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Author SHA1 Message Date
w.pomp bc7f48c65a - workflow update
PyTest / pytest (ubuntu-latest, 3.10) (push) Successful in 22s
PyTest / pytest (ubuntu-latest, 3.12) (push) Successful in 24s
PyTest / pytest (ubuntu-latest, 3.14) (push) Successful in 21s
2026-05-12 15:37:23 +02:00
w.pomp d6c85984b9 - backwards compatibility bugfix
PyTest / pytest (ubuntu-latest, 3.10) (push) Successful in 2m23s
PyTest / pytest (ubuntu-latest, 3.12) (push) Successful in 36s
PyTest / pytest (ubuntu-latest, 3.14) (push) Successful in 36s
2026-05-12 15:30:03 +02:00
w.pomp 8619c0fb34 - add some caching to prevent repeated ray.put and pickling 2026-01-22 20:11:13 +01:00
w.pomp 879da12628 - disable ray dashboard 2026-01-21 16:26:41 +01:00
w.pomp bb74d6e3b0 - add close method to PoolSingleton for backwards compatibility 2026-01-21 15:27:45 +01:00
Wim Pomp 9fdbf49b5c - n_processes can now be changed each time
- block adding tasks if pool is busy
2026-01-09 11:37:55 +01:00
Wim Pomp 1098239af9 recurse when pickling objects with dill 2026-01-08 20:14:08 +01:00
Wim Pomp 81d0362540 - separate output from progress bar 2026-01-08 17:18:26 +01:00
Wim Pomp 2cff1a1515 - add custom pickler back in 2026-01-08 16:25:24 +01:00
Wim Pomp f3737ffd44 - publish to pypi using github action 2026-01-08 11:15:23 +01:00
Wim Pomp d47db7aa14 - publish to pypi using github action 2026-01-08 11:07:19 +01:00
Wim Pomp 0ccd09f079 - publish to pypi using github action 2026-01-08 10:57:50 +01:00
Wim Pomp 43a0cf68b5 - add allow_output option
- update readme
2026-01-08 10:42:50 +01:00
Wim Pomp 6341561380 update pyproject.toml 2026-01-08 01:03:59 +01:00
Wim Pomp 310616d583 update pyproject.toml 2026-01-08 01:00:53 +01:00
Wim Pomp 5528b54ede Now based on ray, which enables nested parallel computations. 2026-01-08 00:48:14 +01:00
Wim Pomp a84bf2d29e Merge remote-tracking branch 'origin/master' 2025-01-06 18:14:40 +01:00
Wim Pomp d0bc749bb4 - add SharedArray to share numpy arrays
- fix async call_later when no event loop is available
2025-01-06 18:14:18 +01:00
Wim Pomp 326a06f9da - add SharedArray to share numpy arrays
- fix async call_later when no event loop is available
2025-01-06 18:01:55 +01:00
Wim Pomp eb92ce006d - make cpu_count a field to PoolSingleton for easy global configuration of number of processes
- remove TypeVars
- manually wrap parfor and pmap
- also redirect output when retrieving task
2024-12-20 16:43:02 +01:00
Wim Pomp 31e07b49eb - statically determine gil/nogil, otherwise we cannot subclass some things 2024-12-05 12:57:46 +01:00
Wim Pomp 7291468fb7 - add async callback to close pool after 10 minutes of inactivity 2024-11-05 15:05:10 +01:00
Wim Pomp 46bd419d3d - add Task class for typing again 2024-11-04 14:52:46 +01:00
Wim Pomp c47650fc30 - add close method to PoolSingleton class again 2024-10-22 11:23:16 +02:00
Wim Pomp 396a1a791d - gmap bugfix 2024-10-21 10:25:17 +02:00
Wim Pomp d6afbc3caf - add PoolSingleton to __init__
- update readme
2024-10-20 13:10:49 +02:00
Wim Pomp 57b3fbe2b2 - nogil version (selected automatically) which uses threads instead of processes 2024-10-20 12:45:51 +02:00
Wim Pomp b3aabc68ab - nogil version (selected automatically) which uses threads instead of processes 2024-10-20 12:45:08 +02:00
Wim Pomp f43734c8be - fix zeros length iterator bug
- fix bug where sometimes not all results are returned
2024-09-13 14:53:42 +02:00
Wim Pomp fb7757828f - fix serial computation
- some more tests
2024-09-11 13:08:03 +02:00
Wim Pomp 4d80316244 - add gmap: function like pmap, but returning a generator instead of a list
- add arguments for returning results out/in order and returning result indices
2024-09-05 18:37:47 +02:00
Wim Pomp 29203dd128 - redirect stdout and stderr in child processes to devnull instead of None
- add parfor.__version__
2024-07-22 17:32:17 +02:00
Wim Pomp 9ce96a7e61 - redirect stdout and stderr in child processes 2024-07-08 17:57:23 +02:00
Wim Pomp b609df8b52 - bugfix: do not restart pool when n_processes = None 2024-05-28 16:35:14 +02:00
Wim Pomp 9783c1d1f2 - introduce n_processes to change the number of processes in the pool 2024-05-24 16:57:35 +02:00
Wim Pomp ac4d599646 - minimum python: 3.10
- typing
- task_error bug fix
- remove some deprecated functions
2024-04-26 18:32:12 +02:00
Wim Pomp 42746d21eb - make ParPoolSingleton.close a class method. 2024-03-19 18:52:20 +01:00
Wim Pomp 6fefdb9be0 - bugfix for argument bar=False 2024-02-09 13:32:18 +01:00
Wim Pomp bb3b87b913 - catch and ignore errors when emptying queue
- timeout on closing pool
- close manager on closing pool
2024-01-29 11:25:22 +01:00
Wim Pomp 0b0c7a798f - Shutdown workers after 10 minutes of inactivity. Restart pool when needed again. 2023-11-18 13:38:01 +01:00
Wim Pomp ad8d9a4efb - Protect reference counter with a lock because changes to a multiprocessing manager dict are not atomic. 2023-11-08 12:50:30 +01:00
Wim Pomp 098d1810c3 - Bugfix 2023-11-07 16:51:02 +01:00
Wim Pomp f22b682b2a - skip KeyboardInterrupts in workers
- silence some warnings
2023-11-07 15:04:54 +01:00
Wim Pomp e936292905 - Implement reference counting to make sure the parent process does not trash the item before all children trashed it. 2023-10-27 17:48:52 +02:00
Wim Pomp 265470e0ac - Use a shared memory approach.
- Track unpickled objects by CouldNotBePickled class.
- Bump minimal python to 3.8.
2023-10-12 14:46:42 +02:00
Wim Pomp 0263b6a4c7 - Copy previous task to prevent unnecessary pickling. 2023-09-13 17:04:55 +02:00
Wim Pomp f3302f6dba - Use a singleton pool to prevent lengthy restarts of the pool, this also means that arguments for pool size have gone.
- Removed qbar and TqdmMeter.
- Wrap chunked function for better error messages.
2023-09-08 17:19:35 +02:00
Wim Pomp 92f162b7d5 - Make processes non-daemonic
- Deprecate terminator argument
2023-08-16 16:46:50 +02:00
Wim Pomp dfee4bc0ea - README update 2023-08-08 17:50:20 +02:00
Wim Pomp 0635c62d42 - bugfix: some iterables caused an error
- pytest tests
- deprecation warnings
- use poetry for installs
2023-08-08 15:05:31 +02:00
Wim Pomp 7e0c0cc45d - bugfix in parpool.get_newest
- make TqdmMeter bar decrease when necessary
2022-06-28 11:08:37 +02:00
Wim Pomp 84f4afbba2 Merge remote-tracking branch 'origin/master' 2022-05-03 15:56:20 +02:00
Wim Pomp 32c5560306 - rename some things to conform to PEP
- pmap and parfor now automatically divide the task in chunks: less pickling is needed this way
- pickle code in a new file: prevent some unpickleble things from getting pickled
- Chunks now supports generators when the length keyword argument is supplied
- TqdmMeter can have a description
2022-05-03 15:56:13 +02:00
Wim Pomp d2c226a37e - rename some things to conform to PEP
- pmap and parfor now automatically divide the task in chunks: less pickling is needed this way
- pickle code in a new file: prevent some unpickleble things from getting pickled
- Chunks now supports generators when the length keyword argument is supplied
- TqdmMeter can have a description
2022-05-03 15:55:11 +02:00
Wim Pomp 865ec70d97 - bug fix in killed process detection 2022-03-22 15:36:07 +01:00
Wim Pomp fcf451cb23 - drop support for python 2
- automatically kill javabridge (if it exists) at the end of a process
- better hashing and tasking
2022-03-03 12:43:00 +01:00
Wim Pomp 4bddca82eb - option for a callback function to update a user defined bar 2021-07-29 21:04:28 +02:00
Wim Pomp 8ed1a5500e - chunks: kwargs to set number of chunks relative to number of cpus 2021-07-17 10:54:00 +02:00
Wim Pomp bc2ae2ea25 - Make progress bar update with chunksize when using chunks.
- Catch exceptions, but not keyboard interrupts.
2021-05-29 11:09:54 +02:00
Wim Pomp 9caeb06c2b - Bugfix 2021-05-25 10:51:14 +02:00
Wim Pomp 6c9c18746b - Make chunks a class, so we can do len(chunks(...)) 2021-05-24 18:59:32 +02:00
Wim Pomp 95ae325028 - Better chunks function, option for both number of chunks or size of chunks. 2021-05-24 18:19:14 +02:00
Wim Pomp 5d57081713 - Better and faster error handling. 2021-03-19 20:39:38 +01:00
Wim Pomp ddc0189bad - Add get_newest method to parpool. 2021-03-06 00:09:16 +01:00
Wim Pomp 6cce9e9b8e - Better error handling 2021-03-05 22:27:00 +01:00
Wim Pomp 61f1429543 - bar for serial case 2021-02-20 15:17:17 +01:00
Wim Pomp 3d99250b98 - force number of workers to be at least 2
- update readme
2021-01-04 12:35:01 +01:00
Wim Pomp 0721e2125c - differentiate use of nP into nP and rP
- default to using one process per cpu core
- update requirements with versions
2021-01-04 12:25:19 +01:00
Wim Pomp b979a0c72a Merge remote-tracking branch 'origin/master' 2020-12-28 13:53:36 +01:00
Wim Pomp d7a2a473d5 Update readme with if __name__ == '__main__': 2020-12-28 13:53:12 +01:00
Wim Pomp a8fefb5d00 Update readme with if __name__ == '__main__': 2020-12-28 13:52:05 +01:00
Wim Pomp a02677dc1d - Fix chunks for when length of input is smaller than chunk size. 2020-11-24 16:34:40 +01:00
w.pomp 2ddf73ed0f - Fix qbar error for OSX. 2020-09-11 17:37:47 +02:00
w.pomp 6c4f2d5132 - Add terminator function. 2020-09-04 18:03:30 +02:00
w.pomp da70cf7a2f - Dill (almost) everything.
- Change dill a little to automatically omit undillable parts of objects.
- README.me Limitations
2020-09-03 11:29:15 +02:00
w.pomp 881496b8f4 - Add github link to setup.py
- Add install_requires
2020-08-31 17:39:52 +02:00
w.pomp 0d07638e98 First commit. 2020-08-31 16:10:12 +02:00
25 changed files with 1251 additions and 28528 deletions
+21 -44
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@@ -1,54 +1,31 @@
name: Publish name: Publish
on: [push, pull_request, workflow_call] on: [workflow_dispatch]
permissions: permissions:
contents: read contents: read
jobs: jobs:
crates_io_publish: publish_pytest:
name: Publish (crates.io) uses: ./.github/workflows/pytest.yml
pypi_publish:
runs-on: ubuntu-latest runs-on: ubuntu-latest
timeout-minutes: 25 needs: [ publish_pytest ]
steps: steps:
- uses: actions/checkout@v4 - name: Checkout
- uses: dtolnay/rust-toolchain@stable uses: actions/checkout@v6
- name: Build sdist
- name: cargo-release Cache uses: actions/setup-python@v6
id: cargo_release_cache
uses: actions/cache@v3
with: with:
path: ~/.cargo/bin/cargo-release python-version: "3.12"
key: ${{ runner.os }}-cargo-release - name: Install build
run: pip install build
- run: cargo install cargo-release - name: Build a binary wheel and a source tarball
if: steps.cargo_release_cache.outputs.cache-hit != 'true' run: python -m build
- name: Publish to PyPI
- name: cargo login uses: pypa/gh-action-pypi-publish@release/v1
run: cargo login ${{ secrets.CRATES_IO_API_TOKEN }} with:
skip-existing: true
# allow-branch HEAD is because GitHub actions switches password: ${{ secrets.PYPI_API_TOKEN }}
# to the tag while building, which is a detached head env:
GITHUB_WORKFLOW_REF: 1.10.1
# Publishing is currently messy, because:
#
# * `peace_rt_model_core` exports `NativeError` or `WebError` depending on the target.
# * `peace_rt_model_web` fails to build when publishing the workspace for a native target.
# * `peace_rt_model_web` still needs its dependencies to be published before it can be
# published.
# * `peace_rt_model_hack` needs `peace_rt_model_web` to be published before it can be
# published.
#
# We *could* pass through `--no-verify` so `cargo` doesn't build the crate before publishing,
# which is reasonable, since this job only runs after the Linux, Windows, and WASM builds
# have passed.
- name: "cargo release publish"
run: |-
cargo release \
publish \
--workspace \
--all-features \
--allow-branch "main" \
--no-confirm \
--no-verify \
--execute
+26
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name: PyTest
on: [push, pull_request, workflow_call]
permissions:
contents: read
jobs:
pytest:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: [ "3.10", "3.12", "3.14" ]
os: [ ubuntu-latest ]
steps:
- name: Checkout
uses: actions/checkout@v6
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v6
with:
python-version: ${{ matrix.python-version }}
- name: Install
run: pip install .[test]
- name: Test with pytest
run: pytest
+6 -73
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@@ -1,73 +1,6 @@
/target /build/
/dist/
# Byte-compiled / optimized / DLL files /parfor.egg-info/
__pycache__/ /.idea/
.pytest_cache/ /.pytest_cache/
*.py[cod] ._*
# C extensions
*.so
# Distribution / packaging
.Python
.venv/
env/
bin/
build/
develop-eggs/
dist/
eggs/
lib/
lib64/
parts/
sdist/
var/
include/
man/
venv/
*.egg-info/
.installed.cfg
*.egg
# Installer logs
pip-log.txt
pip-delete-this-directory.txt
pip-selfcheck.json
# Unit test / coverage reports
htmlcov/
.tox/
.coverage
.cache
nosetests.xml
coverage.xml
# Translations
*.mo
# Mr Developer
.mr.developer.cfg
.project
.pydevproject
# Rope
.ropeproject
# Django stuff:
*.log
*.pot
.DS_Store
# Sphinx documentation
docs/_build/
# PyCharm
.idea/
# VSCode
.vscode/
# Pyenv
.python-version
/Cargo.lock
-32
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[package]
name = "ome-metadata"
version = "0.1.0"
edition = "2024"
rust-version = "1.85.1"
authors = ["Wim Pomp <w.pomp@nki.nl>"]
license = "MIT"
description = "Ome metadata as a rust/python structure."
homepage = "https://github.com/wimpomp/ome-metadata"
repository = "https://github.com/wimpomp/ome-metadata"
readme = "README.md"
keywords = ["bioformats", "imread", "ome", "metadata"]
categories = ["multimedia::images", "science"]
exclude = ["/tests"]
# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
[lib]
name = "ome_metadata"
crate-type = ["cdylib", "rlib"]
[dependencies]
anyhow = "1.0.98"
serde = { version = "1.0.219", features = ["derive"] }
quick-xml = { version = "0.37.5", features = ["serialize"] }
[dependencies.pyo3]
version = "0.24.2"
features = ["extension-module", "abi3-py310", "generate-import-lib", "anyhow"]
optional = true
[features]
python = ["dep:pyo3"]
+163 -20
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@@ -1,25 +1,168 @@
# ome-metadata [![pytest](https://git.wimpomp.nl/wim/parfor/actions/workflows/pytest.yml/badge.svg)](https://git.wimpomp.nl/wim/parfor/actions?workflow=pytest.yml)
Open Microscopy XML metadata (https://www.openmicroscopy.org/Schemas/) as a collection of Rust structs and enums, with translation to Python. # Parfor
Used to parallelize for-loops using parfor in Matlab? This package allows you to do the same in python.
Take any normal serial but parallelizable for-loop and execute it in parallel using easy syntax.
Don't worry about the technical details of using the multiprocessing module, race conditions, queues,
parfor handles all that. Now powered by [ray](https://pypi.org/project/ray/).
## Rust Tested on linux, Windows and OSX with python 3.10 and 3.12.
```
use std::fs::read_to_string;
use ome_metadata::Ome;
let xml = read_to_string($file)?; ## Why is parfor better than just using multiprocessing?
let ome: Ome = xml.parse()?; - Easy to use
let image = &ome.image.unwrap()[0]; - Progress bars are built-in
println!("acquisition date: {:#?}", image.acquisition_date); - Retry the task in the main process upon failure for easy debugging
``` - Using a modified version of dill when ray fails to serialize an object:
a lot more objects can be used when parallelizing
## Python ## How it works
``` [Ray](https://pypi.org/project/ray/) does all the heavy lifting. Parfor now is just a wrapper around ray, adding
from ome_metadata import Ome some ergonomics.
with open($file) as f: ## Installation
xml = f.read() `pip install parfor`
ome = Ome.from_xml(xml)
image = ome.image[0] ## Usage
print(f"acquisition date: {image.acquisition_date}") Parfor decorates a functions and returns the result of that function evaluated in parallel for each iteration of
``` an iterator.
## Requires
numpy, ray, tqdm
## Arguments
To functions `parfor.parfor`, `parfor.pmap` and `parfor.gmap`.
### 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: keyword arguments for tqdm.tqdm
### Return
list with results from applying the function 'fun' to each iteration of the iterable / iterator
## Examples
### Normal serial for loop
<<
from time import sleep
a = 3
fun = []
for i in range(10):
sleep(1)
fun.append(a * i ** 2)
print(fun)
>> [0, 3, 12, 27, 48, 75, 108, 147, 192, 243]
### Using parfor to parallelize
<<
from time import sleep
from parfor import parfor
@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]
<<
@parfor(range(10), (3,), bar=False)
def fun(i, a):
sleep(1)
return a * i ** 2
print(fun)
>> [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]
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]
### 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.
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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
+119
View File
@@ -0,0 +1,119 @@
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()
-38
View File
@@ -1,38 +0,0 @@
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
+22 -24
View File
@@ -1,32 +1,30 @@
[build-system]
requires = ["maturin>=1.8,<2.0"]
build-backend = "maturin"
[project] [project]
name = "ome-metadata" name = "parfor"
keywords = ["bioformats", "imread", "ome", "metadata"] version = "2026.5.0"
requires-python = ">=3.10" description = "A package to mimic the use of parfor as done in Matlab."
classifiers = [ authors = [
"License :: OSI Approved :: MIT License", { name = "Wim Pomp-Pervova", email = "wimpomp@gmail.com" }
"Programming Language :: Rust", ]
"Programming Language :: Python", license = { text = "MIT" }
"Programming Language :: Python :: 3", readme = "README.md"
"Programming Language :: Python :: 3 :: Only", keywords = ["parfor", "concurrency", "multiprocessing", "parallel"]
"Programming Language :: Python :: 3.10", requires-python = ">=3.10"
"Programming Language :: Python :: 3.11", dependencies = [
"Programming Language :: Python :: 3.12", "dill >= 0.3.0",
"Programming Language :: Python :: 3.13", "numpy",
"Programming Language :: Python :: 3.14", "tqdm >= 4.50.0",
"ray",
] ]
dynamic = ["version", "description", "authors", "license", "readme"]
[project.urls] [project.urls]
Repository = "https://github.com/wimpomp/ome-metadata" repository = "https://git.wimpomp.nl/wim/parfor"
[tool.maturin] [project.optional-dependencies]
python-source = "py" test = ["pytest"]
features = ["pyo3/extension-module", "python"]
module-name = "ome_metadata.ome_metadata_rs" [tool.ruff]
line-length = 119
indent-width = 4
[tool.isort] [tool.isort]
line_length = 119 line_length = 119
-51
View File
@@ -1,51 +0,0 @@
#![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"
);
}
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-13
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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(())
}
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@@ -1,416 +0,0 @@
<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"/>
<Plane TheZ="6" TheT="0" TheC="0" DeltaT="9.530999898910522" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="0.04" PositionZUnit="µm"/>
<Plane TheZ="7" TheT="0" TheC="0" DeltaT="10.483999967575073" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="0.54" PositionZUnit="µm"/>
<Plane TheZ="8" TheT="0" TheC="0" DeltaT="11.437000036239624" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="1.04" PositionZUnit="µm"/>
<Plane TheZ="9" TheT="0" TheC="0" DeltaT="12.389999866485596" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="1.54" PositionZUnit="µm"/>
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<Plane TheZ="11" TheT="0" TheC="0" DeltaT="14.294999837875366" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="2.54" PositionZUnit="µm"/>
<Plane TheZ="12" TheT="0" TheC="0" DeltaT="15.247999906539917" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="3.04" PositionZUnit="µm"/>
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<Plane TheZ="0" TheT="1" TheC="0" DeltaT="22.99399995803833" DeltaTUnit="s" PositionX="-2097.2" PositionXUnit="µm" PositionY="-12106.9" PositionYUnit="µm" PositionZ="-2.96" PositionZUnit="µm"/>
<Plane TheZ="1" TheT="1" TheC="0" DeltaT="23.94700002670288" DeltaTUnit="s" PositionX="-2097.2" PositionXUnit="µm" PositionY="-12106.9" PositionYUnit="µm" PositionZ="-2.46" PositionZUnit="µm"/>
<Plane TheZ="2" TheT="1" TheC="0" DeltaT="24.8989999294281" DeltaTUnit="s" PositionX="-2097.2" PositionXUnit="µm" PositionY="-12106.9" PositionYUnit="µm" PositionZ="-1.96" PositionZUnit="µm"/>
<Plane TheZ="3" TheT="1" TheC="0" DeltaT="25.85199999809265" DeltaTUnit="s" PositionX="-2097.2" PositionXUnit="µm" PositionY="-12106.9" PositionYUnit="µm" PositionZ="-1.46" PositionZUnit="µm"/>
<Plane TheZ="4" TheT="1" TheC="0" DeltaT="26.805000066757202" DeltaTUnit="s" PositionX="-2097.2" PositionXUnit="µm" PositionY="-12106.9" PositionYUnit="µm" PositionZ="-0.96" PositionZUnit="µm"/>
<Plane TheZ="5" TheT="1" TheC="0" DeltaT="27.757999897003174" DeltaTUnit="s" PositionX="-2097.2" PositionXUnit="µm" PositionY="-12106.9" PositionYUnit="µm" PositionZ="-0.46" PositionZUnit="µm"/>
<Plane TheZ="6" TheT="1" TheC="0" DeltaT="28.710999965667725" DeltaTUnit="s" PositionX="-2097.2" PositionXUnit="µm" PositionY="-12106.9" PositionYUnit="µm" PositionZ="0.04" PositionZUnit="µm"/>
<Plane TheZ="7" TheT="1" TheC="0" DeltaT="29.664000034332275" DeltaTUnit="s" PositionX="-2097.2" PositionXUnit="µm" PositionY="-12106.9" PositionYUnit="µm" PositionZ="0.54" PositionZUnit="µm"/>
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</OME>
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<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">
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-121
View File
@@ -1,121 +0,0 @@
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</OME>
-12
View File
@@ -1,12 +0,0 @@
<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>
+174
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@@ -0,0 +1,174 @@
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)]