cfg
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*.egg
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|
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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pip-selfcheck.json
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.coverage
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.cache
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nosetests.xml
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coverage.xml
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# Translations
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*.mo
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# Mr Developer
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.mr.developer.cfg
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.project
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.pydevproject
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# Rope
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.ropeproject
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# Django stuff:
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*.log
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*.pot
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.DS_Store
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|
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# Sphinx documentation
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docs/_build/
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|
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# PyCharm
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.idea/
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|
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# VSCode
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.vscode/
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|
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# Pyenv
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.python-version
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/Cargo.lock
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+32
@@ -0,0 +1,32 @@
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[package]
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name = "ome-metadata"
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version = "0.1.0"
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edition = "2024"
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rust-version = "1.85.1"
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authors = ["Wim Pomp <w.pomp@nki.nl>"]
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license = "MIT"
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description = "Ome metadata as a rust/python structure."
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homepage = "https://github.com/wimpomp/ome-metadata"
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repository = "https://github.com/wimpomp/ome-metadata"
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readme = "README.md"
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keywords = ["bioformats", "imread", "ome", "metadata"]
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categories = ["multimedia::images", "science"]
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exclude = ["/tests"]
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# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
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[lib]
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name = "ome_metadata"
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crate-type = ["cdylib", "rlib"]
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[dependencies]
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anyhow = "1.0.98"
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serde = { version = "1.0.219", features = ["derive"] }
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quick-xml = { version = "0.37.5", features = ["serialize"] }
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[dependencies.pyo3]
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version = "0.24.2"
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features = ["extension-module", "abi3-py310", "generate-import-lib", "anyhow"]
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optional = true
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[features]
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python = ["dep:pyo3"]
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@@ -1,168 +1,25 @@
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[](https://git.wimpomp.nl/wim/parfor/actions?workflow=pytest.yml)
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# ome-metadata
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# Parfor
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Used to parallelize for-loops using parfor in Matlab? This package allows you to do the same in python.
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Take any normal serial but parallelizable for-loop and execute it in parallel using easy syntax.
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Don't worry about the technical details of using the multiprocessing module, race conditions, queues,
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parfor handles all that. Now powered by [ray](https://pypi.org/project/ray/).
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Open Microscopy XML metadata (https://www.openmicroscopy.org/Schemas/) as a collection of Rust structs and enums, with translation to Python.
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Tested on linux, Windows and OSX with python 3.10 and 3.12.
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## Rust
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```
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use std::fs::read_to_string;
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use ome_metadata::Ome;
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|
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## Why is parfor better than just using multiprocessing?
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- Easy to use
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- Progress bars are built-in
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- Retry the task in the main process upon failure for easy debugging
|
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- Using a modified version of dill when ray fails to serialize an object:
|
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a lot more objects can be used when parallelizing
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let xml = read_to_string($file)?;
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let ome: Ome = xml.parse()?;
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let image = &ome.image.unwrap()[0];
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println!("acquisition date: {:#?}", image.acquisition_date);
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```
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## How it works
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[Ray](https://pypi.org/project/ray/) does all the heavy lifting. Parfor now is just a wrapper around ray, adding
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some ergonomics.
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## Python
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```
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from ome_metadata import Ome
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## Installation
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`pip install parfor`
|
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|
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## Usage
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Parfor decorates a functions and returns the result of that function evaluated in parallel for each iteration of
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an iterator.
|
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|
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## Requires
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numpy, ray, tqdm
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|
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## Arguments
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To functions `parfor.parfor`, `parfor.pmap` and `parfor.gmap`.
|
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|
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### Required:
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fun: function taking arguments: iteration from iterable, other arguments defined in args & kwargs
|
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iterable: iterable or iterator from which an item is given to fun as a first argument
|
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|
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### Optional:
|
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args: tuple with other unnamed arguments to fun
|
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kwargs: dict with other named arguments to fun
|
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total: give the length of the iterator in cases where len(iterator) results in an error
|
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desc: string with description of the progress bar
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bar: bool enable progress bar,
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or a callback function taking the number of passed iterations as an argument
|
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serial: execute in series instead of parallel if True, None (default): let pmap decide
|
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n_processes: number of processes to use,
|
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the parallel pool will be restarted if the current pool does not have the right number of processes
|
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yield_ordered: return the result in the same order as the iterable
|
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yield_index: return the index of the result too
|
||||
allow_output: allow output from subprocesses
|
||||
**bar_kwargs: keyword arguments for tqdm.tqdm
|
||||
|
||||
### Return
|
||||
list with results from applying the function 'fun' to each iteration of the iterable / iterator
|
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|
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## Examples
|
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### Normal serial for loop
|
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<<
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from time import sleep
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|
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a = 3
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fun = []
|
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for i in range(10):
|
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sleep(1)
|
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fun.append(a * i ** 2)
|
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print(fun)
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>> [0, 3, 12, 27, 48, 75, 108, 147, 192, 243]
|
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|
||||
### Using parfor to parallelize
|
||||
<<
|
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from time import sleep
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from parfor import parfor
|
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@parfor(range(10), (3,))
|
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def fun(i, a):
|
||||
sleep(1)
|
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return a * i ** 2
|
||||
print(fun)
|
||||
|
||||
>> [0, 3, 12, 27, 48, 75, 108, 147, 192, 243]
|
||||
|
||||
<<
|
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@parfor(range(10), (3,), bar=False)
|
||||
def fun(i, a):
|
||||
sleep(1)
|
||||
return a * i ** 2
|
||||
print(fun)
|
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|
||||
>> [0, 3, 12, 27, 48, 75, 108, 147, 192, 243]
|
||||
|
||||
### Using parfor in a script/module/.py-file
|
||||
Parfor should never be executed during the import phase of a .py-file. To prevent that from happening
|
||||
use the `if __name__ == '__main__':` structure:
|
||||
|
||||
<<
|
||||
from time import sleep
|
||||
from parfor import parfor
|
||||
|
||||
if __name__ == '__main__':
|
||||
@parfor(range(10), (3,))
|
||||
def fun(i, a):
|
||||
sleep(1)
|
||||
return a * i ** 2
|
||||
print(fun)
|
||||
|
||||
>> [0, 3, 12, 27, 48, 75, 108, 147, 192, 243]
|
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or:
|
||||
|
||||
<<
|
||||
from time import sleep
|
||||
from parfor import parfor
|
||||
|
||||
def my_fun(*args, **kwargs):
|
||||
@parfor(range(10), (3,))
|
||||
def fun(i, a):
|
||||
sleep(1)
|
||||
return a * i ** 2
|
||||
return fun
|
||||
|
||||
if __name__ == '__main__':
|
||||
print(my_fun())
|
||||
|
||||
>> [0, 3, 12, 27, 48, 75, 108, 147, 192, 243]
|
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|
||||
### If you hate decorators not returning a function
|
||||
pmap maps an iterator to a function like map does, but in parallel
|
||||
|
||||
<<
|
||||
from parfor import pmap
|
||||
from time import sleep
|
||||
def fun(i, a):
|
||||
sleep(1)
|
||||
return a * i ** 2
|
||||
print(pmap(fun, range(10), (3,)))
|
||||
|
||||
>> [0, 3, 12, 27, 48, 75, 108, 147, 192, 243]
|
||||
|
||||
### Using generators
|
||||
If iterators like lists and tuples are too big for the memory, use generators instead.
|
||||
Since generators don't have a predefined length, give parfor the length (total) as an argument (optional).
|
||||
|
||||
<<
|
||||
import numpy as np
|
||||
c = (im for im in imagereader)
|
||||
@parfor(c, total=len(imagereader))
|
||||
def fun(im):
|
||||
return np.mean(im)
|
||||
|
||||
>> [list with means of the images]
|
||||
|
||||
# Extra's
|
||||
## `pmap`
|
||||
The function parfor decorates, it's used similarly to `map`, it returns a list with the results.
|
||||
|
||||
## `gmap`
|
||||
Same as pmap, but returns a generator. Useful to use the result as soon as it's generated.
|
||||
|
||||
## `Chunks`
|
||||
Split a long iterator in bite-sized chunks to parallelize
|
||||
|
||||
## `ParPool`
|
||||
More low-level accessibility to parallel execution. Submit tasks and request the result at any time,
|
||||
(although to avoid breaking causality, submit first, then request), use different functions and function
|
||||
arguments for different tasks.
|
||||
|
||||
## `SharedArray`
|
||||
A numpy arrow that can be shared among processes.
|
||||
with open($file) as f:
|
||||
xml = f.read()
|
||||
ome = Ome.from_xml(xml)
|
||||
image = ome.image[0]
|
||||
print(f"acquisition date: {image.acquisition_date}")
|
||||
```
|
||||
@@ -1,720 +0,0 @@
|
||||
from __future__ import annotations
|
||||
|
||||
import logging
|
||||
import os
|
||||
from collections import OrderedDict
|
||||
from contextlib import ExitStack, redirect_stderr, redirect_stdout
|
||||
from functools import wraps
|
||||
from importlib.metadata import version
|
||||
from io import StringIO
|
||||
from multiprocessing.shared_memory import SharedMemory
|
||||
from traceback import format_exc
|
||||
from typing import (
|
||||
Any,
|
||||
Callable,
|
||||
Generator,
|
||||
Hashable,
|
||||
Iterable,
|
||||
Iterator,
|
||||
NoReturn,
|
||||
Optional,
|
||||
Protocol,
|
||||
Sequence,
|
||||
Sized,
|
||||
)
|
||||
|
||||
import numpy as np
|
||||
import ray
|
||||
from numpy.typing import ArrayLike, DTypeLike
|
||||
from ray.remote_function import RemoteFunction
|
||||
from ray.types import ObjectRef
|
||||
from tqdm.auto import tqdm
|
||||
|
||||
from .pickler import dumps, loads
|
||||
|
||||
__version__ = version("parfor")
|
||||
cpu_count = int(os.cpu_count())
|
||||
|
||||
|
||||
class Bar(Protocol):
|
||||
def update(self, n: int = 1) -> None: ...
|
||||
|
||||
|
||||
class SharedArray(np.ndarray):
|
||||
"""Numpy array whose memory can be shared between processes, so that memory use is reduced and changes in one
|
||||
process are reflected in all other processes. Changes are not atomic, so protect changes with a lock to prevent
|
||||
race conditions!
|
||||
"""
|
||||
|
||||
def __new__(
|
||||
cls,
|
||||
shape: int | Sequence[int],
|
||||
dtype: DTypeLike = float,
|
||||
shm: str | SharedMemory = None,
|
||||
offset: int = 0,
|
||||
strides: tuple[int, int] = None,
|
||||
order: str = None,
|
||||
) -> SharedArray:
|
||||
if isinstance(shm, str):
|
||||
shm = SharedMemory(shm)
|
||||
elif shm is None:
|
||||
shm = SharedMemory(create=True, size=int(np.prod(shape) * np.dtype(dtype).itemsize)) # type: ignore
|
||||
new = super().__new__(cls, shape, dtype, shm.buf, offset, strides, order)
|
||||
new.shm = shm
|
||||
return new # type: ignore
|
||||
|
||||
def __reduce__(
|
||||
self,
|
||||
) -> tuple[
|
||||
Callable[[int | Sequence[int], DTypeLike, str], SharedArray],
|
||||
tuple[int | tuple[int, ...], np.dtype, str],
|
||||
]:
|
||||
return self.__class__, (self.shape, self.dtype, self.shm.name)
|
||||
|
||||
def __enter__(self) -> SharedArray:
|
||||
return self
|
||||
|
||||
def __exit__(self, *args: Any, **kwargs: Any) -> None:
|
||||
if hasattr(self, "shm"):
|
||||
self.shm.close()
|
||||
self.shm.unlink()
|
||||
|
||||
def __del__(self) -> None:
|
||||
if hasattr(self, "shm"):
|
||||
self.shm.close()
|
||||
|
||||
def __array_finalize__(self, obj: np.ndarray | None) -> None:
|
||||
if isinstance(obj, np.ndarray) and not isinstance(obj, SharedArray):
|
||||
raise TypeError("view casting to SharedArray is not implemented because right now we need to make a copy")
|
||||
|
||||
@classmethod
|
||||
def from_array(cls, array: ArrayLike) -> SharedArray:
|
||||
"""copy existing array into a SharedArray"""
|
||||
array = np.asarray(array)
|
||||
new = cls(array.shape, array.dtype)
|
||||
new[:] = array[:]
|
||||
return new
|
||||
|
||||
|
||||
class Chunks(Iterable):
|
||||
"""Yield successive chunks from lists.
|
||||
Usage: chunks(list0, list1, ...)
|
||||
chunks(list0, list1, ..., size=s)
|
||||
chunks(list0, list1, ..., number=n)
|
||||
chunks(list0, list1, ..., ratio=r)
|
||||
size: size of chunks, might change to optimize division between chunks
|
||||
number: number of chunks, coerced to 1 <= n <= len(list0)
|
||||
ratio: number of chunks / number of cpus, coerced to 1 <= n <= len(list0)
|
||||
both size and number or ratio are given: use number or ratio, unless the chunk size would be bigger than size
|
||||
both ratio and number are given: use ratio
|
||||
"""
|
||||
|
||||
def __init__(
|
||||
self,
|
||||
*iterables: Iterable[Any] | Sized,
|
||||
size: int = None,
|
||||
number: int = None,
|
||||
ratio: float = None,
|
||||
length: int = None,
|
||||
) -> None:
|
||||
if length is None:
|
||||
try:
|
||||
length = min(*[len(iterable) for iterable in iterables]) if len(iterables) > 1 else len(iterables[0])
|
||||
except TypeError:
|
||||
raise TypeError(
|
||||
"Cannot determine the length of the iterables(s), so the length must be provided as an argument."
|
||||
)
|
||||
if size is not None and (number is not None or ratio is not None):
|
||||
if number is None:
|
||||
number = int(cpu_count * ratio)
|
||||
if length >= size * number:
|
||||
number = round(length / size)
|
||||
elif size is not None: # size of chunks
|
||||
number = round(length / size)
|
||||
elif ratio is not None: # number of chunks
|
||||
number = int(cpu_count * ratio)
|
||||
self.iterators = [iter(arg) for arg in iterables]
|
||||
self.number_of_items = length
|
||||
self.length = min(length, number)
|
||||
self.lengths = [
|
||||
((i + 1) * self.number_of_items // self.length) - (i * self.number_of_items // self.length)
|
||||
for i in range(self.length)
|
||||
]
|
||||
|
||||
def __iter__(self) -> Iterator[Any]:
|
||||
for i in range(self.length):
|
||||
p, q = (
|
||||
(i * self.number_of_items // self.length),
|
||||
((i + 1) * self.number_of_items // self.length),
|
||||
)
|
||||
if len(self.iterators) == 1:
|
||||
yield [next(self.iterators[0]) for _ in range(q - p)]
|
||||
else:
|
||||
yield [[next(iterator) for _ in range(q - p)] for iterator in self.iterators]
|
||||
|
||||
def __len__(self) -> int:
|
||||
return self.length
|
||||
|
||||
|
||||
class ExternalBar(Iterable):
|
||||
def __init__(
|
||||
self,
|
||||
iterable: Iterable = None,
|
||||
callback: Callable[[int], None] = None,
|
||||
total: int = 0,
|
||||
) -> None:
|
||||
self.iterable = iterable
|
||||
self.callback = callback
|
||||
self.total = total
|
||||
self._n = 0
|
||||
|
||||
def __enter__(self) -> ExternalBar:
|
||||
return self
|
||||
|
||||
def __exit__(self, *args: Any, **kwargs: Any) -> None:
|
||||
return
|
||||
|
||||
def __iter__(self) -> Iterator[Any]:
|
||||
for n, item in enumerate(self.iterable):
|
||||
yield item
|
||||
self.n = n + 1
|
||||
|
||||
def update(self, n: int = 1) -> None:
|
||||
self.n += n
|
||||
|
||||
@property
|
||||
def n(self) -> int:
|
||||
return self._n
|
||||
|
||||
@n.setter
|
||||
def n(self, n: int) -> None:
|
||||
if n != self._n:
|
||||
self._n = n
|
||||
if self.callback is not None:
|
||||
self.callback(n)
|
||||
|
||||
|
||||
def get_worker(n_processes) -> RemoteFunction:
|
||||
n_processes = n_processes or PoolSingleton.cpu_count
|
||||
num_cpus = None if n_processes is None else cpu_count / n_processes
|
||||
|
||||
if not ray.is_initialized():
|
||||
os.environ["RAY_ACCEL_ENV_VAR_OVERRIDE_ON_ZERO"] = "0"
|
||||
ray.init(logging_level=logging.ERROR, log_to_driver=False, include_dashboard=False)
|
||||
|
||||
def worker(task):
|
||||
try:
|
||||
with ExitStack() as stack: # noqa
|
||||
if task.allow_output:
|
||||
out = StringIO()
|
||||
err = StringIO()
|
||||
stack.enter_context(redirect_stdout(out))
|
||||
stack.enter_context(redirect_stderr(err))
|
||||
else:
|
||||
stack.enter_context(redirect_stdout(open(os.devnull, "w")))
|
||||
stack.enter_context(redirect_stderr(open(os.devnull, "w")))
|
||||
try:
|
||||
task()
|
||||
task.status = ("done",)
|
||||
except Exception: # noqa
|
||||
task.status = "task_error", format_exc()
|
||||
if task.allow_output:
|
||||
task.out = out.getvalue()
|
||||
task.err = err.getvalue()
|
||||
except KeyboardInterrupt: # noqa
|
||||
pass
|
||||
|
||||
return task
|
||||
|
||||
if num_cpus:
|
||||
return ray.remote(num_cpus=num_cpus)(worker) # type: ignore
|
||||
else:
|
||||
return ray.remote(worker) # type: ignore
|
||||
|
||||
|
||||
class DequeDict(OrderedDict):
|
||||
def __init__(self, maxlen: int = None, *args: Any, **kwargs: Any) -> None:
|
||||
self.maxlen = maxlen
|
||||
super().__init__(*args, **kwargs)
|
||||
|
||||
def __setitem__(self, *args: Any, **kwargs: Any) -> None:
|
||||
super().__setitem__(*args, **kwargs)
|
||||
self.truncate()
|
||||
|
||||
def truncate(self) -> None:
|
||||
if self.maxlen is not None:
|
||||
while len(self) > self.maxlen:
|
||||
self.popitem(False)
|
||||
|
||||
def update(self, *args: Any, **kwargs: Any) -> None:
|
||||
super().update(*args, **kwargs) # type: ignore
|
||||
self.truncate()
|
||||
|
||||
|
||||
cache = DequeDict(128)
|
||||
|
||||
|
||||
class Task:
|
||||
def __init__(
|
||||
self,
|
||||
handle: Hashable,
|
||||
fun: Callable[[Any, ...], Any],
|
||||
args: tuple[Any, ...] = (),
|
||||
kwargs: dict[str, Any] = None,
|
||||
allow_output: bool = False,
|
||||
) -> None:
|
||||
self.handle = handle
|
||||
self.fun = fun
|
||||
self.args = args
|
||||
self.kwargs = kwargs or {}
|
||||
self.name = fun.__name__ if hasattr(fun, "__name__") else None
|
||||
self.done = False
|
||||
self.result = None
|
||||
self.out = None
|
||||
self.err = None
|
||||
self.future = None
|
||||
self.status = "starting"
|
||||
self.allow_output = allow_output
|
||||
|
||||
@staticmethod
|
||||
def get(item: tuple[bool, Any]) -> Any:
|
||||
if item[0]:
|
||||
return loads(ray.get(item[1]))
|
||||
else:
|
||||
return ray.get(item[1])
|
||||
|
||||
@staticmethod
|
||||
def put(item: Any) -> tuple[bool, Any]:
|
||||
try:
|
||||
h = hash(item)
|
||||
if not h in cache:
|
||||
try:
|
||||
cache[h] = False, ray.put(item)
|
||||
except Exception: # noqa
|
||||
cache[h] = True, ray.put(dumps(item, recurse=True))
|
||||
else:
|
||||
cache.move_to_end(h)
|
||||
return cache[h]
|
||||
except TypeError:
|
||||
try:
|
||||
return False, ray.put(item)
|
||||
except Exception: # noqa
|
||||
return True, ray.put(dumps(item, recurse=True))
|
||||
|
||||
@property
|
||||
def fun(self) -> Callable[[Any, ...], Any]:
|
||||
return self.get(self._fun)
|
||||
|
||||
@fun.setter
|
||||
def fun(self, fun: Callable[[Any, ...], Any]):
|
||||
self._fun = self.put(fun)
|
||||
|
||||
@property
|
||||
def args(self) -> tuple[Any, ...]:
|
||||
return tuple([self.get(arg) for arg in self._args])
|
||||
|
||||
@args.setter
|
||||
def args(self, args: tuple[Any, ...]) -> None:
|
||||
self._args = [self.put(arg) for arg in args]
|
||||
|
||||
@property
|
||||
def kwargs(self) -> dict[str, Any]:
|
||||
return {key: self.get(value) for key, value in self._kwargs.items()}
|
||||
|
||||
@kwargs.setter
|
||||
def kwargs(self, kwargs: dict[str, Any]) -> None:
|
||||
self._kwargs = {key: self.put(value) for key, value in kwargs.items()}
|
||||
|
||||
@property
|
||||
def result(self) -> Any:
|
||||
return self.get(self._result)
|
||||
|
||||
@result.setter
|
||||
def result(self, result: Any) -> None:
|
||||
self._result = self.put(result)
|
||||
|
||||
def __call__(self) -> Task:
|
||||
if not self.done:
|
||||
self.result = self.fun(*self.args, **self.kwargs) # noqa
|
||||
self.done = True
|
||||
return self
|
||||
|
||||
def __repr__(self) -> str:
|
||||
if self.done:
|
||||
return f"Task {self.handle}, result: {self.result}"
|
||||
else:
|
||||
return f"Task {self.handle}"
|
||||
|
||||
|
||||
class ParPool:
|
||||
"""Parallel processing with addition of iterations at any time and request of that result any time after that.
|
||||
The target function and its argument can be changed at any time.
|
||||
"""
|
||||
|
||||
def __init__(
|
||||
self,
|
||||
fun: Callable[[Any, ...], Any] = None,
|
||||
args: tuple[Any] = None,
|
||||
kwargs: dict[str, Any] = None,
|
||||
n_processes: int = None,
|
||||
bar: Bar = None,
|
||||
allow_output: bool = False,
|
||||
):
|
||||
self.handle = 0
|
||||
self.tasks = {}
|
||||
self.bar = bar
|
||||
self.bar_lengths = {}
|
||||
self.allow_output = allow_output
|
||||
self.fun = fun
|
||||
self.args = args
|
||||
self.kwargs = kwargs
|
||||
self.n_processes = n_processes or PoolSingleton.cpu_count
|
||||
self.worker = get_worker(self.n_processes)
|
||||
|
||||
def __getstate__(self) -> NoReturn:
|
||||
raise RuntimeError(f"Cannot pickle {self.__class__.__name__} object.")
|
||||
|
||||
def __enter__(self) -> ParPool:
|
||||
return self
|
||||
|
||||
def __exit__(self, *args: Any, **kwargs: Any) -> None:
|
||||
self.close()
|
||||
|
||||
def __call__(self, n: Any, handle: Hashable = None, barlength: int = 1) -> None:
|
||||
self.add_task(
|
||||
args=(n, *(() if self.args is None else self.args)),
|
||||
handle=handle,
|
||||
barlength=barlength,
|
||||
)
|
||||
|
||||
def close(self) -> None:
|
||||
cache.clear()
|
||||
|
||||
def add_task(
|
||||
self,
|
||||
fun: Callable[[Any, ...], Any] = None,
|
||||
args: tuple[Any, ...] = None,
|
||||
kwargs: dict[str, Any] = None,
|
||||
handle: Hashable = None,
|
||||
barlength: int = 1,
|
||||
allow_output: bool = False,
|
||||
) -> Optional[int]:
|
||||
if handle is None:
|
||||
new_handle = self.handle
|
||||
self.handle += 1
|
||||
else:
|
||||
new_handle = handle
|
||||
if new_handle in self:
|
||||
raise ValueError(f"handle {new_handle} already present")
|
||||
task = Task(
|
||||
new_handle,
|
||||
fun or self.fun,
|
||||
args or self.args,
|
||||
kwargs or self.kwargs,
|
||||
allow_output or self.allow_output,
|
||||
)
|
||||
self.block_until_space_available()
|
||||
task.future = self.worker.remote(task)
|
||||
self.tasks[new_handle] = task
|
||||
self.bar_lengths[new_handle] = barlength
|
||||
if handle is None:
|
||||
return new_handle
|
||||
else:
|
||||
return None
|
||||
|
||||
def __setitem__(self, handle: Hashable, n: Any) -> None:
|
||||
"""Add new iteration."""
|
||||
self(n, handle=handle)
|
||||
|
||||
def __getitem__(self, handle: Hashable) -> Any:
|
||||
"""Request result and delete its record. Wait if result not yet available."""
|
||||
if handle not in self:
|
||||
raise KeyError(f"No task with handle: {handle} in pool")
|
||||
task = self.finalize_task(self.tasks[handle])
|
||||
self.tasks.pop(task.handle)
|
||||
return task.result
|
||||
|
||||
def __contains__(self, handle: Hashable) -> bool:
|
||||
return handle in self.tasks
|
||||
|
||||
def __delitem__(self, handle: Hashable) -> None:
|
||||
self.tasks.pop(handle)
|
||||
|
||||
def finalize_task(self, future: ObjectRef | Task) -> Task:
|
||||
if isinstance(future, Task):
|
||||
task: Task = future
|
||||
future = task.future
|
||||
else:
|
||||
task = None # type: ignore
|
||||
|
||||
if future is not None:
|
||||
task: Task = ray.get(future) # type: ignore
|
||||
code, *args = task.status
|
||||
if task.out:
|
||||
if hasattr(self.bar, "write"):
|
||||
self.bar.write(task.out, end="")
|
||||
else:
|
||||
print(task.out, end="")
|
||||
if task.err:
|
||||
if hasattr(self.bar, "write"):
|
||||
self.bar.write(task.err, end="")
|
||||
else:
|
||||
print(task.err, end="")
|
||||
getattr(self, code)(task, *args)
|
||||
self.tasks[task.handle] = task
|
||||
return task
|
||||
|
||||
def block_until_space_available(self) -> None:
|
||||
if len(self.tasks) < 3 * self.n_processes:
|
||||
return
|
||||
while True:
|
||||
if self.tasks:
|
||||
futures = [task.future for task in self.tasks.values() if task.future is not None]
|
||||
done, busy = ray.wait(futures, num_returns=1, timeout=0.01)
|
||||
for d in done:
|
||||
self.finalize_task(d) # type: ignore
|
||||
if len(busy) < 3 * self.n_processes:
|
||||
return
|
||||
|
||||
def get_newest(self) -> Any:
|
||||
"""Request the newest handle and result and delete its record. Wait if result not yet available."""
|
||||
if self.tasks:
|
||||
done = [task for task in self.tasks.values() if task.future is None]
|
||||
if done:
|
||||
task = done[0]
|
||||
self.tasks.pop(task.handle)
|
||||
return task.handle, task.result
|
||||
while True:
|
||||
futures = [task.future for task in self.tasks.values() if task.future is not None]
|
||||
done, _ = ray.wait(futures, num_returns=1, timeout=0.01)
|
||||
if done:
|
||||
task = self.finalize_task(done[0])
|
||||
self.tasks.pop(task.handle)
|
||||
return task.handle, task.result
|
||||
raise StopIteration
|
||||
|
||||
def task_error(self, task: Task, error: Exception) -> None:
|
||||
if task.handle in self:
|
||||
task = self.tasks[task.handle]
|
||||
print(f"Error from process working on iteration {task.handle}:\n")
|
||||
print(error)
|
||||
print("Retrying in main process...")
|
||||
task()
|
||||
raise Exception(f"Function '{task.name}' cannot be executed by parfor, amend or execute in serial.")
|
||||
|
||||
def done(self, task: Task) -> None:
|
||||
if task.handle in self: # if not, the task was restarted erroneously
|
||||
self.tasks[task.handle] = task
|
||||
if hasattr(self.bar, "update"):
|
||||
self.bar.update(self.bar_lengths.pop(task.handle))
|
||||
|
||||
|
||||
class PoolSingleton:
|
||||
cpu_count: int = os.cpu_count()
|
||||
|
||||
@staticmethod
|
||||
def close(*args, **kwargs) -> None:
|
||||
pass
|
||||
|
||||
|
||||
class Worker:
|
||||
nested: bool = False
|
||||
|
||||
|
||||
def gmap(
|
||||
fun: Callable[[Any, ...], Any],
|
||||
iterable: Iterable[Any] = None,
|
||||
args: tuple[Any, ...] = None,
|
||||
kwargs: dict[str, Any] = None,
|
||||
total: int = None,
|
||||
desc: str = None,
|
||||
bar: Bar | bool = True,
|
||||
serial: bool = None,
|
||||
n_processes: int = None,
|
||||
yield_ordered: bool = True,
|
||||
yield_index: bool = False,
|
||||
allow_output: bool = False,
|
||||
**bar_kwargs: Any,
|
||||
) -> Generator[Any, None, None]:
|
||||
"""map a function fun to each iteration in iterable
|
||||
use as a function: pmap
|
||||
use as a decorator: parfor
|
||||
best use: iterable is a generator and length is given to this function as 'total'
|
||||
|
||||
required:
|
||||
fun: function taking arguments: iteration from iterable, other arguments defined in args & kwargs
|
||||
iterable: iterable or iterator from which an item is given to fun as a first argument
|
||||
optional:
|
||||
args: tuple with other unnamed arguments to fun
|
||||
kwargs: dict with other named arguments to fun
|
||||
total: give the length of the iterator in cases where len(iterator) results in an error
|
||||
desc: string with description of the progress bar
|
||||
bar: bool enable progress bar,
|
||||
or a callback function taking the number of passed iterations as an argument
|
||||
serial: execute in series instead of parallel if True, None (default): let pmap decide
|
||||
n_processes: number of processes to use,
|
||||
the parallel pool will be restarted if the current pool does not have the right number of processes
|
||||
yield_ordered: return the result in the same order as the iterable
|
||||
yield_index: return the index of the result too
|
||||
allow_output: allow output from subprocesses
|
||||
**bar_kwargs: keywords arguments for tqdm.tqdm
|
||||
|
||||
output:
|
||||
list (pmap) or generator (gmap) with results from applying the function \'fun\' to each iteration
|
||||
of the iterable / iterator
|
||||
|
||||
examples:
|
||||
<< from time import sleep
|
||||
<<
|
||||
@parfor(range(10), (3,))
|
||||
def fun(i, a):
|
||||
sleep(1)
|
||||
return a * i ** 2
|
||||
fun
|
||||
>> [0, 3, 12, 27, 48, 75, 108, 147, 192, 243]
|
||||
|
||||
<<
|
||||
def fun(i, a):
|
||||
sleep(1)
|
||||
return a * i ** 2
|
||||
pmap(fun, range(10), (3,))
|
||||
>> [0, 3, 12, 27, 48, 75, 108, 147, 192, 243]
|
||||
|
||||
equivalent to using the deco module:
|
||||
<<
|
||||
@concurrent
|
||||
def fun(i, a):
|
||||
time.sleep(1)
|
||||
return a * i ** 2
|
||||
|
||||
@synchronized
|
||||
def run(iterator, a):
|
||||
res = []
|
||||
for i in iterator:
|
||||
res.append(fun(i, a))
|
||||
return res
|
||||
run(range(10), 3)
|
||||
>> [0, 3, 12, 27, 48, 75, 108, 147, 192, 243]
|
||||
|
||||
all equivalent to the serial for-loop:
|
||||
<<
|
||||
a = 3
|
||||
fun = []
|
||||
for i in range(10):
|
||||
sleep(1)
|
||||
fun.append(a * i ** 2)
|
||||
fun
|
||||
>> [0, 3, 12, 27, 48, 75, 108, 147, 192, 243]
|
||||
"""
|
||||
is_chunked = isinstance(iterable, Chunks)
|
||||
if is_chunked:
|
||||
chunk_fun = fun
|
||||
else:
|
||||
iterable = Chunks(iterable, ratio=5, length=total)
|
||||
|
||||
@wraps(fun)
|
||||
def chunk_fun(iterable: Iterable, *args: Any, **kwargs: Any) -> list[Any]: # noqa
|
||||
return [fun(iteration, *args, **kwargs) for iteration in iterable]
|
||||
|
||||
if args is None:
|
||||
args = ()
|
||||
if kwargs is None:
|
||||
kwargs = {}
|
||||
|
||||
if "total" not in bar_kwargs:
|
||||
bar_kwargs["total"] = sum(iterable.lengths)
|
||||
if "desc" not in bar_kwargs:
|
||||
bar_kwargs["desc"] = desc
|
||||
if "disable" not in bar_kwargs:
|
||||
bar_kwargs["disable"] = not bar
|
||||
if serial is True or (serial is None and len(iterable) < min(cpu_count, 4)): # serial case
|
||||
|
||||
def tqdm_chunks(chunks: Chunks, *args, **kwargs) -> Iterable[Any]: # noqa
|
||||
with tqdm(*args, **kwargs) as b:
|
||||
for chunk, length in zip(chunks, chunks.lengths): # noqa
|
||||
yield chunk
|
||||
b.update(length)
|
||||
|
||||
iterable = (
|
||||
ExternalBar(iterable, bar, sum(iterable.lengths)) if callable(bar) else tqdm_chunks(iterable, **bar_kwargs) # type: ignore
|
||||
)
|
||||
if is_chunked:
|
||||
if yield_index:
|
||||
for i, c in enumerate(iterable):
|
||||
yield i, chunk_fun(c, *args, **kwargs)
|
||||
else:
|
||||
for c in iterable:
|
||||
yield chunk_fun(c, *args, **kwargs)
|
||||
else:
|
||||
if yield_index:
|
||||
for i, c in enumerate(iterable):
|
||||
for q in chunk_fun(c, *args, **kwargs):
|
||||
yield i, q
|
||||
else:
|
||||
for c in iterable:
|
||||
yield from chunk_fun(c, *args, **kwargs)
|
||||
|
||||
else: # parallel case
|
||||
with ExitStack() as stack: # noqa
|
||||
if callable(bar):
|
||||
bar = stack.enter_context(ExternalBar(callback=bar)) # noqa
|
||||
else:
|
||||
bar = stack.enter_context(tqdm(**bar_kwargs))
|
||||
with ParPool(chunk_fun, args, kwargs, n_processes, bar, allow_output) as p: # type: ignore
|
||||
for i, (j, l) in enumerate(zip(iterable, iterable.lengths)): # add work to the queue
|
||||
p(j, handle=i, barlength=l)
|
||||
if bar.total is None or bar.total < i + 1:
|
||||
bar.total = i + 1
|
||||
|
||||
if is_chunked:
|
||||
if yield_ordered:
|
||||
if yield_index:
|
||||
for i in range(len(iterable)):
|
||||
yield i, p[i]
|
||||
else:
|
||||
for i in range(len(iterable)):
|
||||
yield p[i]
|
||||
else:
|
||||
if yield_index:
|
||||
for _ in range(len(iterable)):
|
||||
yield p.get_newest()
|
||||
else:
|
||||
for _ in range(len(iterable)):
|
||||
yield p.get_newest()[1]
|
||||
else:
|
||||
if yield_ordered:
|
||||
if yield_index:
|
||||
for i in range(len(iterable)):
|
||||
for q in p[i]:
|
||||
yield i, q
|
||||
else:
|
||||
for i in range(len(iterable)):
|
||||
yield from p[i]
|
||||
else:
|
||||
if yield_index:
|
||||
for _ in range(len(iterable)):
|
||||
i, n = p.get_newest()
|
||||
for q in n:
|
||||
yield i, q
|
||||
else:
|
||||
for _ in range(len(iterable)):
|
||||
yield from p.get_newest()[1]
|
||||
|
||||
|
||||
def pmap(*args, **kwargs) -> list[Any]:
|
||||
return list(gmap(*args, **kwargs))
|
||||
|
||||
|
||||
def parfor(*args: Any, **kwargs: Any) -> Callable[[Callable[[Any, ...], Any]], list[Any]]:
|
||||
def decfun(fun: Callable[[Any, ...], Any]) -> list[Any]:
|
||||
return pmap(fun, *args, **kwargs)
|
||||
|
||||
return decfun
|
||||
|
||||
|
||||
try:
|
||||
parfor.__doc__ = pmap.__doc__ = gmap.__doc__
|
||||
pmap.__annotations__ = gmap.__annotations__ | pmap.__annotations__
|
||||
parfor.__annotations__ = {key: value for key, value in pmap.__annotations__.items() if key != "fun"}
|
||||
except AttributeError:
|
||||
pass
|
||||
@@ -1,119 +0,0 @@
|
||||
from __future__ import annotations
|
||||
|
||||
import copyreg
|
||||
from io import BytesIO
|
||||
from pickle import PicklingError
|
||||
from typing import Any, Callable
|
||||
|
||||
import dill
|
||||
|
||||
loads = dill.loads
|
||||
|
||||
|
||||
class CouldNotBePickled:
|
||||
def __init__(self, class_name: str) -> None:
|
||||
self.class_name = class_name
|
||||
|
||||
def __repr__(self) -> str:
|
||||
return f"Item of type '{self.class_name}' could not be pickled and was omitted."
|
||||
|
||||
@classmethod
|
||||
def reduce(cls, item: Any) -> tuple[Callable[[str], CouldNotBePickled], tuple[str]]:
|
||||
return cls, (type(item).__name__,)
|
||||
|
||||
|
||||
class Pickler(dill.Pickler):
|
||||
"""Overload dill to ignore unpicklable parts of objects.
|
||||
You probably didn't want to use these parts anyhow.
|
||||
However, if you did, you'll have to find some way to make them picklable.
|
||||
"""
|
||||
|
||||
def save(self, obj: Any, save_persistent_id: bool = True) -> None:
|
||||
"""Copied from pickle and amended."""
|
||||
self.framer.commit_frame()
|
||||
|
||||
# Check for persistent id (defined by a subclass)
|
||||
pid = self.persistent_id(obj)
|
||||
if pid is not None and save_persistent_id:
|
||||
self.save_pers(pid)
|
||||
return
|
||||
|
||||
# Check the memo
|
||||
x = self.memo.get(id(obj))
|
||||
if x is not None:
|
||||
self.write(self.get(x[0]))
|
||||
return
|
||||
|
||||
rv = NotImplemented
|
||||
reduce = getattr(self, "reducer_override", None)
|
||||
if reduce is not None:
|
||||
rv = reduce(obj)
|
||||
|
||||
if rv is NotImplemented:
|
||||
# Check the type dispatch table
|
||||
t = type(obj)
|
||||
f = self.dispatch.get(t)
|
||||
if f is not None:
|
||||
f(self, obj) # Call unbound method with explicit self
|
||||
return
|
||||
|
||||
# Check private dispatch table if any, or else
|
||||
# copyreg.dispatch_table
|
||||
reduce = getattr(self, "dispatch_table", copyreg.dispatch_table).get(t)
|
||||
if reduce is not None:
|
||||
rv = reduce(obj)
|
||||
else:
|
||||
# Check for a class with a custom metaclass; treat as regular
|
||||
# class
|
||||
if issubclass(t, type):
|
||||
self.save_global(obj)
|
||||
return
|
||||
|
||||
# Check for a __reduce_ex__ method, fall back to __reduce__
|
||||
reduce = getattr(obj, "__reduce_ex__", None)
|
||||
try:
|
||||
if reduce is not None:
|
||||
rv = reduce(self.proto)
|
||||
else:
|
||||
reduce = getattr(obj, "__reduce__", None)
|
||||
if reduce is not None:
|
||||
rv = reduce()
|
||||
else:
|
||||
raise PicklingError("Can't pickle %r object: %r" % (t.__name__, obj))
|
||||
except Exception: # noqa
|
||||
rv = CouldNotBePickled.reduce(obj)
|
||||
|
||||
# Check for string returned by reduce(), meaning "save as global"
|
||||
if isinstance(rv, str):
|
||||
try:
|
||||
self.save_global(obj, rv)
|
||||
except Exception: # noqa
|
||||
self.save_global(obj, CouldNotBePickled.reduce(obj))
|
||||
return
|
||||
|
||||
# Assert that reduce() returned a tuple
|
||||
if not isinstance(rv, tuple):
|
||||
raise PicklingError("%s must return string or tuple" % reduce)
|
||||
|
||||
# Assert that it returned an appropriately sized tuple
|
||||
length = len(rv)
|
||||
if not (2 <= length <= 6):
|
||||
raise PicklingError("Tuple returned by %s must have two to six elements" % reduce)
|
||||
|
||||
# Save the reduce() output and finally memoize the object
|
||||
try:
|
||||
self.save_reduce(obj=obj, *rv)
|
||||
except Exception: # noqa
|
||||
self.save_reduce(obj=obj, *CouldNotBePickled.reduce(obj))
|
||||
|
||||
|
||||
def dumps(
|
||||
obj: Any, protocol: str = None, byref: bool = None, fmode: str = None, recurse: bool = True, **kwds: Any
|
||||
) -> bytes:
|
||||
"""pickle an object to a string"""
|
||||
protocol = dill.settings["protocol"] if protocol is None else int(protocol)
|
||||
_kwds = kwds.copy()
|
||||
_kwds.update(dict(byref=byref, fmode=fmode, recurse=recurse))
|
||||
with BytesIO() as file:
|
||||
Pickler(file, protocol, **_kwds).dump(obj)
|
||||
return file.getvalue()
|
||||
@@ -0,0 +1,38 @@
|
||||
from __future__ import annotations
|
||||
|
||||
from . import ome_metadata_rs as rs # noqa
|
||||
|
||||
|
||||
class Ome(dict):
|
||||
@staticmethod
|
||||
def from_xml(xml: str) -> Ome:
|
||||
"""Create the OME structure from an XML string"""
|
||||
new = Ome()
|
||||
new.update(rs.ome(str(xml)))
|
||||
return new
|
||||
|
||||
def __dir__(self) -> list[str]:
|
||||
return list(self.keys()) + list(super().__dir__())
|
||||
|
||||
def __getattr__(self, key: str) -> Ome | OmeList | int | float | str:
|
||||
try:
|
||||
new = self.__getitem__(key)
|
||||
except KeyError:
|
||||
raise AttributeError(f"'Ome' object has no attribute '{key}'")
|
||||
if isinstance(new, dict):
|
||||
return Ome(**new)
|
||||
elif isinstance(new, list):
|
||||
return OmeList(new)
|
||||
else:
|
||||
return new
|
||||
|
||||
|
||||
class OmeList(list):
|
||||
def __getitem__(self, item: int) -> Ome | OmeList | int | float | str:
|
||||
new = super().__getitem__(item)
|
||||
if isinstance(new, dict):
|
||||
return Ome(**new)
|
||||
elif isinstance(new, list):
|
||||
return OmeList(new)
|
||||
else:
|
||||
return new
|
||||
+23
-21
@@ -1,30 +1,32 @@
|
||||
[build-system]
|
||||
requires = ["maturin>=1.8,<2.0"]
|
||||
build-backend = "maturin"
|
||||
|
||||
[project]
|
||||
name = "parfor"
|
||||
version = "2026.5.0"
|
||||
description = "A package to mimic the use of parfor as done in Matlab."
|
||||
authors = [
|
||||
{ name = "Wim Pomp-Pervova", email = "wimpomp@gmail.com" }
|
||||
]
|
||||
license = { text = "MIT" }
|
||||
readme = "README.md"
|
||||
keywords = ["parfor", "concurrency", "multiprocessing", "parallel"]
|
||||
name = "ome-metadata"
|
||||
keywords = ["bioformats", "imread", "ome", "metadata"]
|
||||
requires-python = ">=3.10"
|
||||
dependencies = [
|
||||
"dill >= 0.3.0",
|
||||
"numpy",
|
||||
"tqdm >= 4.50.0",
|
||||
"ray",
|
||||
classifiers = [
|
||||
"License :: OSI Approved :: MIT License",
|
||||
"Programming Language :: Rust",
|
||||
"Programming Language :: Python",
|
||||
"Programming Language :: Python :: 3",
|
||||
"Programming Language :: Python :: 3 :: Only",
|
||||
"Programming Language :: Python :: 3.10",
|
||||
"Programming Language :: Python :: 3.11",
|
||||
"Programming Language :: Python :: 3.12",
|
||||
"Programming Language :: Python :: 3.13",
|
||||
"Programming Language :: Python :: 3.14",
|
||||
]
|
||||
dynamic = ["version", "description", "authors", "license", "readme"]
|
||||
|
||||
[project.urls]
|
||||
repository = "https://git.wimpomp.nl/wim/parfor"
|
||||
Repository = "https://github.com/wimpomp/ome-metadata"
|
||||
|
||||
[project.optional-dependencies]
|
||||
test = ["pytest"]
|
||||
|
||||
[tool.ruff]
|
||||
line-length = 119
|
||||
indent-width = 4
|
||||
[tool.maturin]
|
||||
python-source = "py"
|
||||
features = ["pyo3/extension-module", "python"]
|
||||
module-name = "ome_metadata.ome_metadata_rs"
|
||||
|
||||
[tool.isort]
|
||||
line_length = 119
|
||||
|
||||
+51
@@ -0,0 +1,51 @@
|
||||
#![allow(non_camel_case_types)]
|
||||
pub mod ome;
|
||||
|
||||
#[cfg(feature = "python")]
|
||||
mod py;
|
||||
|
||||
use anyhow::{Error, Result};
|
||||
pub use ome::Ome;
|
||||
use quick_xml::de::from_str;
|
||||
use std::str::FromStr;
|
||||
|
||||
impl FromStr for Ome {
|
||||
type Err = Error;
|
||||
|
||||
fn from_str(s: &str) -> Result<Self> {
|
||||
Ok(from_str(s)?)
|
||||
}
|
||||
}
|
||||
|
||||
#[cfg(test)]
|
||||
mod tests {
|
||||
use super::*;
|
||||
use std::fs::read_to_string;
|
||||
|
||||
macro_rules! test_read {
|
||||
($($name:ident: $file:expr $(,)?)*) => {
|
||||
$(
|
||||
#[test]
|
||||
fn $name() -> Result<()> {
|
||||
let file = read_to_string(format!("tests/{}.xml", $file))?;
|
||||
let _ome: Ome = file.parse()?;
|
||||
Ok(())
|
||||
}
|
||||
)*
|
||||
};
|
||||
}
|
||||
|
||||
test_read!(
|
||||
a: "YTL1849A111_2023_05_04__14_46_19_cellnr_1_track"
|
||||
b: "Experiment-2029"
|
||||
c: "test"
|
||||
d: "4-Pos_001_002"
|
||||
e: "YTL1841B2-2-1_1hr_DMSO_galinduction_1"
|
||||
f: "1xp53-01-AP1"
|
||||
g: "YTL378_JF552"
|
||||
h: "MK022_cE9_1-01-Airyscan Processing-01-Scene-2-P1"
|
||||
i: "beads_2023_05_04__19_00_22"
|
||||
j: "20230511-p53-4x-CMV-1min-4h-01-Airyscan Processing-01"
|
||||
k: "YTL1849A131_2023_05_04__13_36_36"
|
||||
);
|
||||
}
|
||||
+2765
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,13 @@
|
||||
use crate::Ome;
|
||||
use pyo3::prelude::*;
|
||||
|
||||
#[pymodule]
|
||||
#[pyo3(name = "ome_metadata_rs")]
|
||||
fn ome_metadata_rs(m: &Bound<'_, PyModule>) -> PyResult<()> {
|
||||
#[pyfn(m)]
|
||||
fn ome(text: &str) -> PyResult<Ome> {
|
||||
Ok(text.parse()?)
|
||||
}
|
||||
|
||||
Ok(())
|
||||
}
|
||||
@@ -0,0 +1,416 @@
|
||||
<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">
|
||||
<Experimenter ID="Experimenter:0" UserName="r.hoogstraaten"/>
|
||||
<Instrument ID="Instrument:0">
|
||||
<Microscope Type="Inverted"/>
|
||||
<Detector Model="" Offset="0.0" Zoom="1.7" ID="Detector:Airyscan" Type="Other"/>
|
||||
<Detector Model="" ID="Detector:LSM980"/>
|
||||
<Objective Model="C-Apochromat 40x/1.20 W autocorr UV VIS IR" ID="Objective:1" Immersion="Water" LensNA="1.2" NominalMagnification="40.0" WorkingDistance="280.0" WorkingDistanceUnit="µm"/>
|
||||
<Dichroic ID="Dichroic:3"/>
|
||||
<Dichroic ID="Dichroic:4"/>
|
||||
<Dichroic ID="Dichroic:5"/>
|
||||
</Instrument>
|
||||
<Image ID="Image:0" Name="1xp53-01-AP1.czi #1">
|
||||
<AcquisitionDate>2023-12-20T09:44:49.746</AcquisitionDate>
|
||||
<ExperimenterRef ID="Experimenter:0"/>
|
||||
<InstrumentRef ID="Instrument:0"/>
|
||||
<ObjectiveSettings ID="Objective:1" Medium="Water" RefractiveIndex="1.33"/>
|
||||
<StageLabel Name="Scene position #0" X="-2097.1" XUnit="µm" Y="-12106.7" YUnit="µm" Z="-2.96" ZUnit="µm"/>
|
||||
<Pixels ID="Pixels:0" DimensionOrder="XYCZT" Type="uint16" SignificantBits="16" Interleaved="false" BigEndian="false" SizeX="1000" SizeY="1000" SizeZ="15" SizeC="1" SizeT="26" PhysicalSizeX="0.12185920266544126" PhysicalSizeXUnit="µm" PhysicalSizeY="0.12185920266544126" PhysicalSizeYUnit="µm" PhysicalSizeZ="0.5" PhysicalSizeZUnit="µm" TimeIncrement="19.92016" TimeIncrementUnit="s">
|
||||
<Channel ID="Channel:0:0" Name="EGFP" SamplesPerPixel="1" IlluminationType="Epifluorescence" PinholeSize="215.8910436973" PinholeSizeUnit="µm" AcquisitionMode="LaserScanningConfocalMicroscopy" ExcitationWavelength="488.0" ExcitationWavelengthUnit="nm" EmissionWavelength="509.0" EmissionWavelengthUnit="nm" Fluor="EGFP" Color="16735231">
|
||||
<DetectorSettings ID="Detector:Airyscan"/>
|
||||
<LightPath/>
|
||||
</Channel>
|
||||
<MetadataOnly/>
|
||||
<Plane TheZ="0" TheT="0" TheC="0" DeltaT="3.812999963760376" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="-2.96" PositionZUnit="µm"/>
|
||||
<Plane TheZ="1" TheT="0" TheC="0" DeltaT="4.766000032424927" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="-2.46" PositionZUnit="µm"/>
|
||||
<Plane TheZ="2" TheT="0" TheC="0" DeltaT="5.718999862670898" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="-1.96" PositionZUnit="µm"/>
|
||||
<Plane TheZ="3" TheT="0" TheC="0" DeltaT="6.671999931335449" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="-1.46" PositionZUnit="µm"/>
|
||||
<Plane TheZ="4" TheT="0" TheC="0" DeltaT="7.625" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="-0.96" PositionZUnit="µm"/>
|
||||
<Plane TheZ="5" TheT="0" TheC="0" DeltaT="8.577999830245972" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="-0.46" PositionZUnit="µm"/>
|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
</Pixels>
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||||
</Image>
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||||
</OME>
|
||||
File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,88 @@
|
||||
<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">
|
||||
<Instrument ID="Instrument:0">
|
||||
<Detector Manufacturer="HamamatsuHam_DCAM" Model="C13440-20CU" SerialNumber="S/N: 303952" ID="Detector:0:0" Type="Other"/>
|
||||
</Instrument>
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||||
<Image ID="Image:0" Name="4-Pos_001_002">
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||||
<Description>OT/DAPI_filter/DAPI 20% 25 ms/Cy3_filter/Cy3 100% 250 ms/Cy5_filter/Cy5 100% 250ms/40x optovar 1.25/ Z -3 to 3/OD0</Description>
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||||
<InstrumentRef ID="Instrument:0"/>
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||||
<ImagingEnvironment Temperature="0.0" TemperatureUnit="°C"/>
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||||
<Pixels ID="Pixels:0" DimensionOrder="XYZCT" Type="uint16" SignificantBits="16" Interleaved="false" BigEndian="true" SizeX="2048" SizeY="2048" SizeZ="21" SizeC="3" SizeT="1" PhysicalSizeX="0.131" PhysicalSizeXUnit="µm" PhysicalSizeY="0.131" PhysicalSizeYUnit="µm" PhysicalSizeZ="0.2999999999999998" PhysicalSizeZUnit="µm">
|
||||
<Channel ID="Channel:0:0" Name="Cy3-Cy3_filter" SamplesPerPixel="1" Color="-1">
|
||||
<DetectorSettings ID="Detector:0:0" Gain="0.0" Binning="1x1"/>
|
||||
<LightPath/>
|
||||
</Channel>
|
||||
<Channel ID="Channel:0:1" Name="Cy5-Cy5_filter" SamplesPerPixel="1" Color="-1">
|
||||
<DetectorSettings ID="Detector:0:0" Gain="0.0" Binning="1x1"/>
|
||||
<LightPath/>
|
||||
</Channel>
|
||||
<Channel ID="Channel:0:2" Name="DAPI-DAPI_filter" SamplesPerPixel="1" Color="-1">
|
||||
<DetectorSettings ID="Detector:0:0" Gain="0.0" Binning="1x1"/>
|
||||
<LightPath/>
|
||||
</Channel>
|
||||
<MetadataOnly/>
|
||||
<Plane TheZ="0" TheT="0" TheC="0" DeltaT="868802.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-1.8499999999999999" PositionZUnit="µm"/>
|
||||
<Plane TheZ="1" TheT="0" TheC="0" DeltaT="869379.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-1.55" PositionZUnit="µm"/>
|
||||
<Plane TheZ="2" TheT="0" TheC="0" DeltaT="869950.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-1.2499999999999998" PositionZUnit="µm"/>
|
||||
<Plane TheZ="3" TheT="0" TheC="0" DeltaT="870520.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-0.95" PositionZUnit="µm"/>
|
||||
<Plane TheZ="4" TheT="0" TheC="0" DeltaT="871096.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-0.6499999999999999" PositionZUnit="µm"/>
|
||||
<Plane TheZ="5" TheT="0" TheC="0" DeltaT="871664.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-0.34999999999999987" PositionZUnit="µm"/>
|
||||
<Plane TheZ="6" TheT="0" TheC="0" DeltaT="872240.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-0.050000000000000044" PositionZUnit="µm"/>
|
||||
<Plane TheZ="7" TheT="0" TheC="0" DeltaT="872820.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="0.2500000000000002" PositionZUnit="µm"/>
|
||||
<Plane TheZ="8" TheT="0" TheC="0" DeltaT="873394.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="0.55" PositionZUnit="µm"/>
|
||||
<Plane TheZ="9" TheT="0" TheC="0" DeltaT="873965.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="0.8499999999999999" PositionZUnit="µm"/>
|
||||
<Plane TheZ="10" TheT="0" TheC="0" DeltaT="874539.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="1.1500000000000001" PositionZUnit="µm"/>
|
||||
<Plane TheZ="11" TheT="0" TheC="0" DeltaT="875108.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="1.45" PositionZUnit="µm"/>
|
||||
<Plane TheZ="12" TheT="0" TheC="0" DeltaT="875682.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="1.7499999999999998" PositionZUnit="µm"/>
|
||||
<Plane TheZ="13" TheT="0" TheC="0" DeltaT="876252.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="2.05" PositionZUnit="µm"/>
|
||||
<Plane TheZ="14" TheT="0" TheC="0" DeltaT="876826.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="2.3500000000000005" PositionZUnit="µm"/>
|
||||
<Plane TheZ="15" TheT="0" TheC="0" DeltaT="877395.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="2.6500000000000004" PositionZUnit="µm"/>
|
||||
<Plane TheZ="16" TheT="0" TheC="0" DeltaT="877974.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="2.95" PositionZUnit="µm"/>
|
||||
<Plane TheZ="17" TheT="0" TheC="0" DeltaT="878541.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="3.25" PositionZUnit="µm"/>
|
||||
<Plane TheZ="18" TheT="0" TheC="0" DeltaT="879115.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="3.55" PositionZUnit="µm"/>
|
||||
<Plane TheZ="19" TheT="0" TheC="0" DeltaT="879684.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="3.8500000000000005" PositionZUnit="µm"/>
|
||||
<Plane TheZ="20" TheT="0" TheC="0" DeltaT="880258.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="4.15" PositionZUnit="µm"/>
|
||||
<Plane TheZ="0" TheT="0" TheC="1" DeltaT="881421.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-1.8499999999999999" PositionZUnit="µm"/>
|
||||
<Plane TheZ="1" TheT="0" TheC="1" DeltaT="881990.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-1.55" PositionZUnit="µm"/>
|
||||
<Plane TheZ="2" TheT="0" TheC="1" DeltaT="882564.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-1.2499999999999998" PositionZUnit="µm"/>
|
||||
<Plane TheZ="3" TheT="0" TheC="1" DeltaT="883133.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-0.95" PositionZUnit="µm"/>
|
||||
<Plane TheZ="4" TheT="0" TheC="1" DeltaT="883706.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-0.6499999999999999" PositionZUnit="µm"/>
|
||||
<Plane TheZ="5" TheT="0" TheC="1" DeltaT="884276.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-0.34999999999999987" PositionZUnit="µm"/>
|
||||
<Plane TheZ="6" TheT="0" TheC="1" DeltaT="884851.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-0.050000000000000044" PositionZUnit="µm"/>
|
||||
<Plane TheZ="7" TheT="0" TheC="1" DeltaT="885436.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="0.2500000000000002" PositionZUnit="µm"/>
|
||||
<Plane TheZ="8" TheT="0" TheC="1" DeltaT="886010.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="0.55" PositionZUnit="µm"/>
|
||||
<Plane TheZ="9" TheT="0" TheC="1" DeltaT="886577.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="0.8499999999999999" PositionZUnit="µm"/>
|
||||
<Plane TheZ="10" TheT="0" TheC="1" DeltaT="887158.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="1.1500000000000001" PositionZUnit="µm"/>
|
||||
<Plane TheZ="11" TheT="0" TheC="1" DeltaT="887736.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="1.45" PositionZUnit="µm"/>
|
||||
<Plane TheZ="12" TheT="0" TheC="1" DeltaT="888308.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="1.7499999999999998" PositionZUnit="µm"/>
|
||||
<Plane TheZ="13" TheT="0" TheC="1" DeltaT="888878.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="2.05" PositionZUnit="µm"/>
|
||||
<Plane TheZ="14" TheT="0" TheC="1" DeltaT="889452.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="2.3500000000000005" PositionZUnit="µm"/>
|
||||
<Plane TheZ="15" TheT="0" TheC="1" DeltaT="890023.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="2.6500000000000004" PositionZUnit="µm"/>
|
||||
<Plane TheZ="16" TheT="0" TheC="1" DeltaT="890598.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="2.95" PositionZUnit="µm"/>
|
||||
<Plane TheZ="17" TheT="0" TheC="1" DeltaT="891165.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="3.25" PositionZUnit="µm"/>
|
||||
<Plane TheZ="18" TheT="0" TheC="1" DeltaT="891737.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="3.55" PositionZUnit="µm"/>
|
||||
<Plane TheZ="19" TheT="0" TheC="1" DeltaT="892305.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="3.8500000000000005" PositionZUnit="µm"/>
|
||||
<Plane TheZ="20" TheT="0" TheC="1" DeltaT="892878.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="4.15" PositionZUnit="µm"/>
|
||||
<Plane TheZ="0" TheT="0" TheC="2" DeltaT="894099.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-1.8499999999999999" PositionZUnit="µm"/>
|
||||
<Plane TheZ="1" TheT="0" TheC="2" DeltaT="894365.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-1.55" PositionZUnit="µm"/>
|
||||
<Plane TheZ="2" TheT="0" TheC="2" DeltaT="894755.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-1.2499999999999998" PositionZUnit="µm"/>
|
||||
<Plane TheZ="3" TheT="0" TheC="2" DeltaT="895162.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-0.95" PositionZUnit="µm"/>
|
||||
<Plane TheZ="4" TheT="0" TheC="2" DeltaT="895564.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-0.6499999999999999" PositionZUnit="µm"/>
|
||||
<Plane TheZ="5" TheT="0" TheC="2" DeltaT="895985.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-0.34999999999999987" PositionZUnit="µm"/>
|
||||
<Plane TheZ="6" TheT="0" TheC="2" DeltaT="896271.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-0.050000000000000044" PositionZUnit="µm"/>
|
||||
<Plane TheZ="7" TheT="0" TheC="2" DeltaT="896671.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="0.2500000000000002" PositionZUnit="µm"/>
|
||||
<Plane TheZ="8" TheT="0" TheC="2" DeltaT="897106.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="0.55" PositionZUnit="µm"/>
|
||||
<Plane TheZ="9" TheT="0" TheC="2" DeltaT="897393.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="0.8499999999999999" PositionZUnit="µm"/>
|
||||
<Plane TheZ="10" TheT="0" TheC="2" DeltaT="897796.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="1.1500000000000001" PositionZUnit="µm"/>
|
||||
<Plane TheZ="11" TheT="0" TheC="2" DeltaT="898219.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="1.45" PositionZUnit="µm"/>
|
||||
<Plane TheZ="12" TheT="0" TheC="2" DeltaT="898635.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="1.7499999999999998" PositionZUnit="µm"/>
|
||||
<Plane TheZ="13" TheT="0" TheC="2" DeltaT="899068.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="2.05" PositionZUnit="µm"/>
|
||||
<Plane TheZ="14" TheT="0" TheC="2" DeltaT="899353.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="2.3500000000000005" PositionZUnit="µm"/>
|
||||
<Plane TheZ="15" TheT="0" TheC="2" DeltaT="899765.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="2.6500000000000004" PositionZUnit="µm"/>
|
||||
<Plane TheZ="16" TheT="0" TheC="2" DeltaT="900176.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="2.95" PositionZUnit="µm"/>
|
||||
<Plane TheZ="17" TheT="0" TheC="2" DeltaT="900611.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="3.25" PositionZUnit="µm"/>
|
||||
<Plane TheZ="18" TheT="0" TheC="2" DeltaT="900881.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="3.55" PositionZUnit="µm"/>
|
||||
<Plane TheZ="19" TheT="0" TheC="2" DeltaT="901313.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="3.8500000000000005" PositionZUnit="µm"/>
|
||||
<Plane TheZ="20" TheT="0" TheC="2" DeltaT="901598.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="4.15" PositionZUnit="µm"/>
|
||||
</Pixels>
|
||||
</Image>
|
||||
</OME>
|
||||
@@ -0,0 +1,121 @@
|
||||
<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">
|
||||
<Experimenter ID="Experimenter:0" UserName="zeiss"/>
|
||||
<Instrument ID="Instrument:0">
|
||||
<Microscope Type="Inverted"/>
|
||||
<Detector Model="HDCamC15440-20UP-50" ID="Detector:HamamatsuCamera"/>
|
||||
<Detector Model="HDCamC15440-20UP-50" ID="Detector:HamamatsuCamera#2"/>
|
||||
<Objective Model="EC Plan-Neofluar 10x/0.30" ID="Objective:1" Immersion="Air" LensNA="0.3" NominalMagnification="10.0" WorkingDistance="5600.0" WorkingDistanceUnit="µm"/>
|
||||
<FilterSet ID="FilterSet:1">
|
||||
<ExcitationFilterRef ID="Filter:1"/>
|
||||
<ExcitationFilterRef ID="Filter:3"/>
|
||||
<ExcitationFilterRef ID="Filter:5"/>
|
||||
<ExcitationFilterRef ID="Filter:7"/>
|
||||
<DichroicRef ID="Dichroic:1"/>
|
||||
<EmissionFilterRef ID="Filter:2"/>
|
||||
<EmissionFilterRef ID="Filter:4"/>
|
||||
<EmissionFilterRef ID="Filter:6"/>
|
||||
<EmissionFilterRef ID="Filter:8"/>
|
||||
</FilterSet>
|
||||
<FilterSet ID="FilterSet:2">
|
||||
<ExcitationFilterRef ID="Filter:9"/>
|
||||
<ExcitationFilterRef ID="Filter:11"/>
|
||||
<ExcitationFilterRef ID="Filter:13"/>
|
||||
<ExcitationFilterRef ID="Filter:15"/>
|
||||
<DichroicRef ID="Dichroic:2"/>
|
||||
<EmissionFilterRef ID="Filter:10"/>
|
||||
<EmissionFilterRef ID="Filter:12"/>
|
||||
<EmissionFilterRef ID="Filter:14"/>
|
||||
<EmissionFilterRef ID="Filter:16"/>
|
||||
</FilterSet>
|
||||
<Filter ID="Filter:1">
|
||||
<TransmittanceRange CutOut="4095.0" CutOutUnit="nm"/>
|
||||
</Filter>
|
||||
<Filter ID="Filter:2">
|
||||
<TransmittanceRange CutIn="420.0" CutInUnit="nm" CutOut="480.0" CutOutUnit="nm"/>
|
||||
</Filter>
|
||||
<Filter ID="Filter:3">
|
||||
<TransmittanceRange CutOut="4095.0" CutOutUnit="nm"/>
|
||||
</Filter>
|
||||
<Filter ID="Filter:4">
|
||||
<TransmittanceRange CutIn="495.0" CutInUnit="nm" CutOut="550.0" CutOutUnit="nm"/>
|
||||
</Filter>
|
||||
<Filter ID="Filter:5">
|
||||
<TransmittanceRange CutOut="4095.0" CutOutUnit="nm"/>
|
||||
</Filter>
|
||||
<Filter ID="Filter:6">
|
||||
<TransmittanceRange CutIn="575.0" CutInUnit="nm" CutOut="620.0" CutOutUnit="nm"/>
|
||||
</Filter>
|
||||
<Filter ID="Filter:7">
|
||||
<TransmittanceRange CutOut="4095.0" CutOutUnit="nm"/>
|
||||
</Filter>
|
||||
<Filter ID="Filter:8">
|
||||
<TransmittanceRange CutIn="660.0" CutInUnit="nm" CutOut="720.0" CutOutUnit="nm"/>
|
||||
</Filter>
|
||||
<Filter ID="Filter:9">
|
||||
<TransmittanceRange CutOut="4095.0" CutOutUnit="nm"/>
|
||||
</Filter>
|
||||
<Filter ID="Filter:10">
|
||||
<TransmittanceRange CutIn="420.0" CutInUnit="nm" CutOut="480.0" CutOutUnit="nm"/>
|
||||
</Filter>
|
||||
<Filter ID="Filter:11">
|
||||
<TransmittanceRange CutOut="4095.0" CutOutUnit="nm"/>
|
||||
</Filter>
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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|
||||
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|
||||
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|
||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
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||||
<Plane TheZ="94" TheT="0" TheC="0" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.681" PositionZUnit="µm"/>
|
||||
<Plane TheZ="94" TheT="0" TheC="1" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.681" PositionZUnit="µm"/>
|
||||
<Plane TheZ="94" TheT="0" TheC="2" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.681" PositionZUnit="µm"/>
|
||||
<Plane TheZ="94" TheT="0" TheC="3" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.681" PositionZUnit="µm"/>
|
||||
<Plane TheZ="94" TheT="0" TheC="4" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.681" PositionZUnit="µm"/>
|
||||
<Plane TheZ="94" TheT="0" TheC="5" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.681" PositionZUnit="µm"/>
|
||||
<Plane TheZ="95" TheT="0" TheC="0" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.781" PositionZUnit="µm"/>
|
||||
<Plane TheZ="95" TheT="0" TheC="1" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.781" PositionZUnit="µm"/>
|
||||
<Plane TheZ="95" TheT="0" TheC="2" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.781" PositionZUnit="µm"/>
|
||||
<Plane TheZ="95" TheT="0" TheC="3" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.781" PositionZUnit="µm"/>
|
||||
<Plane TheZ="95" TheT="0" TheC="4" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.781" PositionZUnit="µm"/>
|
||||
<Plane TheZ="95" TheT="0" TheC="5" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.781" PositionZUnit="µm"/>
|
||||
<Plane TheZ="96" TheT="0" TheC="0" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.881" PositionZUnit="µm"/>
|
||||
<Plane TheZ="96" TheT="0" TheC="1" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.881" PositionZUnit="µm"/>
|
||||
<Plane TheZ="96" TheT="0" TheC="2" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.881" PositionZUnit="µm"/>
|
||||
<Plane TheZ="96" TheT="0" TheC="3" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.881" PositionZUnit="µm"/>
|
||||
<Plane TheZ="96" TheT="0" TheC="4" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.881" PositionZUnit="µm"/>
|
||||
<Plane TheZ="96" TheT="0" TheC="5" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.881" PositionZUnit="µm"/>
|
||||
<Plane TheZ="97" TheT="0" TheC="0" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.981" PositionZUnit="µm"/>
|
||||
<Plane TheZ="97" TheT="0" TheC="1" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.981" PositionZUnit="µm"/>
|
||||
<Plane TheZ="97" TheT="0" TheC="2" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.981" PositionZUnit="µm"/>
|
||||
<Plane TheZ="97" TheT="0" TheC="3" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.981" PositionZUnit="µm"/>
|
||||
<Plane TheZ="97" TheT="0" TheC="4" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.981" PositionZUnit="µm"/>
|
||||
<Plane TheZ="97" TheT="0" TheC="5" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.981" PositionZUnit="µm"/>
|
||||
<Plane TheZ="98" TheT="0" TheC="0" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.081" PositionZUnit="µm"/>
|
||||
<Plane TheZ="98" TheT="0" TheC="1" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.081" PositionZUnit="µm"/>
|
||||
<Plane TheZ="98" TheT="0" TheC="2" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.081" PositionZUnit="µm"/>
|
||||
<Plane TheZ="98" TheT="0" TheC="3" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.081" PositionZUnit="µm"/>
|
||||
<Plane TheZ="98" TheT="0" TheC="4" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.081" PositionZUnit="µm"/>
|
||||
<Plane TheZ="98" TheT="0" TheC="5" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.081" PositionZUnit="µm"/>
|
||||
<Plane TheZ="99" TheT="0" TheC="0" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.181" PositionZUnit="µm"/>
|
||||
<Plane TheZ="99" TheT="0" TheC="1" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.181" PositionZUnit="µm"/>
|
||||
<Plane TheZ="99" TheT="0" TheC="2" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.181" PositionZUnit="µm"/>
|
||||
<Plane TheZ="99" TheT="0" TheC="3" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.181" PositionZUnit="µm"/>
|
||||
<Plane TheZ="99" TheT="0" TheC="4" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.181" PositionZUnit="µm"/>
|
||||
<Plane TheZ="99" TheT="0" TheC="5" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.181" PositionZUnit="µm"/>
|
||||
<Plane TheZ="100" TheT="0" TheC="0" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.281" PositionZUnit="µm"/>
|
||||
<Plane TheZ="100" TheT="0" TheC="1" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.281" PositionZUnit="µm"/>
|
||||
<Plane TheZ="100" TheT="0" TheC="2" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.281" PositionZUnit="µm"/>
|
||||
<Plane TheZ="100" TheT="0" TheC="3" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.281" PositionZUnit="µm"/>
|
||||
<Plane TheZ="100" TheT="0" TheC="4" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.281" PositionZUnit="µm"/>
|
||||
<Plane TheZ="100" TheT="0" TheC="5" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.281" PositionZUnit="µm"/>
|
||||
</Pixels>
|
||||
</Image>
|
||||
</OME>
|
||||
@@ -0,0 +1,12 @@
|
||||
<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">
|
||||
<Image ID="Image:0" Name="test.tif">
|
||||
<AcquisitionDate>2025-01-29T14:42:42</AcquisitionDate>
|
||||
<Description/>
|
||||
<Pixels ID="Pixels:0" DimensionOrder="XYCZT" Type="int8" SignificantBits="8" Interleaved="false" BigEndian="false" SizeX="2" SizeY="2" SizeZ="1" SizeC="1" SizeT="1">
|
||||
<Channel ID="Channel:0:0" SamplesPerPixel="1">
|
||||
<LightPath/>
|
||||
</Channel>
|
||||
<MetadataOnly/>
|
||||
</Pixels>
|
||||
</Image>
|
||||
</OME>
|
||||
@@ -1,174 +0,0 @@
|
||||
from __future__ import annotations
|
||||
|
||||
from dataclasses import dataclass
|
||||
from os import getpid
|
||||
from time import sleep
|
||||
from typing import Any, Iterator, Optional, Sequence
|
||||
|
||||
import numpy as np
|
||||
import pytest
|
||||
|
||||
from parfor import Chunks, ParPool, SharedArray, parfor, pmap
|
||||
|
||||
|
||||
class SequenceIterator:
|
||||
def __init__(self, sequence: Sequence) -> None:
|
||||
self._sequence = sequence
|
||||
self._index = 0
|
||||
|
||||
def __iter__(self) -> SequenceIterator:
|
||||
return self
|
||||
|
||||
def __next__(self) -> Any:
|
||||
if self._index < len(self._sequence):
|
||||
item = self._sequence[self._index]
|
||||
self._index += 1
|
||||
return item
|
||||
else:
|
||||
raise StopIteration
|
||||
|
||||
def __len__(self) -> int:
|
||||
return len(self._sequence)
|
||||
|
||||
|
||||
class Iterable:
|
||||
def __init__(self, sequence: Sequence) -> None:
|
||||
self.sequence = sequence
|
||||
|
||||
def __iter__(self) -> SequenceIterator:
|
||||
return SequenceIterator(self.sequence)
|
||||
|
||||
|
||||
def iterators() -> tuple[Iterator, Optional[int]]:
|
||||
yield range(10), None
|
||||
yield list(range(10)), None
|
||||
yield (i for i in range(10)), 10
|
||||
yield SequenceIterator(range(10)), None
|
||||
yield Iterable(range(10)), 10
|
||||
|
||||
|
||||
@pytest.mark.parametrize("iterator", iterators())
|
||||
def test_chunks(iterator: tuple[Iterator, Optional[int]]) -> None:
|
||||
chunks = Chunks(iterator[0], size=2, length=iterator[1])
|
||||
assert list(chunks) == [[0, 1], [2, 3], [4, 5], [6, 7], [8, 9]]
|
||||
|
||||
|
||||
def test_parpool() -> None:
|
||||
def fun(i, j, k) -> int: # noqa
|
||||
return i * j * k
|
||||
|
||||
with ParPool(fun, (3,), {"k": 2}) as pool: # noqa
|
||||
for i in range(10):
|
||||
pool[i] = i
|
||||
|
||||
assert [pool[i] for i in range(10)] == [0, 6, 12, 18, 24, 30, 36, 42, 48, 54]
|
||||
|
||||
|
||||
def test_parfor() -> None:
|
||||
@parfor(range(10), (3,), {"k": 2})
|
||||
def fun(i, j, k):
|
||||
return i * j * k
|
||||
|
||||
assert fun == [0, 6, 12, 18, 24, 30, 36, 42, 48, 54]
|
||||
|
||||
|
||||
@pytest.mark.parametrize("serial", (True, False))
|
||||
def test_pmap(serial) -> None:
|
||||
def fun(i, j, k):
|
||||
return i * j * k
|
||||
|
||||
assert pmap(fun, range(10), (3,), {"k": 2}, serial=serial) == [
|
||||
0,
|
||||
6,
|
||||
12,
|
||||
18,
|
||||
24,
|
||||
30,
|
||||
36,
|
||||
42,
|
||||
48,
|
||||
54,
|
||||
]
|
||||
|
||||
|
||||
@pytest.mark.parametrize("serial", (True, False))
|
||||
def test_pmap_with_idx(serial) -> None:
|
||||
def fun(i, j, k):
|
||||
return i * j * k
|
||||
|
||||
assert pmap(fun, range(10), (3,), {"k": 2}, serial=serial, yield_index=True) == [
|
||||
(0, 0),
|
||||
(1, 6),
|
||||
(2, 12),
|
||||
(3, 18),
|
||||
(4, 24),
|
||||
(5, 30),
|
||||
(6, 36),
|
||||
(7, 42),
|
||||
(8, 48),
|
||||
(9, 54),
|
||||
]
|
||||
|
||||
|
||||
@pytest.mark.parametrize("serial", (True, False))
|
||||
def test_pmap_chunks(serial) -> None:
|
||||
def fun(i, j, k):
|
||||
return [i_ * j * k for i_ in i]
|
||||
|
||||
chunks = Chunks(range(10), size=2)
|
||||
assert pmap(fun, chunks, (3,), {"k": 2}, serial=serial) == [
|
||||
[0, 6],
|
||||
[12, 18],
|
||||
[24, 30],
|
||||
[36, 42],
|
||||
[48, 54],
|
||||
]
|
||||
|
||||
|
||||
def test_id_reuse() -> None:
|
||||
def fun(i):
|
||||
return i[0].a
|
||||
|
||||
@dataclass
|
||||
class T:
|
||||
a: int = 3
|
||||
|
||||
def gen(total):
|
||||
for i in range(total):
|
||||
t = T(i)
|
||||
yield t
|
||||
del t
|
||||
|
||||
a = pmap(fun, Chunks(gen(1000), size=1, length=1000), total=1000) # noqa
|
||||
assert all([i == j for i, j in enumerate(a)])
|
||||
|
||||
|
||||
@pytest.mark.parametrize("n_processes", (2, 4, 6))
|
||||
def test_n_processes(n_processes) -> None:
|
||||
@parfor(range(12), n_processes=n_processes)
|
||||
def fun(i): # noqa
|
||||
sleep(0.25)
|
||||
return getpid()
|
||||
|
||||
assert len(set(fun)) <= n_processes
|
||||
|
||||
|
||||
def test_shared_array() -> None:
|
||||
def fun(i, a):
|
||||
a[i] = i
|
||||
|
||||
with SharedArray(100, int) as arr:
|
||||
pmap(fun, range(len(arr)), (arr,))
|
||||
b = np.array(arr)
|
||||
|
||||
assert np.all(b == np.arange(len(arr)))
|
||||
|
||||
|
||||
def test_nesting() -> None:
|
||||
def a(i):
|
||||
return i**2
|
||||
|
||||
def b(i):
|
||||
return pmap(a, range(i, i + 50))
|
||||
|
||||
assert pmap(b, range(10)) == [[i**2 for i in range(j, j + 50)] for j in range(10)]
|
||||
Reference in New Issue
Block a user