- workflow update

- block adding tasks if pool is busy

.github/workflows/publish.yml

@@ -1,54 +1,31 @@
 name: Publish
 
-on: [push, pull_request, workflow_call]
+on: [workflow_dispatch]
 
 permissions:
   contents: read
 
 jobs:
-  crates_io_publish:
-    name: Publish (crates.io)
+  publish_pytest:
+    uses: ./.github/workflows/pytest.yml
+  pypi_publish:
     runs-on: ubuntu-latest
-    timeout-minutes: 25
+    needs: [ publish_pytest ]
     steps:
-      - uses: actions/checkout@v4
-      - uses: dtolnay/rust-toolchain@stable
-
-      - name: cargo-release Cache
-        id: cargo_release_cache
-        uses: actions/cache@v3
+      - name: Checkout
+        uses: actions/checkout@v6
+      - name: Build sdist
+        uses: actions/setup-python@v6
         with:
-          path: ~/.cargo/bin/cargo-release
-          key: ${{ runner.os }}-cargo-release
-
-      - run: cargo install cargo-release
-        if: steps.cargo_release_cache.outputs.cache-hit != 'true'
-
-      - name: cargo login
-        run: cargo login ${{ secrets.CRATES_IO_API_TOKEN }}
-
-      # allow-branch HEAD is because GitHub actions switches
-      # to the tag while building, which is a detached head
-
-      # 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
+          python-version: "3.12"
+      - name: Install build
+        run: pip install build
+      - name: Build a binary wheel and a source tarball
+        run: python -m build
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          skip-existing: true
+          password: ${{ secrets.PYPI_API_TOKEN }}
+        env:
+          GITHUB_WORKFLOW_REF: 1.10.1

.github/workflows/pytest.yml

@@ -0,0 +1,26 @@
+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

.gitignore

@@ -1,73 +1,6 @@
-/target
-
-# Byte-compiled / optimized / DLL files
-__pycache__/
-.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
+/build/
+/dist/
+/parfor.egg-info/
+/.idea/
+/.pytest_cache/
+._*

Cargo.toml

@@ -1,32 +0,0 @@
-[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"]

README.md

@@ -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
-``` 
-use std::fs::read_to_string;
-use ome_metadata::Ome;
+Tested on linux, Windows and OSX with python 3.10 and 3.12.
 
-let xml = read_to_string($file)?;
-let ome: Ome = xml.parse()?;
-let image = &ome.image.unwrap()[0];
-println!("acquisition date: {:#?}", image.acquisition_date);
-```
+## Why is parfor better than just using multiprocessing?
+- Easy to use
+- Progress bars are built-in
+- 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
-```
-from ome_metadata import Ome
+## How it works
+[Ray](https://pypi.org/project/ray/) does all the heavy lifting. Parfor now is just a wrapper around ray, adding
+some ergonomics.
 
-with open($file) as f:
-    xml = f.read()
-ome = Ome.from_xml(xml)
-image = ome.image[0]
-print(f"acquisition date: {image.acquisition_date}")
-```
+## Installation
+`pip install parfor`
+
+## Usage
+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.

parfor/__init__.py

@@ -0,0 +1,720 @@
+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

parfor/pickler.py

@@ -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()

py/ome_metadata/__init__.py

@@ -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

pyproject.toml

@@ -1,32 +1,30 @@
-[build-system]
-requires = ["maturin>=1.8,<2.0"]
-build-backend = "maturin"
-
 [project]
-name = "ome-metadata"
-keywords = ["bioformats", "imread", "ome", "metadata"]
-requires-python = ">=3.10"
-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",
+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"]
+requires-python = ">=3.10"
+dependencies = [
+    "dill >= 0.3.0",
+    "numpy",
+    "tqdm >= 4.50.0",
+    "ray",
 ]
-dynamic = ["version", "description", "authors", "license", "readme"]
 
 [project.urls]
-Repository = "https://github.com/wimpomp/ome-metadata"
+repository = "https://git.wimpomp.nl/wim/parfor"
 
-[tool.maturin]
-python-source = "py"
-features = ["pyo3/extension-module", "python"]
-module-name = "ome_metadata.ome_metadata_rs"
+[project.optional-dependencies]
+test = ["pytest"]
+
+[tool.ruff]
+line-length = 119
+indent-width = 4
 
 [tool.isort]
 line_length = 119

src/lib.rs

@@ -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"
-    );
-}

src/py.rs

@@ -1,13 +0,0 @@
-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(())
-}

tests/1xp53-01-AP1.xml

@@ -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"/>
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tests/4-Pos_001_002.xml

@@ -1,88 +0,0 @@
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-      <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"/>
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-      <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"/>
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-      <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>

tests/Experiment-2029.xml

@@ -1,121 +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="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"/>
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-    <Filter ID="Filter:12">
-      <TransmittanceRange CutIn="495.0" CutInUnit="nm" CutOut="550.0" CutOutUnit="nm"/>
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-    <Filter ID="Filter:13">
-      <TransmittanceRange CutOut="4095.0" CutOutUnit="nm"/>
-    </Filter>
-    <Filter ID="Filter:14">
-      <TransmittanceRange CutIn="575.0" CutInUnit="nm" CutOut="620.0" CutOutUnit="nm"/>
-    </Filter>
-    <Filter ID="Filter:15">
-      <TransmittanceRange CutOut="4095.0" CutOutUnit="nm"/>
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-    <Filter ID="Filter:16">
-      <TransmittanceRange CutIn="660.0" CutInUnit="nm" CutOut="720.0" CutOutUnit="nm"/>
-    </Filter>
-    <Dichroic ID="Dichroic:1"/>
-    <Dichroic ID="Dichroic:2"/>
-  </Instrument>
-  <Image ID="Image:0" Name="Experiment-2029.czi #1">
-    <AcquisitionDate>2023-11-27T13:35:29.360</AcquisitionDate>
-    <ExperimenterRef ID="Experimenter:0"/>
-    <InstrumentRef ID="Instrument:0"/>
-    <ObjectiveSettings ID="Objective:1" Medium="Air" RefractiveIndex="1.000293"/>
-    <StageLabel Name="Scene position #0" X="-0.1" XUnit="µm" Y="0.0" YUnit="µm" Z="0.0" ZUnit="µm"/>
-    <Pixels ID="Pixels:0" DimensionOrder="XYCZT" Type="uint16" SignificantBits="16" Interleaved="false" BigEndian="false" SizeX="1280" SizeY="1280" SizeZ="1" SizeC="2" SizeT="10" PhysicalSizeX="0.6310679611650485" PhysicalSizeXUnit="µm" PhysicalSizeY="0.6310679611650485" PhysicalSizeYUnit="µm" TimeIncrement="1.015" TimeIncrementUnit="s">
-      <Channel ID="Channel:0:0" Name="Hamamatsu Camera" SamplesPerPixel="1" IlluminationType="Epifluorescence" AcquisitionMode="Other" ExcitationWavelength="488.0" ExcitationWavelengthUnit="nm" EmissionWavelength="597.5" EmissionWavelengthUnit="nm" Fluor="Dye1" Color="10040319">
-        <DetectorSettings ID="Detector:HamamatsuCamera" Gain="0.0" Binning="1x1"/>
-        <FilterSetRef ID="FilterSet:1"/>
-        <LightPath/>
-      </Channel>
-      <Channel ID="Channel:0:1" Name="Hamamatsu Camera #2" SamplesPerPixel="1" IlluminationType="Epifluorescence" AcquisitionMode="Other" ExcitationWavelength="488.0" ExcitationWavelengthUnit="nm" Fluor="Dye2" Color="-16776961">
-        <DetectorSettings ID="Detector:HamamatsuCamera#2" Binning="1x1"/>
-        <FilterSetRef ID="FilterSet:2"/>
-        <LightPath/>
-      </Channel>
-      <MetadataOnly/>
-      <Plane TheZ="0" TheT="0" TheC="0" DeltaT="0.2760000228881836" DeltaTUnit="s" ExposureTime="27.32513" ExposureTimeUnit="s" PositionX="-0.1" PositionXUnit="µm" PositionY="0.0" PositionYUnit="µm" PositionZ="0.0" PositionZUnit="µm"/>
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-      <Plane TheZ="0" TheT="1" TheC="0" DeltaT="0.2780001163482666" DeltaTUnit="s" ExposureTime="27.32513" ExposureTimeUnit="s" PositionX="-0.1" PositionXUnit="µm" PositionY="0.0" PositionYUnit="µm" PositionZ="0.0" PositionZUnit="µm"/>
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tests/YTL1841B2-2-1_1hr_DMSO_galinduction_1.xml

@@ -1,11 +0,0 @@
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-  <Image ID="Image:0" Name="max.tif">
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tests/YTL1849A111_2023_05_04__14_46_19_cellnr_1_track.xml

@@ -1,21 +0,0 @@
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-  <Image ID="Image:0" Name="YTL1849A111_2023_05_04__14_46_19_cellnr_1_track.tif">
-    <AcquisitionDate>2023-05-10T21:20:56</AcquisitionDate>
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-      <MetadataOnly/>
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-  </Image>
-</OME>

tests/YTL378_JF552.xml

@@ -1,106 +0,0 @@
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-  <Instrument ID="Instrument:0">
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-    <Filter ID="Filter:0:1"/>
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-    <Filter ID="Filter:1:1"/>
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-    <Microscope Type="Other"/>
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-    <Filter ID="Filter:2:1"/>
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tests/beads_2023_05_04__19_00_22.xml

@@ -1,652 +0,0 @@
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-    </Pixels>
-  </Image>
-</OME>

tests/test.xml

@@ -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>

tests/test_parfor.py

@@ -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)]