- Python: tree of python objects instead of tree of dicts

- Rust: more derives

.github/workflows/publish.yml

@@ -1,31 +0,0 @@
-name: Publish
-
-on: [workflow_dispatch]
-
-permissions:
-  contents: read
-
-jobs:
-  publish_pytest:
-    uses: ./.github/workflows/pytest.yml
-  pypi_publish:
-    runs-on: ubuntu-latest
-    needs: [ publish_pytest ]
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v6
-      - name: Build sdist
-        uses: actions/setup-python@v6
-        with:
-          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/publish_crates.yml

@@ -0,0 +1,66 @@
+name: Publish
+
+on: [workflow_dispatch]
+
+permissions:
+  contents: read
+
+jobs:
+  crates_io_publish:
+    name: Publish (crates.io)
+    runs-on: ubuntu-latest
+    timeout-minutes: 25
+    steps:
+      - uses: actions/checkout@v6
+      - name: Restore cache
+        uses: actions/cache/restore@v4
+        with:
+          path: |
+            ~/.cargo
+          key: cache-ubuntu-cargo-publish
+
+      - name: Install Rust
+        run: |-
+          export PATH="$HOME/.cargo/bin:$PATH"
+          if ! command -v rustc >/dev/null 2>&1; then
+            curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
+          else
+            rustup update
+          fi
+          cargo install cargo-release
+        shell: bash
+
+      # 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: |-
+          export PATH="$HOME/.osxcross/bin:$PATH"
+          cargo login ${{ secrets.CRATES_IO_API_TOKEN }}
+          cargo release \
+            publish \
+            --workspace \
+            --all-features \
+            --allow-branch "main" \
+            --no-confirm \
+            --no-verify \
+            --execute
+
+      - name: Store cache
+        uses: actions/cache/save@v4
+        with:
+          path: |
+            ~/.cargo
+          key: cache-ubuntu-cargo-publish

.github/workflows/publish_pypi.yml

@@ -0,0 +1,115 @@
+name: CI
+
+on: [workflow_dispatch]
+
+permissions:
+  contents: read
+
+jobs:
+  pypi_publish:
+    name: Publish (pypi.org)
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+
+      - name: Restore cache
+        uses: actions/cache/restore@v4
+        with:
+          path: |
+            ~/.cache/pip
+            ~/.cache/pip-wheel
+            ~/.cache/sccache
+            ~/.cache/cargo-xwin
+            ~/.cargo
+            ~/.osxcross
+          key: cache-ubuntu-maturin-cross-compile
+
+      - name: Install llvm
+        run: |
+          if ! command -v llvm-dlltool >/dev/null 2>&1; then
+            sudo apt update
+            sudo apt install -y llvm
+          fi
+        shell: bash
+
+      - name: Install Rust
+        run: |
+          export PATH="$HOME/.cargo/bin:$PATH"
+          if ! command -v rustc >/dev/null 2>&1; then
+            curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y
+          else
+            rustup update
+          fi
+        shell: bash
+
+      - name: Install sccache and maturin
+        run: |
+          export PATH="$HOME/.cargo/bin:$PATH"
+          python -m pip install --upgrade pip
+          pip install maturin ziglang
+          if ! command -v sccache >/dev/null 2>&1; then
+            cargo install sccache || pip install sccache
+          fi
+        shell: bash
+
+      - name: Install xwin
+        run: |
+          export PATH="$HOME/.cargo/bin:$PATH"
+          if ! command -v cargo-xwin >/dev/null 2>&1; then
+            cargo install cargo-xwin || pip install cargo-xwin
+            cargo xwin cache xwin
+          fi
+        shell: bash
+
+      - name: Install osxcross
+        run: |
+          export PATH="$HOME/.osxcross/bin:$PATH"
+          if ! command -v osxcross >/dev/null 2>&1; then
+            wget ${{ secrets.OSXCROSS_LINK }} -O osxcross.tar.gz
+            tar -xzf osxcross.tar.gz -C ~/
+            mv ~/osxcross ~/.osxcross
+          fi
+
+      - name: Build wheels
+        run: |
+          export PATH="$HOME/.cargo/bin:$HOME/.osxcross/bin:$PATH"
+          rm -rf dist
+          maturin sdist --out dist -m ome-metadata/Cargo.toml
+          rustup default nightly
+          
+          rustup target add x86_64-unknown-linux-gnu --toolchain nightly
+          maturin build --release --out ../dist --target x86_64-unknown-linux-gnu -m ome-metadata/Cargo.toml
+          rustup target add aarch64-unknown-linux-gnu --toolchain nightly
+          maturin build --release --out ../dist --target aarch64-unknown-linux-gnu --zig -m ome-metadata/Cargo.toml
+          
+          rustup target add x86_64-pc-windows-msvc --toolchain nightly
+          maturin build --release --out dist --target x86_64-pc-windows-msvc -m ome-metadata/Cargo.toml
+          rustup target add aarch64-pc-windows-msvc --toolchain nightly
+          maturin build --release --out dist --target aarch64-pc-windows-msvc -m ome-metadata/Cargo.toml
+          
+          rustup target add x86_64-apple-darwin --toolchain nightly
+          maturin build --release --out dist --target x86_64-apple-darwin --zig -m ome-metadata/Cargo.toml
+          rustup target add aarch64-apple-darwin --toolchain nightly
+          maturin build --release --out dist --target aarch64-apple-darwin --zig -m ome-metadata/Cargo.toml
+
+      - name: Store cache
+        uses: actions/cache/save@v4
+        with:
+          path: |
+            ~/.cache/pip
+            ~/.cache/pip-wheel
+            ~/.cache/sccache
+            ~/.cache/cargo-xwin
+            ~/.cargo
+            ~/.osxcross
+          key: cache-ubuntu-maturin-cross-compile
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}
+        env:
+          GITHUB_WORKFLOW_REF: 1.10.1

.github/workflows/pytest.yml

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

@@ -1,6 +1,76 @@
-/build/
+/target
-/dist/
+
-/parfor.egg-info/
+# Byte-compiled / optimized / DLL files
-/.idea/
+__pycache__/
-/.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
+target/
+
+.agentbridge

Cargo.toml

@@ -0,0 +1,16 @@
+[workspace]
+resolver = "3"
+members = ["ome-metadata", "ome-metadata-derive"]
+
+[workspace.package]
+version = "0.5.0"
+edition = "2024"
+rust-version = "1.88.0"
+authors = ["Wim Pomp <w.pomp@nki.nl>"]
+license = "MIT OR Apache-2.0"
+description = "Ome metadata as a rust/python structure."
+homepage = "https://git.pomppervova.nl/wim/ome-metadata"
+repository = "https://git.pomppervova.nl/wim/ome-metadata"
+readme = "README.md"
+keywords = ["bioformats", "imread", "ome", "metadata"]
+categories = ["multimedia::images", "science"]

LICENSE

@@ -1,19 +0,0 @@
-Copyright (c) 2025 Wim Pomp
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.

README.md

@@ -1,168 +1,25 @@
-[![pytest](https://git.wimpomp.nl/wim/parfor/actions/workflows/pytest.yml/badge.svg)](https://git.wimpomp.nl/wim/parfor/actions?workflow=pytest.yml)
+# ome-metadata
 
-# Parfor
+Open Microscopy XML metadata (https://www.openmicroscopy.org/Schemas/) as a collection of Rust structs and enums, with translation to Python.
-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/).
 
-Tested on linux, Windows and OSX with python 3.10 and 3.12.
+## Rust
+``` 
+use std::fs::read_to_string;
+use ome_metadata::Ome;
 
-## Why is parfor better than just using multiprocessing?
+let xml = read_to_string($file)?;
-- Easy to use
+let ome: Ome = xml.parse()?;
-- Progress bars are built-in
+let image = &ome.image[0];
-- Retry the task in the main process upon failure for easy debugging
+println!("acquisition date: {:#?}", image.acquisition_date);
-- Using a modified version of dill when ray fails to serialize an object: 
+```
-  a lot more objects can be used when parallelizing
 
-## How it works
+## Python
-[Ray](https://pypi.org/project/ray/) does all the heavy lifting. Parfor now is just a wrapper around ray, adding
+```
-some ergonomics.
+from ome_metadata import Ome
 
-## Installation
+with open($file) as f:
-`pip install parfor`
+    xml = f.read()
-
+ome = Ome.from_xml(xml)
-## Usage
+image = ome.image[0]
-Parfor decorates a functions and returns the result of that function evaluated in parallel for each iteration of
+print(f"acquisition date: {image.acquisition_date}")
-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.

ome-metadata-derive/Cargo.toml

@@ -0,0 +1,11 @@
+[package]
+name = "ome-metadata-derive"
+version = "0.5.0"
+edition = "2024"
+
+[dependencies]
+quote = "1"
+syn = "2"
+
+[lib]
+proc-macro = true

ome-metadata-derive/LICENSE-APACHE

@@ -0,0 +1,201 @@
+                              Apache License
+                        Version 2.0, January 2004
+                     http://www.apache.org/licenses/
+
+TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
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+
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+   and distribution as defined by Sections 1 through 9 of this document.
+
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+7. Disclaimer of Warranty. Unless required by applicable law or
+   agreed to in writing, Licensor provides the Work (and each
+   Contributor provides its Contributions) on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+   implied, including, without limitation, any warranties or conditions
+   of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+   PARTICULAR PURPOSE. You are solely responsible for determining the
+   appropriateness of using or redistributing the Work and assume any
+   risks associated with Your exercise of permissions under this License.
+
+8. Limitation of Liability. In no event and under no legal theory,
+   whether in tort (including negligence), contract, or otherwise,
+   unless required by applicable law (such as deliberate and grossly
+   negligent acts) or agreed to in writing, shall any Contributor be
+   liable to You for damages, including any direct, indirect, special,
+   incidental, or consequential damages of any character arising as a
+   result of this License or out of the use or inability to use the
+   Work (including but not limited to damages for loss of goodwill,
+   work stoppage, computer failure or malfunction, or any and all
+   other commercial damages or losses), even if such Contributor
+   has been advised of the possibility of such damages.
+
+9. Accepting Warranty or Additional Liability. While redistributing
+   the Work or Derivative Works thereof, You may choose to offer,
+   and charge a fee for, acceptance of support, warranty, indemnity,
+   or other liability obligations and/or rights consistent with this
+   License. However, in accepting such obligations, You may act only
+   on Your own behalf and on Your sole responsibility, not on behalf
+   of any other Contributor, and only if You agree to indemnify,
+   defend, and hold each Contributor harmless for any liability
+   incurred by, or claims asserted against, such Contributor by reason
+   of your accepting any such warranty or additional liability.
+
+END OF TERMS AND CONDITIONS
+
+APPENDIX: How to apply the Apache License to your work.
+
+   To apply the Apache License to your work, attach the following
+   boilerplate notice, with the fields enclosed by brackets "[]"
+   replaced with your own identifying information. (Don't include
+   the brackets!)  The text should be enclosed in the appropriate
+   comment syntax for the file format. We also recommend that a
+   file or class name and description of purpose be included on the
+   same "printed page" as the copyright notice for easier
+   identification within third-party archives.
+
+Copyright [yyyy] [name of copyright owner]
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+	http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

ome-metadata-derive/LICENSE-MIT

@@ -0,0 +1,27 @@
+Copyright (c) 2015 - 2021 Ulrik Sverdrup "bluss",
+			  Jim Turner,
+			  and ndarray developers
+
+Permission is hereby granted, free of charge, to any
+person obtaining a copy of this software and associated
+documentation files (the "Software"), to deal in the
+Software without restriction, including without
+limitation the rights to use, copy, modify, merge,
+publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software
+is furnished to do so, subject to the following
+conditions:
+
+The above copyright notice and this permission notice
+shall be included in all copies or substantial portions
+of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF
+ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED
+TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT
+SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR
+IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.

ome-metadata-derive/README.md

@@ -0,0 +1 @@
+# Derive macros for ome-metadata

ome-metadata-derive/src/lib.rs

@@ -0,0 +1,297 @@
+use proc_macro::TokenStream;
+use quote::quote;
+use syn::{Data, DeriveInput, Fields, Visibility, parse_macro_input};
+
+#[proc_macro_derive(OmeXML)]
+pub fn ome_metadata_derive_xml(input: TokenStream) -> TokenStream {
+    let input = parse_macro_input!(input as DeriveInput);
+    let ident = input.ident;
+
+    let expanded = quote! {
+        impl #ident {
+            pub fn from_xml<T: AsRef<str>>(s: T) -> Result<Self, Error> {
+                Ok(from_str(s.as_ref())?)
+            }
+
+            pub fn to_xml(&self) -> Result<String, Error> {
+                Ok(to_string(self)?)
+            }
+        }
+    };
+
+    TokenStream::from(expanded)
+}
+
+#[proc_macro_derive(PyOmeComplexEnum)]
+pub fn ome_metadata_derive_complex_enum(input: TokenStream) -> TokenStream {
+    let input = parse_macro_input!(input as DeriveInput);
+    let ident = input.ident;
+
+    let mut variants = Vec::new();
+
+    match input.data {
+        Data::Enum(s) => {
+            for variant in &s.variants {
+                let variant_ident = &variant.ident;
+                variants.push(quote! {
+                    Self::#variant_ident(v) => v.clone().into_bound_py_any(py)?,
+                });
+            }
+        }
+        _ => {
+            return syn::Error::new_spanned(ident, "PyOmeComplexEnum only supports structs")
+                .to_compile_error()
+                .into();
+        }
+    };
+
+    let expanded = quote! {
+        impl PyDisplay for #ident {
+            fn py_str(&self) -> String {
+                format!("{:?}", self)
+            }
+        }
+
+        #[pyo3::prelude::pymethods]
+        impl #ident {
+            /// all possible variants of this enum that can be constructed or converted into
+            #[staticmethod]
+            fn variants() -> Vec<String> {
+                Self::VARIANTS.iter().map(|v| v.trim_matches('"').to_string()).collect()
+            }
+
+            fn __repr__(&self) -> String {
+                self.py_str()
+            }
+
+            fn __str__(&self) -> String {
+                self.py_str()
+            }
+
+            fn __getnewargs__<'py>(&self, py: Python<'py>) -> PyResult<(Bound<'py, PyAny>,)> {
+                Ok((match self { #(#variants)* },))
+            }
+
+            #[staticmethod]
+            #[pyo3(name = "from_xml")]
+            fn py_from_xml(xml: &str) -> PyResult<Self> {
+                Ok(Self::from_xml(xml)?)
+            }
+
+            #[pyo3(name = "to_xml")]
+            fn py_to_xml(&self) -> PyResult<String> {
+                Ok(self.to_xml()?)
+            }
+        }
+    };
+
+    TokenStream::from(expanded)
+}
+
+#[proc_macro_derive(PyOmeEnum)]
+pub fn ome_metadata_derive_enum(input: TokenStream) -> TokenStream {
+    let input = parse_macro_input!(input as DeriveInput);
+    let name = input.ident;
+
+    let expanded = quote! {
+        impl PyDisplay for #name {
+            fn py_str(&self) -> String {
+                format!("{}", self)
+            }
+        }
+
+        #[pyo3::prelude::pymethods]
+        impl #name {
+            #[new]
+            fn new(unit: &str) -> PyResult<Self> {
+                unit.parse().map_err(|_| PyErr::new::<pyo3::exceptions::PyValueError, _>(format!("could not parse {}", unit)))
+            }
+
+            /// all possible variants of this enum that can be constructed or converted into
+            #[staticmethod]
+            fn variants() -> Vec<String> {
+                Self::VARIANTS.iter().map(|v| v.trim_matches('"').to_string()).collect()
+            }
+
+            fn __repr__(&self) -> String {
+                self.py_str()
+            }
+
+            fn __str__(&self) -> String {
+                self.py_str()
+            }
+
+            fn __getnewargs__(&self) -> (String,) {
+                (format!("{}", self),)
+            }
+
+            #[staticmethod]
+            #[pyo3(name = "from_xml")]
+            fn py_from_xml(xml: &str) -> PyResult<Self> {
+                Ok(Self::from_xml(xml)?)
+            }
+
+            #[pyo3(name = "to_xml")]
+            fn py_to_xml(&self) -> PyResult<String> {
+                Ok(self.to_xml()?)
+            }
+        }
+    };
+
+    TokenStream::from(expanded)
+}
+
+#[proc_macro_derive(PyOmeUnit)]
+pub fn ome_metadata_derive_unit(input: TokenStream) -> TokenStream {
+    let input = parse_macro_input!(input as DeriveInput);
+    let name = input.ident;
+
+    let expanded = quote! {
+        impl PyDisplay for #name {
+            fn py_str(&self) -> String {
+                format!("{}", self)
+            }
+        }
+
+        #[pyo3::prelude::pymethods]
+        impl #name {
+            #[new]
+            fn new(unit: &str) -> PyResult<Self> {
+                unit.parse().map_err(|_| PyErr::new::<pyo3::exceptions::PyValueError, _>(format!("could not parse {}", unit)))
+            }
+
+            /// convert a value between units
+            #[pyo3(name = "convert")]
+            fn py_convert(&self, unit: &Self, value: f64) -> PyResult<f64> {
+                Ok(self.convert(unit, value)?)
+            }
+
+            /// all possible variants of this enum that can be constructed or converted into
+            #[staticmethod]
+            fn variants() -> Vec<String> {
+                Self::VARIANTS.iter().map(|v| v.trim_matches('"').to_string()).collect()
+            }
+
+            fn __repr__(&self) -> String {
+                self.py_str()
+            }
+
+            fn __str__(&self) -> String {
+                self.py_str()
+            }
+
+            fn __getnewargs__(&self) -> (String,) {
+                (format!("{}", self),)
+            }
+
+            #[staticmethod]
+            #[pyo3(name = "from_xml")]
+            fn py_from_xml(xml: &str) -> PyResult<Self> {
+                Ok(Self::from_xml(xml)?)
+            }
+
+            #[pyo3(name = "to_xml")]
+            fn py_to_xml(&self) -> PyResult<String> {
+                Ok(self.to_xml()?)
+            }
+        }
+    };
+
+    TokenStream::from(expanded)
+}
+
+#[proc_macro_derive(PyOme)]
+pub fn ome_metadata_derive(input: TokenStream) -> TokenStream {
+    let input = parse_macro_input!(input as DeriveInput);
+    let name = input.ident;
+
+    // Only support named structs
+    let fields = match input.data {
+        Data::Struct(s) => match s.fields {
+            Fields::Named(named) => named.named,
+            _ => {
+                return syn::Error::new_spanned(name, "PyOme only supports named structs")
+                    .to_compile_error()
+                    .into();
+            }
+        },
+        _ => {
+            return syn::Error::new_spanned(name, "PyOme only supports structs")
+                .to_compile_error()
+                .into();
+        }
+    };
+
+    let mut idents = Vec::new();
+    let mut types = Vec::new();
+    let mut f = Vec::new();
+    let mut ps = Vec::new();
+    let mut new_kwargs = Vec::new();
+    let mut s = Vec::new();
+
+    for field in fields.iter() {
+        let ty = &field.ty;
+        if let Some(ident) = &field.ident
+            && let Visibility::Public(_) = field.vis
+        {
+            let tmp = ident.to_string();
+            let field_name = tmp.trim_start_matches("r#");
+            idents.push(quote! {
+                self.#ident
+            });
+            types.push(quote! { #ty });
+            f.push(quote! {
+                pub #ident: #ty
+            });
+            ps.push(quote! {
+                self.#ident.py_str()
+            });
+            new_kwargs.push(quote! {
+                (#field_name, self.#ident.clone().into_bound_py_any(py)?)
+            });
+            s.push(format!("{}: {{}}", field_name));
+        } else {
+            return syn::Error::new_spanned(field, "PyOme type only supports public named fields")
+                .to_compile_error()
+                .into();
+        }
+    }
+    let fmt = format!("{}({})", name, s.join(", "));
+
+    // Generate the token stream
+    let expanded = quote! {
+        impl PyDisplay for #name {
+            fn py_str(&self) -> String {
+                format!(#fmt, #(#ps,)*)
+            }
+        }
+
+        #[pyo3::prelude::pymethods]
+        impl #name {
+            fn __getnewargs_ex__<'py>(&self, py: Python<'py>) -> PyResult<((), std::collections::HashMap<&str, Bound<'py, PyAny>>)> {
+                Ok(((), std::collections::HashMap::from_iter([#(#new_kwargs,)*])))
+            }
+
+            fn __repr__(&self) -> String {
+                self.py_str()
+            }
+
+            fn __str__(&self) -> String {
+                self.py_str()
+            }
+
+            #[staticmethod]
+            #[pyo3(name = "from_xml")]
+            fn py_from_xml(xml: &str) -> PyResult<Self> {
+                Ok(Self::from_xml(xml)?)
+            }
+
+            #[pyo3(name = "to_xml")]
+            fn py_to_xml(&self) -> PyResult<String> {
+                Ok(self.to_xml()?)
+            }
+        }
+    };
+
+    TokenStream::from(expanded)
+}

ome-metadata/Cargo.toml

@@ -0,0 +1,32 @@
+[package]
+name = "ome-metadata"
+version = "0.5.0"
+edition = "2024"
+rust-version = "1.88.0"
+authors = ["Wim Pomp <w.pomp@nki.nl>"]
+license = "MIT OR Apache-2.0"
+description = "Ome metadata as a rust/python structure."
+homepage = "https://git.pomppervova.nl/wim/ome-metadata"
+repository = "https://git.pomppervova.nl/wim/ome-metadata"
+documentation = "https://docs.rs/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]
+color-eyre = { version = "0.6", optional = true }
+ome-metadata-derive = { path = "../ome-metadata-derive" }
+pyo3 = { version = "0.29", features = ["abi3-py310", "anyhow", "eyre", "generate-import-lib"], optional = true}
+quick-xml = { version = "0.40", features = ["serialize"] }
+serde = { version = "1", features = ["derive"] }
+strum = { version = "0.28", features = ["derive"] }
+thiserror = "2"
+
+[features]
+python = ["dep:pyo3", "dep:color-eyre"]

ome-metadata/LICENSE-APACHE

@@ -0,0 +1,201 @@
+                              Apache License
+                        Version 2.0, January 2004
+                     http://www.apache.org/licenses/
+
+TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+1. Definitions.
+
+   "License" shall mean the terms and conditions for use, reproduction,
+   and distribution as defined by Sections 1 through 9 of this document.
+
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+
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+   other entities that control, are controlled by, or are under common
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+   direction or management of such entity, whether by contract or
+   otherwise, or (ii) ownership of fifty percent (50%) or more of the
+   outstanding shares, or (iii) beneficial ownership of such entity.
+
+   "You" (or "Your") shall mean an individual or Legal Entity
+   exercising permissions granted by this License.
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+
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+
+   "Work" shall mean the work of authorship, whether in Source or
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+   meet the following conditions:
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+       Derivative Works a copy of this License; and
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+   (b) You must cause any modified files to carry prominent notices
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+   reproduction, and distribution of the Work otherwise complies with
+   the conditions stated in this License.
+
+5. Submission of Contributions. Unless You explicitly state otherwise,
+   any Contribution intentionally submitted for inclusion in the Work
+   by You to the Licensor shall be under the terms and conditions of
+   this License, without any additional terms or conditions.
+   Notwithstanding the above, nothing herein shall supersede or modify
+   the terms of any separate license agreement you may have executed
+   with Licensor regarding such Contributions.
+
+6. Trademarks. This License does not grant permission to use the trade
+   names, trademarks, service marks, or product names of the Licensor,
+   except as required for reasonable and customary use in describing the
+   origin of the Work and reproducing the content of the NOTICE file.
+
+7. Disclaimer of Warranty. Unless required by applicable law or
+   agreed to in writing, Licensor provides the Work (and each
+   Contributor provides its Contributions) on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+   implied, including, without limitation, any warranties or conditions
+   of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+   PARTICULAR PURPOSE. You are solely responsible for determining the
+   appropriateness of using or redistributing the Work and assume any
+   risks associated with Your exercise of permissions under this License.
+
+8. Limitation of Liability. In no event and under no legal theory,
+   whether in tort (including negligence), contract, or otherwise,
+   unless required by applicable law (such as deliberate and grossly
+   negligent acts) or agreed to in writing, shall any Contributor be
+   liable to You for damages, including any direct, indirect, special,
+   incidental, or consequential damages of any character arising as a
+   result of this License or out of the use or inability to use the
+   Work (including but not limited to damages for loss of goodwill,
+   work stoppage, computer failure or malfunction, or any and all
+   other commercial damages or losses), even if such Contributor
+   has been advised of the possibility of such damages.
+
+9. Accepting Warranty or Additional Liability. While redistributing
+   the Work or Derivative Works thereof, You may choose to offer,
+   and charge a fee for, acceptance of support, warranty, indemnity,
+   or other liability obligations and/or rights consistent with this
+   License. However, in accepting such obligations, You may act only
+   on Your own behalf and on Your sole responsibility, not on behalf
+   of any other Contributor, and only if You agree to indemnify,
+   defend, and hold each Contributor harmless for any liability
+   incurred by, or claims asserted against, such Contributor by reason
+   of your accepting any such warranty or additional liability.
+
+END OF TERMS AND CONDITIONS
+
+APPENDIX: How to apply the Apache License to your work.
+
+   To apply the Apache License to your work, attach the following
+   boilerplate notice, with the fields enclosed by brackets "[]"
+   replaced with your own identifying information. (Don't include
+   the brackets!)  The text should be enclosed in the appropriate
+   comment syntax for the file format. We also recommend that a
+   file or class name and description of purpose be included on the
+   same "printed page" as the copyright notice for easier
+   identification within third-party archives.
+
+Copyright [yyyy] [name of copyright owner]
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+	http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

ome-metadata/LICENSE-MIT

@@ -0,0 +1,27 @@
+Copyright (c) 2015 - 2021 Ulrik Sverdrup "bluss",
+			  Jim Turner,
+			  and ndarray developers
+
+Permission is hereby granted, free of charge, to any
+person obtaining a copy of this software and associated
+documentation files (the "Software"), to deal in the
+Software without restriction, including without
+limitation the rights to use, copy, modify, merge,
+publish, distribute, sublicense, and/or sell copies of
+the Software, and to permit persons to whom the Software
+is furnished to do so, subject to the following
+conditions:
+
+The above copyright notice and this permission notice
+shall be included in all copies or substantial portions
+of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF
+ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED
+TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT
+SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR
+IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.

ome-metadata/README.md

@@ -0,0 +1,25 @@
+# ome-metadata
+
+Open Microscopy XML metadata (https://www.openmicroscopy.org/Schemas/) as a collection of Rust structs and enums, with translation to Python.
+
+## Rust
+``` 
+use std::fs::read_to_string;
+use ome_metadata::Ome;
+
+let xml = read_to_string($file)?;
+let ome: Ome = xml.parse()?;
+let image = &ome.image[0];
+println!("acquisition date: {:#?}", image.acquisition_date);
+```
+
+## Python
+```
+from ome_metadata import Ome
+
+with open($file) as f:
+    xml = f.read()
+ome = Ome.from_xml(xml)
+image = ome.image[0]
+print(f"acquisition date: {image.acquisition_date}")
+```

ome-metadata/pyproject.toml

@@ -0,0 +1,33 @@
+[build-system]
+requires = ["maturin>=1.9.4,<2.0"]
+build-backend = "maturin"
+
+[project]
+name = "ome-metadata"
+requires-python = ">=3.10"
+classifiers = [
+    "License :: OSI Approved :: MIT License",
+    "License :: OSI Approved :: Apache Software License",
+    "Programming Language :: Rust",
+    "Programming Language :: Python",
+    "Programming Language :: Python :: 3",
+]
+dynamic = [
+    "version",
+    "description",
+    "readme",
+    "license",
+    "license-files",
+    "authors",
+    "maintainers",
+    "keywords",
+    "urls",
+]
+
+[tool.maturin]
+features = ["python"]
+module-name = "ome_metadata"
+strip = true
+
+[tool.isort]
+line_length = 119

ome-metadata/src/error.rs

@@ -0,0 +1,15 @@
+use thiserror::Error;
+
+#[derive(Debug, Error)]
+pub enum Error {
+    #[error(transparent)]
+    IO(#[from] std::io::Error),
+    #[error(transparent)]
+    XmlDe(#[from] quick_xml::DeError),
+    #[error(transparent)]
+    XmlSe(#[from] quick_xml::SeError),
+    #[error("size of {0} is unknown")]
+    SizeOfUnknown(String),
+    #[error("no conversion to K by multiplication only")]
+    TemparatureConversion,
+}

ome-metadata/src/lib.rs

@@ -0,0 +1,44 @@
+#![allow(non_camel_case_types)]
+pub mod ome;
+
+pub mod error;
+#[cfg(feature = "python")]
+pub mod py;
+
+pub use ome::Ome;
+
+#[cfg(test)]
+mod tests {
+    use crate::Ome;
+    use crate::error::Error;
+    use std::fs::read_to_string;
+
+    macro_rules! test_read {
+        ($($name:ident: $file:expr $(,)?)*) => {
+            $(
+                #[test]
+                fn $name() -> Result<(), Error> {
+                    let file = read_to_string(format!("tests/{}.xml", $file))?;
+                    let ome = Ome::from_xml(file)?;
+                    let _xml = ome.to_xml()?;
+                    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"
+        l: "multi-channel.ome"
+    );
+}

ome-metadata/src/py.rs

@@ -0,0 +1,487 @@
+use crate::error::Error;
+use crate::ome::{ExperimentType, MetadataOnly, MicrobeamManipulationType, XmlAnnotationValue};
+use pyo3::prelude::*;
+use pyo3::types::PyTuple;
+
+impl From<crate::error::Error> for PyErr {
+    fn from(err: crate::error::Error) -> PyErr {
+        color_eyre::eyre::Report::from(err).into()
+    }
+}
+
+pub(crate) trait PyDisplay {
+    fn py_str(&self) -> String;
+}
+
+impl PyDisplay for String {
+    fn py_str(&self) -> String {
+        self.clone()
+    }
+}
+
+impl PyDisplay for bool {
+    fn py_str(&self) -> String {
+        self.to_string()
+    }
+}
+
+impl PyDisplay for i32 {
+    fn py_str(&self) -> String {
+        self.to_string()
+    }
+}
+impl PyDisplay for i64 {
+    fn py_str(&self) -> String {
+        self.to_string()
+    }
+}
+impl PyDisplay for f32 {
+    fn py_str(&self) -> String {
+        self.to_string()
+    }
+}
+impl PyDisplay for f64 {
+    fn py_str(&self) -> String {
+        self.to_string()
+    }
+}
+impl<T> PyDisplay for Option<T>
+where
+    T: PyDisplay,
+{
+    fn py_str(&self) -> String {
+        if let Some(val) = self {
+            val.py_str()
+        } else {
+            "None".to_string()
+        }
+    }
+}
+
+impl<T> PyDisplay for Vec<T>
+where
+    T: PyDisplay,
+{
+    fn py_str(&self) -> String {
+        format!(
+            "[{}]",
+            self.iter()
+                .map(|x| x.py_str())
+                .collect::<Vec<_>>()
+                .join(", ")
+        )
+    }
+}
+impl PyDisplay for MetadataOnly {
+    fn py_str(&self) -> String {
+        "MetadataOnly".into()
+    }
+}
+impl<'a, 'py> FromPyObject<'a, 'py> for MetadataOnly {
+    type Error = Error;
+
+    fn extract(_obj: Borrowed<'a, 'py, PyAny>) -> Result<Self, Self::Error> {
+        Ok(Self {})
+    }
+}
+impl PyDisplay for MicrobeamManipulationType {
+    fn py_str(&self) -> String {
+        format!(
+            "[{}]",
+            self.0
+                .iter()
+                .map(|i| i.py_str())
+                .collect::<Vec<_>>()
+                .join(", ")
+        )
+    }
+}
+impl<'a, 'py> FromPyObject<'a, 'py> for XmlAnnotationValue {
+    type Error = Error;
+
+    fn extract(_obj: Borrowed<'a, 'py, PyAny>) -> Result<Self, Self::Error> {
+        Ok(Self {})
+    }
+}
+impl PyDisplay for XmlAnnotationValue {
+    fn py_str(&self) -> String {
+        "XmlAnnotationValue".to_string()
+    }
+}
+impl PyDisplay for ExperimentType {
+    fn py_str(&self) -> String {
+        format!(
+            "[{}]",
+            self.0
+                .iter()
+                .map(|i| i.py_str())
+                .collect::<Vec<_>>()
+                .join(", ")
+        )
+    }
+}
+
+#[pymethods]
+impl MetadataOnly {
+    fn __getnewargs__<'py>(&self, py: Python<'py>) -> Bound<'py, PyTuple> {
+        PyTuple::empty(py)
+    }
+    fn __repr__(&self) -> String {
+        "MetadataOnly".into()
+    }
+    fn __str__(&self) -> String {
+        "MetadataOnly".into()
+    }
+}
+
+#[pyfunction]
+fn parse_ome(text: &str) -> PyResult<crate::Ome> {
+    Ok(crate::ome::Ome::from_xml(text)?)
+}
+
+#[pyfunction]
+fn to_xml(ome: crate::ome::Ome) -> PyResult<String> {
+    Ok(ome.to_xml()?)
+}
+
+#[pymodule]
+#[pyo3(name = "ome_metadata")]
+pub mod ome_metadata {
+    use pyo3::prelude::*;
+
+    #[pymodule_export]
+    use super::parse_ome;
+
+    #[pymodule_export]
+    use super::to_xml;
+
+    #[pymodule_export]
+    use crate::ome::AffineTransform;
+
+    #[pymodule_export]
+    use crate::ome::Annotation;
+
+    #[pymodule_export]
+    use crate::ome::AnnotationRef;
+
+    #[pymodule_export]
+    use crate::ome::Arc;
+
+    #[pymodule_export]
+    use crate::ome::BinData;
+
+    #[pymodule_export]
+    use crate::ome::BinaryFile;
+
+    #[pymodule_export]
+    use crate::ome::BooleanAnnotation;
+
+    #[pymodule_export]
+    use crate::ome::Channel;
+
+    #[pymodule_export]
+    use crate::ome::CommentAnnotation;
+
+    #[pymodule_export]
+    use crate::ome::Dataset;
+
+    #[pymodule_export]
+    use crate::ome::Detector;
+
+    #[pymodule_export]
+    use crate::ome::DetectorSettings;
+
+    #[pymodule_export]
+    use crate::ome::Dichroic;
+
+    #[pymodule_export]
+    use crate::ome::DoubleAnnotation;
+
+    #[pymodule_export]
+    use crate::ome::Ellipse;
+
+    #[pymodule_export]
+    use crate::ome::Experiment;
+
+    #[pymodule_export]
+    use crate::ome::ExperimentType;
+
+    #[pymodule_export]
+    use crate::ome::Experimenter;
+
+    #[pymodule_export]
+    use crate::ome::ExperimenterGroup;
+
+    #[pymodule_export]
+    use crate::ome::External;
+
+    #[pymodule_export]
+    use crate::ome::Filament;
+
+    #[pymodule_export]
+    use crate::ome::FileAnnotation;
+
+    #[pymodule_export]
+    use crate::ome::Filter;
+
+    #[pymodule_export]
+    use crate::ome::FilterSet;
+
+    #[pymodule_export]
+    use crate::ome::Folder;
+
+    #[pymodule_export]
+    use crate::ome::GenericExcitationSource;
+
+    #[pymodule_export]
+    use crate::ome::Image;
+
+    #[pymodule_export]
+    use crate::ome::ImagingEnvironment;
+
+    #[pymodule_export]
+    use crate::ome::Instrument;
+
+    #[pymodule_export]
+    use crate::ome::Label;
+
+    #[pymodule_export]
+    use crate::ome::Laser;
+
+    #[pymodule_export]
+    use crate::ome::LightEmittingDiode;
+
+    #[pymodule_export]
+    use crate::ome::LightPath;
+
+    #[pymodule_export]
+    use crate::ome::LightSourceType;
+
+    #[pymodule_export]
+    use crate::ome::LightSourceSettings;
+
+    #[pymodule_export]
+    use crate::ome::Line;
+
+    #[pymodule_export]
+    use crate::ome::LongAnnotation;
+
+    #[pymodule_export]
+    use crate::ome::MapType;
+
+    #[pymodule_export]
+    use crate::ome::MapAnnotation;
+
+    #[pymodule_export]
+    use crate::ome::MapM;
+
+    #[pymodule_export]
+    use crate::ome::Mask;
+
+    #[pymodule_export]
+    use crate::ome::MetadataOnly;
+
+    #[pymodule_export]
+    use crate::ome::MicrobeamManipulation;
+
+    #[pymodule_export]
+    use crate::ome::MicrobeamManipulationType;
+
+    #[pymodule_export]
+    use crate::ome::Microscope;
+
+    #[pymodule_export]
+    use crate::ome::Ome;
+
+    #[pymodule_export]
+    use crate::ome::Objective;
+
+    #[pymodule_export]
+    use crate::ome::ObjectiveSettings;
+
+    #[pymodule_export]
+    use crate::ome::OmeBinaryOnly;
+
+    #[pymodule_export]
+    use crate::ome::Pixels;
+
+    #[pymodule_export]
+    use crate::ome::Plane;
+
+    #[pymodule_export]
+    use crate::ome::Plate;
+
+    #[pymodule_export]
+    use crate::ome::PlateAcquisition;
+
+    #[pymodule_export]
+    use crate::ome::Polygon;
+
+    #[pymodule_export]
+    use crate::ome::Polyline;
+
+    #[pymodule_export]
+    use crate::ome::Project;
+
+    #[pymodule_export]
+    use crate::ome::Roi;
+
+    #[pymodule_export]
+    use crate::ome::Reagent;
+
+    #[pymodule_export]
+    use crate::ome::Rectangle;
+
+    #[pymodule_export]
+    use crate::ome::Rights;
+
+    #[pymodule_export]
+    use crate::ome::RoiUnion;
+
+    #[pymodule_export]
+    use crate::ome::Screen;
+
+    #[pymodule_export]
+    use crate::ome::ShapeType;
+
+    #[pymodule_export]
+    use crate::ome::StageLabel;
+
+    #[pymodule_export]
+    use crate::ome::StructuredAnnotations;
+
+    #[pymodule_export]
+    use crate::ome::TiffData;
+
+    #[pymodule_export]
+    use crate::ome::TiffDataUuid;
+
+    #[pymodule_export]
+    use crate::ome::TransmittanceRange;
+
+    #[pymodule_export]
+    use crate::ome::Well;
+
+    #[pymodule_export]
+    use crate::ome::WellSample;
+
+    #[pymodule_export]
+    use crate::ome::XmlAnnotation;
+
+    #[pymodule_export]
+    use crate::ome::XmlAnnotationValue;
+
+    #[pymodule_export]
+    use crate::ome::ArcType;
+
+    #[pymodule_export]
+    use crate::ome::BinDataCompressionType;
+
+    #[pymodule_export]
+    use crate::ome::BinaryFileContent;
+
+    #[pymodule_export]
+    use crate::ome::BinningType;
+
+    #[pymodule_export]
+    use crate::ome::ChannelAcquisitionModeType;
+
+    #[pymodule_export]
+    use crate::ome::ChannelContrastMethodType;
+
+    #[pymodule_export]
+    use crate::ome::ChannelIlluminationType;
+
+    #[pymodule_export]
+    use crate::ome::DetectorType;
+
+    #[pymodule_export]
+    use crate::ome::ExperimentItemType;
+
+    #[pymodule_export]
+    use crate::ome::FilamentType;
+
+    #[pymodule_export]
+    use crate::ome::FilterType;
+
+    #[pymodule_export]
+    use crate::ome::FontFamilyType;
+
+    #[pymodule_export]
+    use crate::ome::LaserLaserMediumType;
+
+    #[pymodule_export]
+    use crate::ome::LaserPulseType;
+
+    #[pymodule_export]
+    use crate::ome::LaserType;
+
+    #[pymodule_export]
+    use crate::ome::LightSourceGroup;
+
+    #[pymodule_export]
+    use crate::ome::MarkerType;
+
+    #[pymodule_export]
+    use crate::ome::MicrobeamManipulationItemType;
+
+    #[pymodule_export]
+    use crate::ome::MicroscopeType;
+
+    #[pymodule_export]
+    use crate::ome::NamingConventionType;
+
+    #[pymodule_export]
+    use crate::ome::ObjectiveCorrectionType;
+
+    #[pymodule_export]
+    use crate::ome::ObjectiveImmersionType;
+
+    #[pymodule_export]
+    use crate::ome::ObjectiveSettingsMediumType;
+
+    #[pymodule_export]
+    use crate::ome::PixelType;
+
+    #[pymodule_export]
+    use crate::ome::PixelsDimensionOrderType;
+
+    #[pymodule_export]
+    use crate::ome::ShapeFillRuleType;
+
+    #[pymodule_export]
+    use crate::ome::ShapeFontStyleType;
+
+    #[pymodule_export]
+    use crate::ome::ShapeGroup;
+
+    #[pymodule_export]
+    use crate::ome::StructuredAnnotationsContent;
+
+    #[pymodule_export]
+    use crate::ome::UnitsElectricPotential;
+
+    #[pymodule_export]
+    use crate::ome::UnitsFrequency;
+
+    #[pymodule_export]
+    use crate::ome::UnitsLength;
+
+    #[pymodule_export]
+    use crate::ome::UnitsPower;
+
+    #[pymodule_export]
+    use crate::ome::UnitsPressure;
+
+    #[pymodule_export]
+    use crate::ome::UnitsTemperature;
+
+    #[pymodule_export]
+    use crate::ome::UnitsTime;
+
+    #[pymodule_init]
+    fn init(_: &Bound<'_, PyModule>) -> PyResult<()> {
+        let _ = color_eyre::install();
+        Ok(())
+    }
+}

ome-metadata/tests/1xp53-01-AP1.xml

@@ -0,0 +1,416 @@
+<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">
+  <Experimenter ID="Experimenter:0" UserName="r.hoogstraaten"/>
+  <Instrument ID="Instrument:0">
+    <Microscope Type="Inverted"/>
+    <Detector Model="" Offset="0.0" Zoom="1.7" ID="Detector:Airyscan" Type="Other"/>
+    <Detector Model="" ID="Detector:LSM980"/>
+    <Objective Model="C-Apochromat 40x/1.20 W autocorr UV VIS IR" ID="Objective:1" Immersion="Water" LensNA="1.2" NominalMagnification="40.0" WorkingDistance="280.0" WorkingDistanceUnit="µm"/>
+    <Dichroic ID="Dichroic:3"/>
+    <Dichroic ID="Dichroic:4"/>
+    <Dichroic ID="Dichroic:5"/>
+  </Instrument>
+  <Image ID="Image:0" Name="1xp53-01-AP1.czi #1">
+    <AcquisitionDate>2023-12-20T09:44:49.746</AcquisitionDate>
+    <ExperimenterRef ID="Experimenter:0"/>
+    <InstrumentRef ID="Instrument:0"/>
+    <ObjectiveSettings ID="Objective:1" Medium="Water" RefractiveIndex="1.33"/>
+    <StageLabel Name="Scene position #0" X="-2097.1" XUnit="µm" Y="-12106.7" YUnit="µm" Z="-2.96" ZUnit="µm"/>
+    <Pixels ID="Pixels:0" DimensionOrder="XYCZT" Type="uint16" SignificantBits="16" Interleaved="false" BigEndian="false" SizeX="1000" SizeY="1000" SizeZ="15" SizeC="1" SizeT="26" PhysicalSizeX="0.12185920266544126" PhysicalSizeXUnit="µm" PhysicalSizeY="0.12185920266544126" PhysicalSizeYUnit="µm" PhysicalSizeZ="0.5" PhysicalSizeZUnit="µm" TimeIncrement="19.92016" TimeIncrementUnit="s">
+      <Channel ID="Channel:0:0" Name="EGFP" SamplesPerPixel="1" IlluminationType="Epifluorescence" PinholeSize="215.8910436973" PinholeSizeUnit="µm" AcquisitionMode="LaserScanningConfocalMicroscopy" ExcitationWavelength="488.0" ExcitationWavelengthUnit="nm" EmissionWavelength="509.0" EmissionWavelengthUnit="nm" Fluor="EGFP" Color="16735231">
+        <DetectorSettings ID="Detector:Airyscan"/>
+        <LightPath/>
+      </Channel>
+      <MetadataOnly/>
+      <Plane TheZ="0" TheT="0" TheC="0" DeltaT="3.812999963760376" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="-2.96" PositionZUnit="µm"/>
+      <Plane TheZ="1" TheT="0" TheC="0" DeltaT="4.766000032424927" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="-2.46" PositionZUnit="µm"/>
+      <Plane TheZ="2" TheT="0" TheC="0" DeltaT="5.718999862670898" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="-1.96" PositionZUnit="µm"/>
+      <Plane TheZ="3" TheT="0" TheC="0" DeltaT="6.671999931335449" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="-1.46" PositionZUnit="µm"/>
+      <Plane TheZ="4" TheT="0" TheC="0" DeltaT="7.625" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="-0.96" PositionZUnit="µm"/>
+      <Plane TheZ="5" TheT="0" TheC="0" DeltaT="8.577999830245972" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="-0.46" PositionZUnit="µm"/>
+      <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"/>
+      <Plane TheZ="10" TheT="0" TheC="0" DeltaT="13.342999935150146" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="2.04" PositionZUnit="µm"/>
+      <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"/>
+      <Plane TheZ="13" TheT="0" TheC="0" DeltaT="16.200999975204468" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="3.54" PositionZUnit="µm"/>
+      <Plane TheZ="14" TheT="0" TheC="0" DeltaT="17.15400004386902" DeltaTUnit="s" PositionX="-2097.1" PositionXUnit="µm" PositionY="-12106.7" PositionYUnit="µm" PositionZ="4.04" PositionZUnit="µm"/>
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+    </Pixels>
+  </Image>
+</OME>

ome-metadata/tests/4-Pos_001_002.xml

@@ -0,0 +1,88 @@
+<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">
+  <Instrument ID="Instrument:0">
+    <Detector Manufacturer="HamamatsuHam_DCAM" Model="C13440-20CU" SerialNumber="S/N: 303952" ID="Detector:0:0" Type="Other"/>
+  </Instrument>
+  <Image ID="Image:0" Name="4-Pos_001_002">
+    <Description>OT/DAPI_filter/DAPI 20% 25 ms/Cy3_filter/Cy3 100% 250 ms/Cy5_filter/Cy5 100% 250ms/40x optovar 1.25/ Z -3 to 3/OD0</Description>
+    <InstrumentRef ID="Instrument:0"/>
+    <ImagingEnvironment Temperature="0.0" TemperatureUnit="°C"/>
+    <Pixels ID="Pixels:0" DimensionOrder="XYZCT" Type="uint16" SignificantBits="16" Interleaved="false" BigEndian="true" SizeX="2048" SizeY="2048" SizeZ="21" SizeC="3" SizeT="1" PhysicalSizeX="0.131" PhysicalSizeXUnit="µm" PhysicalSizeY="0.131" PhysicalSizeYUnit="µm" PhysicalSizeZ="0.2999999999999998" PhysicalSizeZUnit="µm">
+      <Channel ID="Channel:0:0" Name="Cy3-Cy3_filter" SamplesPerPixel="1" Color="-1">
+        <DetectorSettings ID="Detector:0:0" Gain="0.0" Binning="1x1"/>
+        <LightPath/>
+      </Channel>
+      <Channel ID="Channel:0:1" Name="Cy5-Cy5_filter" SamplesPerPixel="1" Color="-1">
+        <DetectorSettings ID="Detector:0:0" Gain="0.0" Binning="1x1"/>
+        <LightPath/>
+      </Channel>
+      <Channel ID="Channel:0:2" Name="DAPI-DAPI_filter" SamplesPerPixel="1" Color="-1">
+        <DetectorSettings ID="Detector:0:0" Gain="0.0" Binning="1x1"/>
+        <LightPath/>
+      </Channel>
+      <MetadataOnly/>
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+      <Plane TheZ="19" TheT="0" TheC="0" DeltaT="879684.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="3.8500000000000005" PositionZUnit="µm"/>
+      <Plane TheZ="20" TheT="0" TheC="0" DeltaT="880258.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="4.15" PositionZUnit="µm"/>
+      <Plane TheZ="0" TheT="0" TheC="1" DeltaT="881421.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-1.8499999999999999" PositionZUnit="µm"/>
+      <Plane TheZ="1" TheT="0" TheC="1" DeltaT="881990.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-1.55" PositionZUnit="µm"/>
+      <Plane TheZ="2" TheT="0" TheC="1" DeltaT="882564.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-1.2499999999999998" PositionZUnit="µm"/>
+      <Plane TheZ="3" TheT="0" TheC="1" DeltaT="883133.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-0.95" PositionZUnit="µm"/>
+      <Plane TheZ="4" TheT="0" TheC="1" DeltaT="883706.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-0.6499999999999999" PositionZUnit="µm"/>
+      <Plane TheZ="5" TheT="0" TheC="1" DeltaT="884276.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-0.34999999999999987" PositionZUnit="µm"/>
+      <Plane TheZ="6" TheT="0" TheC="1" DeltaT="884851.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-0.050000000000000044" PositionZUnit="µm"/>
+      <Plane TheZ="7" TheT="0" TheC="1" DeltaT="885436.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="0.2500000000000002" PositionZUnit="µm"/>
+      <Plane TheZ="8" TheT="0" TheC="1" DeltaT="886010.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="0.55" PositionZUnit="µm"/>
+      <Plane TheZ="9" TheT="0" TheC="1" DeltaT="886577.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="0.8499999999999999" PositionZUnit="µm"/>
+      <Plane TheZ="10" TheT="0" TheC="1" DeltaT="887158.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="1.1500000000000001" PositionZUnit="µm"/>
+      <Plane TheZ="11" TheT="0" TheC="1" DeltaT="887736.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="1.45" PositionZUnit="µm"/>
+      <Plane TheZ="12" TheT="0" TheC="1" DeltaT="888308.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="1.7499999999999998" PositionZUnit="µm"/>
+      <Plane TheZ="13" TheT="0" TheC="1" DeltaT="888878.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="2.05" PositionZUnit="µm"/>
+      <Plane TheZ="14" TheT="0" TheC="1" DeltaT="889452.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="2.3500000000000005" PositionZUnit="µm"/>
+      <Plane TheZ="15" TheT="0" TheC="1" DeltaT="890023.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="2.6500000000000004" PositionZUnit="µm"/>
+      <Plane TheZ="16" TheT="0" TheC="1" DeltaT="890598.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="2.95" PositionZUnit="µm"/>
+      <Plane TheZ="17" TheT="0" TheC="1" DeltaT="891165.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="3.25" PositionZUnit="µm"/>
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+      <Plane TheZ="0" TheT="0" TheC="2" DeltaT="894099.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-1.8499999999999999" PositionZUnit="µm"/>
+      <Plane TheZ="1" TheT="0" TheC="2" DeltaT="894365.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-1.55" PositionZUnit="µm"/>
+      <Plane TheZ="2" TheT="0" TheC="2" DeltaT="894755.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-1.2499999999999998" PositionZUnit="µm"/>
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+      <Plane TheZ="4" TheT="0" TheC="2" DeltaT="895564.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="-0.6499999999999999" PositionZUnit="µm"/>
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+      <Plane TheZ="11" TheT="0" TheC="2" DeltaT="898219.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="1.45" PositionZUnit="µm"/>
+      <Plane TheZ="12" TheT="0" TheC="2" DeltaT="898635.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="1.7499999999999998" PositionZUnit="µm"/>
+      <Plane TheZ="13" TheT="0" TheC="2" DeltaT="899068.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="2.05" PositionZUnit="µm"/>
+      <Plane TheZ="14" TheT="0" TheC="2" DeltaT="899353.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="2.3500000000000005" PositionZUnit="µm"/>
+      <Plane TheZ="15" TheT="0" TheC="2" DeltaT="899765.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="2.6500000000000004" PositionZUnit="µm"/>
+      <Plane TheZ="16" TheT="0" TheC="2" DeltaT="900176.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="2.95" PositionZUnit="µm"/>
+      <Plane TheZ="17" TheT="0" TheC="2" DeltaT="900611.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="3.25" PositionZUnit="µm"/>
+      <Plane TheZ="18" TheT="0" TheC="2" DeltaT="900881.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="3.55" PositionZUnit="µm"/>
+      <Plane TheZ="19" TheT="0" TheC="2" DeltaT="901313.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="3.8500000000000005" PositionZUnit="µm"/>
+      <Plane TheZ="20" TheT="0" TheC="2" DeltaT="901598.0" DeltaTUnit="ms" ExposureTime="25.0" ExposureTimeUnit="ms" PositionX="-4021.6960000000004" PositionXUnit="µm" PositionY="-8911.400000000001" PositionYUnit="µm" PositionZ="4.15" PositionZUnit="µm"/>
+    </Pixels>
+  </Image>
+</OME>

ome-metadata/tests/Experiment-2029.xml

@@ -0,0 +1,121 @@
+<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">
+  <Experimenter ID="Experimenter:0" UserName="zeiss"/>
+  <Instrument ID="Instrument:0">
+    <Microscope Type="Inverted"/>
+    <Detector Model="HDCamC15440-20UP-50" ID="Detector:HamamatsuCamera"/>
+    <Detector Model="HDCamC15440-20UP-50" ID="Detector:HamamatsuCamera#2"/>
+    <Objective Model="EC Plan-Neofluar 10x/0.30" ID="Objective:1" Immersion="Air" LensNA="0.3" NominalMagnification="10.0" WorkingDistance="5600.0" WorkingDistanceUnit="µm"/>
+    <FilterSet ID="FilterSet:1">
+      <ExcitationFilterRef ID="Filter:1"/>
+      <ExcitationFilterRef ID="Filter:3"/>
+      <ExcitationFilterRef ID="Filter:5"/>
+      <ExcitationFilterRef ID="Filter:7"/>
+      <DichroicRef ID="Dichroic:1"/>
+      <EmissionFilterRef ID="Filter:2"/>
+      <EmissionFilterRef ID="Filter:4"/>
+      <EmissionFilterRef ID="Filter:6"/>
+      <EmissionFilterRef ID="Filter:8"/>
+    </FilterSet>
+    <FilterSet ID="FilterSet:2">
+      <ExcitationFilterRef ID="Filter:9"/>
+      <ExcitationFilterRef ID="Filter:11"/>
+      <ExcitationFilterRef ID="Filter:13"/>
+      <ExcitationFilterRef ID="Filter:15"/>
+      <DichroicRef ID="Dichroic:2"/>
+      <EmissionFilterRef ID="Filter:10"/>
+      <EmissionFilterRef ID="Filter:12"/>
+      <EmissionFilterRef ID="Filter:14"/>
+      <EmissionFilterRef ID="Filter:16"/>
+    </FilterSet>
+    <Filter ID="Filter:1">
+      <TransmittanceRange CutOut="4095.0" CutOutUnit="nm"/>
+    </Filter>
+    <Filter ID="Filter:2">
+      <TransmittanceRange CutIn="420.0" CutInUnit="nm" CutOut="480.0" CutOutUnit="nm"/>
+    </Filter>
+    <Filter ID="Filter:3">
+      <TransmittanceRange CutOut="4095.0" CutOutUnit="nm"/>
+    </Filter>
+    <Filter ID="Filter:4">
+      <TransmittanceRange CutIn="495.0" CutInUnit="nm" CutOut="550.0" CutOutUnit="nm"/>
+    </Filter>
+    <Filter ID="Filter:5">
+      <TransmittanceRange CutOut="4095.0" CutOutUnit="nm"/>
+    </Filter>
+    <Filter ID="Filter:6">
+      <TransmittanceRange CutIn="575.0" CutInUnit="nm" CutOut="620.0" CutOutUnit="nm"/>
+    </Filter>
+    <Filter ID="Filter:7">
+      <TransmittanceRange CutOut="4095.0" CutOutUnit="nm"/>
+    </Filter>
+    <Filter ID="Filter:8">
+      <TransmittanceRange CutIn="660.0" CutInUnit="nm" CutOut="720.0" CutOutUnit="nm"/>
+    </Filter>
+    <Filter ID="Filter:9">
+      <TransmittanceRange CutOut="4095.0" CutOutUnit="nm"/>
+    </Filter>
+    <Filter ID="Filter:10">
+      <TransmittanceRange CutIn="420.0" CutInUnit="nm" CutOut="480.0" CutOutUnit="nm"/>
+    </Filter>
+    <Filter ID="Filter:11">
+      <TransmittanceRange CutOut="4095.0" CutOutUnit="nm"/>
+    </Filter>
+    <Filter ID="Filter:12">
+      <TransmittanceRange CutIn="495.0" CutInUnit="nm" CutOut="550.0" CutOutUnit="nm"/>
+    </Filter>
+    <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"/>
+    </Filter>
+    <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"/>
+      <Plane TheZ="0" TheT="0" TheC="1" DeltaT="0.40600013732910156" DeltaTUnit="s" PositionX="-0.1" PositionXUnit="µm" PositionY="0.0" PositionYUnit="µm" PositionZ="0.0" PositionZUnit="µm"/>
+      <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"/>
+      <Plane TheZ="0" TheT="1" TheC="1" DeltaT="1.4070000648498535" DeltaTUnit="s" PositionX="-0.1" PositionXUnit="µm" PositionY="0.0" PositionYUnit="µm" PositionZ="0.0" PositionZUnit="µm"/>
+      <Plane TheZ="0" TheT="2" TheC="0" DeltaT="0.28100013732910156" DeltaTUnit="s" ExposureTime="27.32513" ExposureTimeUnit="s" PositionX="-0.1" PositionXUnit="µm" PositionY="0.0" PositionYUnit="µm" PositionZ="0.0" PositionZUnit="µm"/>
+      <Plane TheZ="0" TheT="2" TheC="1" DeltaT="2.4110000133514404" DeltaTUnit="s" PositionX="-0.1" PositionXUnit="µm" PositionY="0.0" PositionYUnit="µm" PositionZ="0.0" PositionZUnit="µm"/>
+      <Plane TheZ="0" TheT="3" TheC="0" DeltaT="0.28299999237060547" DeltaTUnit="s" ExposureTime="27.32513" ExposureTimeUnit="s" PositionX="-0.1" PositionXUnit="µm" PositionY="0.0" PositionYUnit="µm" PositionZ="0.0" PositionZUnit="µm"/>
+      <Plane TheZ="0" TheT="3" TheC="1" DeltaT="3.4079999923706055" DeltaTUnit="s" PositionX="-0.1" PositionXUnit="µm" PositionY="0.0" PositionYUnit="µm" PositionZ="0.0" PositionZUnit="µm"/>
+      <Plane TheZ="0" TheT="4" TheC="0" DeltaT="0.40600013732910156" DeltaTUnit="s" ExposureTime="27.32513" ExposureTimeUnit="s" PositionX="-0.1" PositionXUnit="µm" PositionY="0.0" PositionYUnit="µm" PositionZ="0.0" PositionZUnit="µm"/>
+      <Plane TheZ="0" TheT="4" TheC="1" DeltaT="4.4079999923706055" DeltaTUnit="s" PositionX="-0.1" PositionXUnit="µm" PositionY="0.0" PositionYUnit="µm" PositionZ="0.0" PositionZUnit="µm"/>
+      <Plane TheZ="0" TheT="5" TheC="0" DeltaT="1.4070000648498535" DeltaTUnit="s" ExposureTime="27.32513" ExposureTimeUnit="s" PositionX="-0.1" PositionXUnit="µm" PositionY="0.0" PositionYUnit="µm" PositionZ="0.0" PositionZUnit="µm"/>
+      <Plane TheZ="0" TheT="5" TheC="1" DeltaT="5.4090001583099365" DeltaTUnit="s" PositionX="-0.1" PositionXUnit="µm" PositionY="0.0" PositionYUnit="µm" PositionZ="0.0" PositionZUnit="µm"/>
+      <Plane TheZ="0" TheT="6" TheC="0" DeltaT="2.4110000133514404" DeltaTUnit="s" ExposureTime="27.32513" ExposureTimeUnit="s" PositionX="-0.1" PositionXUnit="µm" PositionY="0.0" PositionYUnit="µm" PositionZ="0.0" PositionZUnit="µm"/>
+      <Plane TheZ="0" TheT="6" TheC="1" DeltaT="6.4100000858306885" DeltaTUnit="s" PositionX="-0.1" PositionXUnit="µm" PositionY="0.0" PositionYUnit="µm" PositionZ="0.0" PositionZUnit="µm"/>
+      <Plane TheZ="0" TheT="7" TheC="0" DeltaT="3.4079999923706055" DeltaTUnit="s" ExposureTime="27.32513" ExposureTimeUnit="s" PositionX="-0.1" PositionXUnit="µm" PositionY="0.0" PositionYUnit="µm" PositionZ="0.0" PositionZUnit="µm"/>
+      <Plane TheZ="0" TheT="7" TheC="1" DeltaT="7.4100000858306885" DeltaTUnit="s" PositionX="-0.1" PositionXUnit="µm" PositionY="0.0" PositionYUnit="µm" PositionZ="0.0" PositionZUnit="µm"/>
+      <Plane TheZ="0" TheT="8" TheC="0" DeltaT="4.4079999923706055" 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="9" TheC="0" DeltaT="5.4090001583099365" DeltaTUnit="s" ExposureTime="27.32513" ExposureTimeUnit="s" PositionX="-0.1" PositionXUnit="µm" PositionY="0.0" PositionYUnit="µm" PositionZ="0.0" PositionZUnit="µm"/>
+      <Plane TheZ="0" TheT="9" TheC="1" DeltaT="9.41100001335144" DeltaTUnit="s" PositionX="-0.1" PositionXUnit="µm" PositionY="0.0" PositionYUnit="µm" PositionZ="0.0" PositionZUnit="µm"/>
+    </Pixels>
+  </Image>
+</OME>

ome-metadata/tests/YTL1841B2-2-1_1hr_DMSO_galinduction_1.xml

@@ -0,0 +1,11 @@
+<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="max.tif">
+    <Description/>
+    <Pixels ID="Pixels:0" DimensionOrder="XYCZT" Type="uint16" SignificantBits="16" Interleaved="false" BigEndian="true" SizeX="1024" SizeY="1024" SizeZ="1" SizeC="1" SizeT="1">
+      <Channel ID="Channel:0:0" SamplesPerPixel="1">
+        <LightPath/>
+      </Channel>
+      <MetadataOnly/>
+    </Pixels>
+  </Image>
+</OME>

ome-metadata/tests/YTL1849A111_2023_05_04__14_46_19_cellnr_1_track.xml

@@ -0,0 +1,21 @@
+<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="YTL1849A111_2023_05_04__14_46_19_cellnr_1_track.tif">
+    <AcquisitionDate>2023-05-10T21:20:56</AcquisitionDate>
+    <Description/>
+    <Pixels ID="Pixels:0" DimensionOrder="XYCZT" Type="uint16" SignificantBits="16" Interleaved="false" BigEndian="false" SizeX="400" SizeY="100" SizeZ="1" SizeC="4" SizeT="241" PhysicalSizeX="0.0970873786407767" PhysicalSizeXUnit="µm" PhysicalSizeY="0.0970873786407767" PhysicalSizeYUnit="µm">
+      <Channel ID="Channel:0:0" SamplesPerPixel="1">
+        <LightPath/>
+      </Channel>
+      <Channel ID="Channel:0:1" SamplesPerPixel="1">
+        <LightPath/>
+      </Channel>
+      <Channel ID="Channel:0:2" SamplesPerPixel="1">
+        <LightPath/>
+      </Channel>
+      <Channel ID="Channel:0:3" SamplesPerPixel="1">
+        <LightPath/>
+      </Channel>
+      <MetadataOnly/>
+    </Pixels>
+  </Image>
+</OME>

ome-metadata/tests/YTL378_JF552.xml

@@ -0,0 +1,106 @@
+<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">
+  <Instrument ID="Instrument:0">
+    <Microscope Type="Other"/>
+    <Objective ID="Objective:0:0" Correction="Other" Immersion="Other"/>
+    <Filter ID="Filter:0:0"/>
+    <Filter ID="Filter:0:1"/>
+  </Instrument>
+  <Instrument ID="Instrument:1">
+    <Microscope Type="Other"/>
+    <Objective ID="Objective:1:0" Correction="Other" Immersion="Other"/>
+    <Filter ID="Filter:1:0"/>
+    <Filter ID="Filter:1:1"/>
+  </Instrument>
+  <Instrument ID="Instrument:2">
+    <Microscope Type="Other"/>
+    <Objective ID="Objective:2:0" Correction="Other" Immersion="Other"/>
+    <Filter ID="Filter:2:0"/>
+    <Filter ID="Filter:2:1"/>
+  </Instrument>
+  <Instrument ID="Instrument:3">
+    <Microscope Type="Other"/>
+    <Objective ID="Objective:3:0" Correction="Other" Immersion="Other"/>
+    <Filter ID="Filter:3:0"/>
+    <Filter ID="Filter:3:1"/>
+  </Instrument>
+  <Image ID="Image:0" Name="Image001">
+    <AcquisitionDate>2018-10-09T13:14:54</AcquisitionDate>
+    <InstrumentRef ID="Instrument:0"/>
+    <ObjectiveSettings ID="Objective:0:0"/>
+    <Pixels ID="Pixels:0" DimensionOrder="XYCZT" Type="uint16" SignificantBits="16" Interleaved="false" BigEndian="false" SizeX="1024" SizeY="1024" SizeZ="1" SizeC="2" SizeT="1" PhysicalSizeX="0.1" PhysicalSizeXUnit="µm" PhysicalSizeY="0.1" PhysicalSizeYUnit="µm">
+      <Channel ID="Channel:0:0" SamplesPerPixel="1" Color="16711935">
+        <LightPath>
+          <EmissionFilterRef ID="Filter:0:0"/>
+        </LightPath>
+      </Channel>
+      <Channel ID="Channel:0:1" SamplesPerPixel="1" Color="-16776961">
+        <LightPath>
+          <EmissionFilterRef ID="Filter:0:1"/>
+        </LightPath>
+      </Channel>
+      <MetadataOnly/>
+      <Plane TheZ="0" TheT="0" TheC="0" DeltaT="0.0" DeltaTUnit="s"/>
+      <Plane TheZ="0" TheT="0" TheC="1" DeltaT="0.7779998779296875" DeltaTUnit="s"/>
+    </Pixels>
+  </Image>
+  <Image ID="Image:1" Name="Image002">
+    <AcquisitionDate>2018-10-09T13:53:56</AcquisitionDate>
+    <InstrumentRef ID="Instrument:1"/>
+    <ObjectiveSettings ID="Objective:1:0"/>
+    <Pixels ID="Pixels:1" DimensionOrder="XYCZT" Type="uint16" SignificantBits="16" Interleaved="false" BigEndian="false" SizeX="1024" SizeY="1024" SizeZ="1" SizeC="2" SizeT="1" PhysicalSizeX="0.1" PhysicalSizeXUnit="µm" PhysicalSizeY="0.1" PhysicalSizeYUnit="µm">
+      <Channel ID="Channel:1:0" SamplesPerPixel="1" Color="16711935">
+        <LightPath>
+          <EmissionFilterRef ID="Filter:1:0"/>
+        </LightPath>
+      </Channel>
+      <Channel ID="Channel:1:1" SamplesPerPixel="1" Color="-16776961">
+        <LightPath>
+          <EmissionFilterRef ID="Filter:1:1"/>
+        </LightPath>
+      </Channel>
+      <MetadataOnly/>
+      <Plane TheZ="0" TheT="0" TheC="0" DeltaT="0.0" DeltaTUnit="s"/>
+      <Plane TheZ="0" TheT="0" TheC="1" DeltaT="0.7840003967285156" DeltaTUnit="s"/>
+    </Pixels>
+  </Image>
+  <Image ID="Image:2" Name="Image003">
+    <AcquisitionDate>2018-10-09T13:54:44</AcquisitionDate>
+    <InstrumentRef ID="Instrument:2"/>
+    <ObjectiveSettings ID="Objective:2:0"/>
+    <Pixels ID="Pixels:2" DimensionOrder="XYCZT" Type="uint16" SignificantBits="16" Interleaved="false" BigEndian="false" SizeX="1024" SizeY="1024" SizeZ="1" SizeC="2" SizeT="1" PhysicalSizeX="0.1" PhysicalSizeXUnit="µm" PhysicalSizeY="0.1" PhysicalSizeYUnit="µm">
+      <Channel ID="Channel:2:0" SamplesPerPixel="1" Color="16711935">
+        <LightPath>
+          <EmissionFilterRef ID="Filter:2:0"/>
+        </LightPath>
+      </Channel>
+      <Channel ID="Channel:2:1" SamplesPerPixel="1" Color="-16776961">
+        <LightPath>
+          <EmissionFilterRef ID="Filter:2:1"/>
+        </LightPath>
+      </Channel>
+      <MetadataOnly/>
+      <Plane TheZ="0" TheT="0" TheC="0" DeltaT="0.0" DeltaTUnit="s"/>
+      <Plane TheZ="0" TheT="0" TheC="1" DeltaT="0.7699985504150391" DeltaTUnit="s"/>
+    </Pixels>
+  </Image>
+  <Image ID="Image:3" Name="Image004">
+    <AcquisitionDate>2018-10-09T13:55:44</AcquisitionDate>
+    <InstrumentRef ID="Instrument:3"/>
+    <ObjectiveSettings ID="Objective:3:0"/>
+    <Pixels ID="Pixels:3" DimensionOrder="XYCZT" Type="uint16" SignificantBits="16" Interleaved="false" BigEndian="false" SizeX="1024" SizeY="1024" SizeZ="1" SizeC="2" SizeT="1" PhysicalSizeX="0.1" PhysicalSizeXUnit="µm" PhysicalSizeY="0.1" PhysicalSizeYUnit="µm">
+      <Channel ID="Channel:3:0" SamplesPerPixel="1" Color="16711935">
+        <LightPath>
+          <EmissionFilterRef ID="Filter:3:0"/>
+        </LightPath>
+      </Channel>
+      <Channel ID="Channel:3:1" SamplesPerPixel="1" Color="-16776961">
+        <LightPath>
+          <EmissionFilterRef ID="Filter:3:1"/>
+        </LightPath>
+      </Channel>
+      <MetadataOnly/>
+      <Plane TheZ="0" TheT="0" TheC="0" DeltaT="0.0" DeltaTUnit="s"/>
+      <Plane TheZ="0" TheT="0" TheC="1" DeltaT="0.7729988098144531" DeltaTUnit="s"/>
+    </Pixels>
+  </Image>
+</OME>

ome-metadata/tests/beads_2023_05_04__19_00_22.xml

@@ -0,0 +1,652 @@
+<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="w.pomp"/>
+  <Instrument ID="Instrument:0">
+    <Microscope/>
+    <Detector Model="" Gain="1.0" Zoom="1.0" AmplificationGain="100.0" ID="Detector:0:0" Type="Other"/>
+    <Detector Model="" Gain="0.0" Zoom="1.0" AmplificationGain="100.0" ID="Detector:0:1" Type="Other"/>
+    <Detector Model="" Gain="0.0" Zoom="1.0" AmplificationGain="100.0" ID="Detector:1:0" Type="Other"/>
+    <Detector Model="" Gain="0.0" Zoom="1.0" AmplificationGain="100.0" ID="Detector:1:1" Type="Other"/>
+    <Detector Model="" Gain="0.0" Zoom="1.0" AmplificationGain="100.0" ID="Detector:2:0" Type="Other"/>
+    <Detector Model="" Gain="0.0" Zoom="1.0" AmplificationGain="100.0" ID="Detector:2:1" Type="Other"/>
+    <Objective Model="alpha Plan-Apochromat 100x/1.57 Oil-HI DIC Korr M27 Elyra" ID="Objective:0" Immersion="Other" LensNA="1.5700000000000003" NominalMagnification="100.0"/>
+  </Instrument>
+  <Image ID="Image:0" Name="Image 25 #1">
+    <ExperimenterRef ID="Experimenter:0"/>
+    <InstrumentRef ID="Instrument:0"/>
+    <ObjectiveSettings ID="Objective:0" Medium="Other" RefractiveIndex="1.661"/>
+    <StageLabel Name="Scene position #0" X="2219.1" XUnit="µm" Y="4321.9" YUnit="µm" Z="324.281" ZUnit="µm"/>
+    <Pixels ID="Pixels:0" DimensionOrder="XYCZT" Type="uint16" SignificantBits="16" Interleaved="false" BigEndian="false" SizeX="512" SizeY="512" SizeZ="101" SizeC="6" SizeT="1" PhysicalSizeX="0.09708737864077668" PhysicalSizeXUnit="µm" PhysicalSizeY="0.09708737864077668" PhysicalSizeYUnit="µm" PhysicalSizeZ="0.09999999999999994" PhysicalSizeZUnit="µm">
+      <Channel ID="Channel:0:0" Name="TV1-T1" SamplesPerPixel="1" IlluminationType="Epifluorescence" AcquisitionMode="TIRF" ExcitationWavelength="561.0" ExcitationWavelengthUnit="nm" EmissionWavelength="561.0" EmissionWavelengthUnit="nm" Color="-6094593">
+        <DetectorSettings ID="Detector:0:0" Binning="1x1"/>
+        <LightPath/>
+      </Channel>
+      <Channel ID="Channel:0:1" Name="TV2-T1" SamplesPerPixel="1" IlluminationType="Epifluorescence" AcquisitionMode="TIRF" ExcitationWavelength="561.0" ExcitationWavelengthUnit="nm" EmissionWavelength="561.0" EmissionWavelengthUnit="nm" Color="-1">
+        <DetectorSettings ID="Detector:0:1" Binning="1x1"/>
+        <LightPath/>
+      </Channel>
+      <Channel ID="Channel:0:2" Name="TV1-T2" SamplesPerPixel="1" IlluminationType="Epifluorescence" AcquisitionMode="TIRF" ExcitationWavelength="488.00000000000006" ExcitationWavelengthUnit="nm" EmissionWavelength="488.00000000000006" EmissionWavelengthUnit="nm" Color="16711935">
+        <DetectorSettings ID="Detector:1:0" Binning="1x1"/>
+        <LightPath/>
+      </Channel>
+      <Channel ID="Channel:0:3" Name="TV2-T2" SamplesPerPixel="1" IlluminationType="Epifluorescence" AcquisitionMode="TIRF" ExcitationWavelength="488.00000000000006" ExcitationWavelengthUnit="nm" EmissionWavelength="488.00000000000006" EmissionWavelengthUnit="nm" Color="-1">
+        <DetectorSettings ID="Detector:1:1" Binning="1x1"/>
+        <LightPath/>
+      </Channel>
+      <Channel ID="Channel:0:4" Name="TV1-T3" SamplesPerPixel="1" IlluminationType="Epifluorescence" AcquisitionMode="TIRF" ExcitationWavelength="642.0000000000001" ExcitationWavelengthUnit="nm" EmissionWavelength="642.0000000000001" EmissionWavelengthUnit="nm" Color="-16776961">
+        <DetectorSettings ID="Detector:2:0" Binning="1x1"/>
+        <LightPath/>
+      </Channel>
+      <Channel ID="Channel:0:5" Name="TV2-T3" SamplesPerPixel="1" IlluminationType="Epifluorescence" AcquisitionMode="TIRF" ExcitationWavelength="642.0000000000001" ExcitationWavelengthUnit="nm" EmissionWavelength="642.0000000000001" EmissionWavelengthUnit="nm" Color="-1">
+        <DetectorSettings ID="Detector:2:1" Binning="1x1"/>
+        <LightPath/>
+      </Channel>
+      <MetadataOnly/>
+      <Plane TheZ="0" TheT="0" TheC="0" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="324.281" PositionZUnit="µm"/>
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+      <Plane TheZ="89" TheT="0" TheC="0" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.181" PositionZUnit="µm"/>
+      <Plane TheZ="89" TheT="0" TheC="1" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.181" PositionZUnit="µm"/>
+      <Plane TheZ="89" TheT="0" TheC="2" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.181" PositionZUnit="µm"/>
+      <Plane TheZ="89" TheT="0" TheC="3" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.181" PositionZUnit="µm"/>
+      <Plane TheZ="89" TheT="0" TheC="4" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.181" PositionZUnit="µm"/>
+      <Plane TheZ="89" TheT="0" TheC="5" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.181" PositionZUnit="µm"/>
+      <Plane TheZ="90" TheT="0" TheC="0" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.281" PositionZUnit="µm"/>
+      <Plane TheZ="90" TheT="0" TheC="1" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.281" PositionZUnit="µm"/>
+      <Plane TheZ="90" TheT="0" TheC="2" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.281" PositionZUnit="µm"/>
+      <Plane TheZ="90" TheT="0" TheC="3" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.281" PositionZUnit="µm"/>
+      <Plane TheZ="90" TheT="0" TheC="4" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.281" PositionZUnit="µm"/>
+      <Plane TheZ="90" TheT="0" TheC="5" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.281" PositionZUnit="µm"/>
+      <Plane TheZ="91" TheT="0" TheC="0" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.381" PositionZUnit="µm"/>
+      <Plane TheZ="91" TheT="0" TheC="1" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.381" PositionZUnit="µm"/>
+      <Plane TheZ="91" TheT="0" TheC="2" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.381" PositionZUnit="µm"/>
+      <Plane TheZ="91" TheT="0" TheC="3" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.381" PositionZUnit="µm"/>
+      <Plane TheZ="91" TheT="0" TheC="4" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.381" PositionZUnit="µm"/>
+      <Plane TheZ="91" TheT="0" TheC="5" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.381" PositionZUnit="µm"/>
+      <Plane TheZ="92" TheT="0" TheC="0" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.481" PositionZUnit="µm"/>
+      <Plane TheZ="92" TheT="0" TheC="1" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.481" PositionZUnit="µm"/>
+      <Plane TheZ="92" TheT="0" TheC="2" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.481" PositionZUnit="µm"/>
+      <Plane TheZ="92" TheT="0" TheC="3" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.481" PositionZUnit="µm"/>
+      <Plane TheZ="92" TheT="0" TheC="4" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.481" PositionZUnit="µm"/>
+      <Plane TheZ="92" TheT="0" TheC="5" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.481" PositionZUnit="µm"/>
+      <Plane TheZ="93" TheT="0" TheC="0" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.581" PositionZUnit="µm"/>
+      <Plane TheZ="93" TheT="0" TheC="1" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.581" PositionZUnit="µm"/>
+      <Plane TheZ="93" TheT="0" TheC="2" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.581" PositionZUnit="µm"/>
+      <Plane TheZ="93" TheT="0" TheC="3" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.581" PositionZUnit="µm"/>
+      <Plane TheZ="93" TheT="0" TheC="4" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.581" PositionZUnit="µm"/>
+      <Plane TheZ="93" TheT="0" TheC="5" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.581" PositionZUnit="µm"/>
+      <Plane TheZ="94" TheT="0" TheC="0" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.681" PositionZUnit="µm"/>
+      <Plane TheZ="94" TheT="0" TheC="1" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.681" PositionZUnit="µm"/>
+      <Plane TheZ="94" TheT="0" TheC="2" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.681" PositionZUnit="µm"/>
+      <Plane TheZ="94" TheT="0" TheC="3" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.681" PositionZUnit="µm"/>
+      <Plane TheZ="94" TheT="0" TheC="4" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.681" PositionZUnit="µm"/>
+      <Plane TheZ="94" TheT="0" TheC="5" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.681" PositionZUnit="µm"/>
+      <Plane TheZ="95" TheT="0" TheC="0" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.781" PositionZUnit="µm"/>
+      <Plane TheZ="95" TheT="0" TheC="1" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.781" PositionZUnit="µm"/>
+      <Plane TheZ="95" TheT="0" TheC="2" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.781" PositionZUnit="µm"/>
+      <Plane TheZ="95" TheT="0" TheC="3" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.781" PositionZUnit="µm"/>
+      <Plane TheZ="95" TheT="0" TheC="4" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.781" PositionZUnit="µm"/>
+      <Plane TheZ="95" TheT="0" TheC="5" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.781" PositionZUnit="µm"/>
+      <Plane TheZ="96" TheT="0" TheC="0" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.881" PositionZUnit="µm"/>
+      <Plane TheZ="96" TheT="0" TheC="1" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.881" PositionZUnit="µm"/>
+      <Plane TheZ="96" TheT="0" TheC="2" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.881" PositionZUnit="µm"/>
+      <Plane TheZ="96" TheT="0" TheC="3" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.881" PositionZUnit="µm"/>
+      <Plane TheZ="96" TheT="0" TheC="4" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.881" PositionZUnit="µm"/>
+      <Plane TheZ="96" TheT="0" TheC="5" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.881" PositionZUnit="µm"/>
+      <Plane TheZ="97" TheT="0" TheC="0" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.981" PositionZUnit="µm"/>
+      <Plane TheZ="97" TheT="0" TheC="1" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.981" PositionZUnit="µm"/>
+      <Plane TheZ="97" TheT="0" TheC="2" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.981" PositionZUnit="µm"/>
+      <Plane TheZ="97" TheT="0" TheC="3" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.981" PositionZUnit="µm"/>
+      <Plane TheZ="97" TheT="0" TheC="4" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.981" PositionZUnit="µm"/>
+      <Plane TheZ="97" TheT="0" TheC="5" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="333.981" PositionZUnit="µm"/>
+      <Plane TheZ="98" TheT="0" TheC="0" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.081" PositionZUnit="µm"/>
+      <Plane TheZ="98" TheT="0" TheC="1" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.081" PositionZUnit="µm"/>
+      <Plane TheZ="98" TheT="0" TheC="2" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.081" PositionZUnit="µm"/>
+      <Plane TheZ="98" TheT="0" TheC="3" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.081" PositionZUnit="µm"/>
+      <Plane TheZ="98" TheT="0" TheC="4" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.081" PositionZUnit="µm"/>
+      <Plane TheZ="98" TheT="0" TheC="5" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.081" PositionZUnit="µm"/>
+      <Plane TheZ="99" TheT="0" TheC="0" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.181" PositionZUnit="µm"/>
+      <Plane TheZ="99" TheT="0" TheC="1" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.181" PositionZUnit="µm"/>
+      <Plane TheZ="99" TheT="0" TheC="2" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.181" PositionZUnit="µm"/>
+      <Plane TheZ="99" TheT="0" TheC="3" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.181" PositionZUnit="µm"/>
+      <Plane TheZ="99" TheT="0" TheC="4" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.181" PositionZUnit="µm"/>
+      <Plane TheZ="99" TheT="0" TheC="5" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.181" PositionZUnit="µm"/>
+      <Plane TheZ="100" TheT="0" TheC="0" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.281" PositionZUnit="µm"/>
+      <Plane TheZ="100" TheT="0" TheC="1" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.281" PositionZUnit="µm"/>
+      <Plane TheZ="100" TheT="0" TheC="2" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.281" PositionZUnit="µm"/>
+      <Plane TheZ="100" TheT="0" TheC="3" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.281" PositionZUnit="µm"/>
+      <Plane TheZ="100" TheT="0" TheC="4" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.281" PositionZUnit="µm"/>
+      <Plane TheZ="100" TheT="0" TheC="5" DeltaT="30479.35022952419" DeltaTUnit="s" PositionX="2219.1" PositionXUnit="µm" PositionY="4321.9" PositionYUnit="µm" PositionZ="334.281" PositionZUnit="µm"/>
+    </Pixels>
+  </Image>
+</OME>

ome-metadata/tests/multi-channel.ome.xml

@@ -0,0 +1 @@
+<?xml version="1.0" encoding="UTF-8"?><OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Creator="OME Bio-Formats 5.2.2" UUID="urn:uuid:bebd2be7-8253-4b90-be93-4df567ffe1be" 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="multi-channel.ome.tif"><Pixels BigEndian="true" DimensionOrder="XYZCT" ID="Pixels:0" Interleaved="false" SignificantBits="8" SizeC="3" SizeT="1" SizeX="439" SizeY="167" SizeZ="1" Type="int8"><Channel ID="Channel:0:0" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:1" SamplesPerPixel="1"><LightPath/></Channel><Channel ID="Channel:0:2" SamplesPerPixel="1"><LightPath/></Channel><TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1"><UUID FileName="multi-channel.ome.tif">urn:uuid:bebd2be7-8253-4b90-be93-4df567ffe1be</UUID></TiffData><TiffData FirstC="1" FirstT="0" FirstZ="0" IFD="1" PlaneCount="1"><UUID FileName="multi-channel.ome.tif">urn:uuid:bebd2be7-8253-4b90-be93-4df567ffe1be</UUID></TiffData><TiffData FirstC="2" FirstT="0" FirstZ="0" IFD="2" PlaneCount="1"><UUID FileName="multi-channel.ome.tif">urn:uuid:bebd2be7-8253-4b90-be93-4df567ffe1be</UUID></TiffData></Pixels></Image></OME>

ome-metadata/tests/test.xml

@@ -0,0 +1,12 @@
+<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2016-06" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.openmicroscopy.org/Schemas/OME/2016-06 http://www.openmicroscopy.org/Schemas/OME/2016-06/ome.xsd">
+  <Image ID="Image:0" Name="test.tif">
+    <AcquisitionDate>2025-01-29T14:42:42</AcquisitionDate>
+    <Description/>
+    <Pixels ID="Pixels:0" DimensionOrder="XYCZT" Type="int8" SignificantBits="8" Interleaved="false" BigEndian="false" SizeX="2" SizeY="2" SizeZ="1" SizeC="1" SizeT="1">
+      <Channel ID="Channel:0:0" SamplesPerPixel="1">
+        <LightPath/>
+      </Channel>
+      <MetadataOnly/>
+    </Pixels>
+  </Image>
+</OME>

parfor/__init__.py

@@ -1,720 +0,0 @@
-from __future__ import annotations
-
-import logging
-import os
-from collections import OrderedDict
-from contextlib import ExitStack, redirect_stderr, redirect_stdout
-from functools import wraps
-from importlib.metadata import version
-from io import StringIO
-from multiprocessing.shared_memory import SharedMemory
-from traceback import format_exc
-from typing import (
-    Any,
-    Callable,
-    Generator,
-    Hashable,
-    Iterable,
-    Iterator,
-    NoReturn,
-    Optional,
-    Protocol,
-    Sequence,
-    Sized,
-)
-
-import numpy as np
-import ray
-from numpy.typing import ArrayLike, DTypeLike
-from ray.remote_function import RemoteFunction
-from ray.types import ObjectRef
-from tqdm.auto import tqdm
-
-from .pickler import dumps, loads
-
-__version__ = version("parfor")
-cpu_count = int(os.cpu_count())
-
-
-class Bar(Protocol):
-    def update(self, n: int = 1) -> None: ...
-
-
-class SharedArray(np.ndarray):
-    """Numpy array whose memory can be shared between processes, so that memory use is reduced and changes in one
-    process are reflected in all other processes. Changes are not atomic, so protect changes with a lock to prevent
-    race conditions!
-    """
-
-    def __new__(
-        cls,
-        shape: int | Sequence[int],
-        dtype: DTypeLike = float,
-        shm: str | SharedMemory = None,
-        offset: int = 0,
-        strides: tuple[int, int] = None,
-        order: str = None,
-    ) -> SharedArray:
-        if isinstance(shm, str):
-            shm = SharedMemory(shm)
-        elif shm is None:
-            shm = SharedMemory(create=True, size=int(np.prod(shape) * np.dtype(dtype).itemsize))  # type: ignore
-        new = super().__new__(cls, shape, dtype, shm.buf, offset, strides, order)
-        new.shm = shm
-        return new  # type: ignore
-
-    def __reduce__(
-        self,
-    ) -> tuple[
-        Callable[[int | Sequence[int], DTypeLike, str], SharedArray],
-        tuple[int | tuple[int, ...], np.dtype, str],
-    ]:
-        return self.__class__, (self.shape, self.dtype, self.shm.name)
-
-    def __enter__(self) -> SharedArray:
-        return self
-
-    def __exit__(self, *args: Any, **kwargs: Any) -> None:
-        if hasattr(self, "shm"):
-            self.shm.close()
-            self.shm.unlink()
-
-    def __del__(self) -> None:
-        if hasattr(self, "shm"):
-            self.shm.close()
-
-    def __array_finalize__(self, obj: np.ndarray | None) -> None:
-        if isinstance(obj, np.ndarray) and not isinstance(obj, SharedArray):
-            raise TypeError("view casting to SharedArray is not implemented because right now we need to make a copy")
-
-    @classmethod
-    def from_array(cls, array: ArrayLike) -> SharedArray:
-        """copy existing array into a SharedArray"""
-        array = np.asarray(array)
-        new = cls(array.shape, array.dtype)
-        new[:] = array[:]
-        return new
-
-
-class Chunks(Iterable):
-    """Yield successive chunks from lists.
-    Usage: chunks(list0, list1, ...)
-           chunks(list0, list1, ..., size=s)
-           chunks(list0, list1, ..., number=n)
-           chunks(list0, list1, ..., ratio=r)
-    size:   size of chunks, might change to optimize division between chunks
-    number: number of chunks, coerced to 1 <= n <= len(list0)
-    ratio:  number of chunks / number of cpus, coerced to 1 <= n <= len(list0)
-    both size and number or ratio are given: use number or ratio, unless the chunk size would be bigger than size
-    both ratio and number are given: use ratio
-    """
-
-    def __init__(
-        self,
-        *iterables: Iterable[Any] | Sized,
-        size: int = None,
-        number: int = None,
-        ratio: float = None,
-        length: int = None,
-    ) -> None:
-        if length is None:
-            try:
-                length = min(*[len(iterable) for iterable in iterables]) if len(iterables) > 1 else len(iterables[0])
-            except TypeError:
-                raise TypeError(
-                    "Cannot determine the length of the iterables(s), so the length must be provided as an argument."
-                )
-        if size is not None and (number is not None or ratio is not None):
-            if number is None:
-                number = int(cpu_count * ratio)
-            if length >= size * number:
-                number = round(length / size)
-        elif size is not None:  # size of chunks
-            number = round(length / size)
-        elif ratio is not None:  # number of chunks
-            number = int(cpu_count * ratio)
-        self.iterators = [iter(arg) for arg in iterables]
-        self.number_of_items = length
-        self.length = min(length, number)
-        self.lengths = [
-            ((i + 1) * self.number_of_items // self.length) - (i * self.number_of_items // self.length)
-            for i in range(self.length)
-        ]
-
-    def __iter__(self) -> Iterator[Any]:
-        for i in range(self.length):
-            p, q = (
-                (i * self.number_of_items // self.length),
-                ((i + 1) * self.number_of_items // self.length),
-            )
-            if len(self.iterators) == 1:
-                yield [next(self.iterators[0]) for _ in range(q - p)]
-            else:
-                yield [[next(iterator) for _ in range(q - p)] for iterator in self.iterators]
-
-    def __len__(self) -> int:
-        return self.length
-
-
-class ExternalBar(Iterable):
-    def __init__(
-        self,
-        iterable: Iterable = None,
-        callback: Callable[[int], None] = None,
-        total: int = 0,
-    ) -> None:
-        self.iterable = iterable
-        self.callback = callback
-        self.total = total
-        self._n = 0
-
-    def __enter__(self) -> ExternalBar:
-        return self
-
-    def __exit__(self, *args: Any, **kwargs: Any) -> None:
-        return
-
-    def __iter__(self) -> Iterator[Any]:
-        for n, item in enumerate(self.iterable):
-            yield item
-            self.n = n + 1
-
-    def update(self, n: int = 1) -> None:
-        self.n += n
-
-    @property
-    def n(self) -> int:
-        return self._n
-
-    @n.setter
-    def n(self, n: int) -> None:
-        if n != self._n:
-            self._n = n
-            if self.callback is not None:
-                self.callback(n)
-
-
-def get_worker(n_processes) -> RemoteFunction:
-    n_processes = n_processes or PoolSingleton.cpu_count
-    num_cpus = None if n_processes is None else cpu_count / n_processes
-
-    if not ray.is_initialized():
-        os.environ["RAY_ACCEL_ENV_VAR_OVERRIDE_ON_ZERO"] = "0"
-        ray.init(logging_level=logging.ERROR, log_to_driver=False, include_dashboard=False)
-
-    def worker(task):
-        try:
-            with ExitStack() as stack:  # noqa
-                if task.allow_output:
-                    out = StringIO()
-                    err = StringIO()
-                    stack.enter_context(redirect_stdout(out))
-                    stack.enter_context(redirect_stderr(err))
-                else:
-                    stack.enter_context(redirect_stdout(open(os.devnull, "w")))
-                    stack.enter_context(redirect_stderr(open(os.devnull, "w")))
-                try:
-                    task()
-                    task.status = ("done",)
-                except Exception:  # noqa
-                    task.status = "task_error", format_exc()
-                if task.allow_output:
-                    task.out = out.getvalue()
-                    task.err = err.getvalue()
-        except KeyboardInterrupt:  # noqa
-            pass
-
-        return task
-
-    if num_cpus:
-        return ray.remote(num_cpus=num_cpus)(worker)  # type: ignore
-    else:
-        return ray.remote(worker)  # type: ignore
-
-
-class DequeDict(OrderedDict):
-    def __init__(self, maxlen: int = None, *args: Any, **kwargs: Any) -> None:
-        self.maxlen = maxlen
-        super().__init__(*args, **kwargs)
-
-    def __setitem__(self, *args: Any, **kwargs: Any) -> None:
-        super().__setitem__(*args, **kwargs)
-        self.truncate()
-
-    def truncate(self) -> None:
-        if self.maxlen is not None:
-            while len(self) > self.maxlen:
-                self.popitem(False)
-
-    def update(self, *args: Any, **kwargs: Any) -> None:
-        super().update(*args, **kwargs)  # type: ignore
-        self.truncate()
-
-
-cache = DequeDict(128)
-
-
-class Task:
-    def __init__(
-        self,
-        handle: Hashable,
-        fun: Callable[[Any, ...], Any],
-        args: tuple[Any, ...] = (),
-        kwargs: dict[str, Any] = None,
-        allow_output: bool = False,
-    ) -> None:
-        self.handle = handle
-        self.fun = fun
-        self.args = args
-        self.kwargs = kwargs or {}
-        self.name = fun.__name__ if hasattr(fun, "__name__") else None
-        self.done = False
-        self.result = None
-        self.out = None
-        self.err = None
-        self.future = None
-        self.status = "starting"
-        self.allow_output = allow_output
-
-    @staticmethod
-    def get(item: tuple[bool, Any]) -> Any:
-        if item[0]:
-            return loads(ray.get(item[1]))
-        else:
-            return ray.get(item[1])
-
-    @staticmethod
-    def put(item: Any) -> tuple[bool, Any]:
-        try:
-            h = hash(item)
-            if not h in cache:
-                try:
-                    cache[h] = False, ray.put(item)
-                except Exception:  # noqa
-                    cache[h] = True, ray.put(dumps(item, recurse=True))
-            else:
-                cache.move_to_end(h)
-            return cache[h]
-        except TypeError:
-            try:
-                return False, ray.put(item)
-            except Exception:  # noqa
-                return True, ray.put(dumps(item, recurse=True))
-
-    @property
-    def fun(self) -> Callable[[Any, ...], Any]:
-        return self.get(self._fun)
-
-    @fun.setter
-    def fun(self, fun: Callable[[Any, ...], Any]):
-        self._fun = self.put(fun)
-
-    @property
-    def args(self) -> tuple[Any, ...]:
-        return tuple([self.get(arg) for arg in self._args])
-
-    @args.setter
-    def args(self, args: tuple[Any, ...]) -> None:
-        self._args = [self.put(arg) for arg in args]
-
-    @property
-    def kwargs(self) -> dict[str, Any]:
-        return {key: self.get(value) for key, value in self._kwargs.items()}
-
-    @kwargs.setter
-    def kwargs(self, kwargs: dict[str, Any]) -> None:
-        self._kwargs = {key: self.put(value) for key, value in kwargs.items()}
-
-    @property
-    def result(self) -> Any:
-        return self.get(self._result)
-
-    @result.setter
-    def result(self, result: Any) -> None:
-        self._result = self.put(result)
-
-    def __call__(self) -> Task:
-        if not self.done:
-            self.result = self.fun(*self.args, **self.kwargs)  # noqa
-            self.done = True
-        return self
-
-    def __repr__(self) -> str:
-        if self.done:
-            return f"Task {self.handle}, result: {self.result}"
-        else:
-            return f"Task {self.handle}"
-
-
-class ParPool:
-    """Parallel processing with addition of iterations at any time and request of that result any time after that.
-    The target function and its argument can be changed at any time.
-    """
-
-    def __init__(
-        self,
-        fun: Callable[[Any, ...], Any] = None,
-        args: tuple[Any] = None,
-        kwargs: dict[str, Any] = None,
-        n_processes: int = None,
-        bar: Bar = None,
-        allow_output: bool = False,
-    ):
-        self.handle = 0
-        self.tasks = {}
-        self.bar = bar
-        self.bar_lengths = {}
-        self.allow_output = allow_output
-        self.fun = fun
-        self.args = args
-        self.kwargs = kwargs
-        self.n_processes = n_processes or PoolSingleton.cpu_count
-        self.worker = get_worker(self.n_processes)
-
-    def __getstate__(self) -> NoReturn:
-        raise RuntimeError(f"Cannot pickle {self.__class__.__name__} object.")
-
-    def __enter__(self) -> ParPool:
-        return self
-
-    def __exit__(self, *args: Any, **kwargs: Any) -> None:
-        self.close()
-
-    def __call__(self, n: Any, handle: Hashable = None, barlength: int = 1) -> None:
-        self.add_task(
-            args=(n, *(() if self.args is None else self.args)),
-            handle=handle,
-            barlength=barlength,
-        )
-
-    def close(self) -> None:
-        cache.clear()
-
-    def add_task(
-        self,
-        fun: Callable[[Any, ...], Any] = None,
-        args: tuple[Any, ...] = None,
-        kwargs: dict[str, Any] = None,
-        handle: Hashable = None,
-        barlength: int = 1,
-        allow_output: bool = False,
-    ) -> Optional[int]:
-        if handle is None:
-            new_handle = self.handle
-            self.handle += 1
-        else:
-            new_handle = handle
-        if new_handle in self:
-            raise ValueError(f"handle {new_handle} already present")
-        task = Task(
-            new_handle,
-            fun or self.fun,
-            args or self.args,
-            kwargs or self.kwargs,
-            allow_output or self.allow_output,
-        )
-        self.block_until_space_available()
-        task.future = self.worker.remote(task)
-        self.tasks[new_handle] = task
-        self.bar_lengths[new_handle] = barlength
-        if handle is None:
-            return new_handle
-        else:
-            return None
-
-    def __setitem__(self, handle: Hashable, n: Any) -> None:
-        """Add new iteration."""
-        self(n, handle=handle)
-
-    def __getitem__(self, handle: Hashable) -> Any:
-        """Request result and delete its record. Wait if result not yet available."""
-        if handle not in self:
-            raise KeyError(f"No task with handle: {handle} in pool")
-        task = self.finalize_task(self.tasks[handle])
-        self.tasks.pop(task.handle)
-        return task.result
-
-    def __contains__(self, handle: Hashable) -> bool:
-        return handle in self.tasks
-
-    def __delitem__(self, handle: Hashable) -> None:
-        self.tasks.pop(handle)
-
-    def finalize_task(self, future: ObjectRef | Task) -> Task:
-        if isinstance(future, Task):
-            task: Task = future
-            future = task.future
-        else:
-            task = None  # type: ignore
-
-        if future is not None:
-            task: Task = ray.get(future)  # type: ignore
-            code, *args = task.status
-            if task.out:
-                if hasattr(self.bar, "write"):
-                    self.bar.write(task.out, end="")
-                else:
-                    print(task.out, end="")
-            if task.err:
-                if hasattr(self.bar, "write"):
-                    self.bar.write(task.err, end="")
-                else:
-                    print(task.err, end="")
-            getattr(self, code)(task, *args)
-            self.tasks[task.handle] = task
-        return task
-
-    def block_until_space_available(self) -> None:
-        if len(self.tasks) < 3 * self.n_processes:
-            return
-        while True:
-            if self.tasks:
-                futures = [task.future for task in self.tasks.values() if task.future is not None]
-                done, busy = ray.wait(futures, num_returns=1, timeout=0.01)
-                for d in done:
-                    self.finalize_task(d)  # type: ignore
-                if len(busy) < 3 * self.n_processes:
-                    return
-
-    def get_newest(self) -> Any:
-        """Request the newest handle and result and delete its record. Wait if result not yet available."""
-        if self.tasks:
-            done = [task for task in self.tasks.values() if task.future is None]
-            if done:
-                task = done[0]
-                self.tasks.pop(task.handle)
-                return task.handle, task.result
-            while True:
-                futures = [task.future for task in self.tasks.values() if task.future is not None]
-                done, _ = ray.wait(futures, num_returns=1, timeout=0.01)
-                if done:
-                    task = self.finalize_task(done[0])
-                    self.tasks.pop(task.handle)
-                    return task.handle, task.result
-        raise StopIteration
-
-    def task_error(self, task: Task, error: Exception) -> None:
-        if task.handle in self:
-            task = self.tasks[task.handle]
-            print(f"Error from process working on iteration {task.handle}:\n")
-            print(error)
-            print("Retrying in main process...")
-            task()
-            raise Exception(f"Function '{task.name}' cannot be executed by parfor, amend or execute in serial.")
-
-    def done(self, task: Task) -> None:
-        if task.handle in self:  # if not, the task was restarted erroneously
-            self.tasks[task.handle] = task
-            if hasattr(self.bar, "update"):
-                self.bar.update(self.bar_lengths.pop(task.handle))
-
-
-class PoolSingleton:
-    cpu_count: int = os.cpu_count()
-
-    @staticmethod
-    def close(*args, **kwargs) -> None:
-        pass
-
-
-class Worker:
-    nested: bool = False
-
-
-def gmap(
-    fun: Callable[[Any, ...], Any],
-    iterable: Iterable[Any] = None,
-    args: tuple[Any, ...] = None,
-    kwargs: dict[str, Any] = None,
-    total: int = None,
-    desc: str = None,
-    bar: Bar | bool = True,
-    serial: bool = None,
-    n_processes: int = None,
-    yield_ordered: bool = True,
-    yield_index: bool = False,
-    allow_output: bool = False,
-    **bar_kwargs: Any,
-) -> Generator[Any, None, None]:
-    """map a function fun to each iteration in iterable
-    use as a function: pmap
-    use as a decorator: parfor
-    best use: iterable is a generator and length is given to this function as 'total'
-
-    required:
-        fun:    function taking arguments: iteration from  iterable, other arguments defined in args & kwargs
-        iterable: iterable or iterator from which an item is given to fun as a first argument
-    optional:
-        args:   tuple with other unnamed arguments to fun
-        kwargs: dict with other named arguments to fun
-        total:  give the length of the iterator in cases where len(iterator) results in an error
-        desc:   string with description of the progress bar
-        bar:    bool enable progress bar,
-                    or a callback function taking the number of passed iterations as an argument
-        serial: execute in series instead of parallel if True, None (default): let pmap decide
-        n_processes: number of processes to use,
-            the parallel pool will be restarted if the current pool does not have the right number of processes
-        yield_ordered: return the result in the same order as the iterable
-        yield_index: return the index of the result too
-        allow_output: allow output from subprocesses
-        **bar_kwargs: keywords arguments for tqdm.tqdm
-
-    output:
-        list (pmap) or generator (gmap) with results from applying the function \'fun\' to each iteration
-         of the iterable / iterator
-
-    examples:
-        << from time import sleep
-        <<
-        @parfor(range(10), (3,))
-        def fun(i, a):
-            sleep(1)
-            return a * i ** 2
-        fun
-        >> [0, 3, 12, 27, 48, 75, 108, 147, 192, 243]
-
-        <<
-        def fun(i, a):
-            sleep(1)
-            return a * i ** 2
-        pmap(fun, range(10), (3,))
-        >> [0, 3, 12, 27, 48, 75, 108, 147, 192, 243]
-
-        equivalent to using the deco module:
-        <<
-        @concurrent
-        def fun(i, a):
-            time.sleep(1)
-            return a * i ** 2
-
-        @synchronized
-        def run(iterator, a):
-            res = []
-            for i in iterator:
-                res.append(fun(i, a))
-            return res
-        run(range(10), 3)
-        >> [0, 3, 12, 27, 48, 75, 108, 147, 192, 243]
-
-        all equivalent to the serial for-loop:
-        <<
-        a = 3
-        fun = []
-        for i in range(10):
-            sleep(1)
-            fun.append(a * i ** 2)
-        fun
-        >> [0, 3, 12, 27, 48, 75, 108, 147, 192, 243]
-    """
-    is_chunked = isinstance(iterable, Chunks)
-    if is_chunked:
-        chunk_fun = fun
-    else:
-        iterable = Chunks(iterable, ratio=5, length=total)
-
-        @wraps(fun)
-        def chunk_fun(iterable: Iterable, *args: Any, **kwargs: Any) -> list[Any]:  # noqa
-            return [fun(iteration, *args, **kwargs) for iteration in iterable]
-
-    if args is None:
-        args = ()
-    if kwargs is None:
-        kwargs = {}
-
-    if "total" not in bar_kwargs:
-        bar_kwargs["total"] = sum(iterable.lengths)
-    if "desc" not in bar_kwargs:
-        bar_kwargs["desc"] = desc
-    if "disable" not in bar_kwargs:
-        bar_kwargs["disable"] = not bar
-    if serial is True or (serial is None and len(iterable) < min(cpu_count, 4)):  # serial case
-
-        def tqdm_chunks(chunks: Chunks, *args, **kwargs) -> Iterable[Any]:  # noqa
-            with tqdm(*args, **kwargs) as b:
-                for chunk, length in zip(chunks, chunks.lengths):  # noqa
-                    yield chunk
-                    b.update(length)
-
-        iterable = (
-            ExternalBar(iterable, bar, sum(iterable.lengths)) if callable(bar) else tqdm_chunks(iterable, **bar_kwargs)  # type: ignore
-        )
-        if is_chunked:
-            if yield_index:
-                for i, c in enumerate(iterable):
-                    yield i, chunk_fun(c, *args, **kwargs)
-            else:
-                for c in iterable:
-                    yield chunk_fun(c, *args, **kwargs)
-        else:
-            if yield_index:
-                for i, c in enumerate(iterable):
-                    for q in chunk_fun(c, *args, **kwargs):
-                        yield i, q
-            else:
-                for c in iterable:
-                    yield from chunk_fun(c, *args, **kwargs)
-
-    else:  # parallel case
-        with ExitStack() as stack:  # noqa
-            if callable(bar):
-                bar = stack.enter_context(ExternalBar(callback=bar))  # noqa
-            else:
-                bar = stack.enter_context(tqdm(**bar_kwargs))
-            with ParPool(chunk_fun, args, kwargs, n_processes, bar, allow_output) as p:  # type: ignore
-                for i, (j, l) in enumerate(zip(iterable, iterable.lengths)):  # add work to the queue
-                    p(j, handle=i, barlength=l)
-                    if bar.total is None or bar.total < i + 1:
-                        bar.total = i + 1
-
-                if is_chunked:
-                    if yield_ordered:
-                        if yield_index:
-                            for i in range(len(iterable)):
-                                yield i, p[i]
-                        else:
-                            for i in range(len(iterable)):
-                                yield p[i]
-                    else:
-                        if yield_index:
-                            for _ in range(len(iterable)):
-                                yield p.get_newest()
-                        else:
-                            for _ in range(len(iterable)):
-                                yield p.get_newest()[1]
-                else:
-                    if yield_ordered:
-                        if yield_index:
-                            for i in range(len(iterable)):
-                                for q in p[i]:
-                                    yield i, q
-                        else:
-                            for i in range(len(iterable)):
-                                yield from p[i]
-                    else:
-                        if yield_index:
-                            for _ in range(len(iterable)):
-                                i, n = p.get_newest()
-                                for q in n:
-                                    yield i, q
-                        else:
-                            for _ in range(len(iterable)):
-                                yield from p.get_newest()[1]
-
-
-def pmap(*args, **kwargs) -> list[Any]:
-    return list(gmap(*args, **kwargs))
-
-
-def parfor(*args: Any, **kwargs: Any) -> Callable[[Callable[[Any, ...], Any]], list[Any]]:
-    def decfun(fun: Callable[[Any, ...], Any]) -> list[Any]:
-        return pmap(fun, *args, **kwargs)
-
-    return decfun
-
-
-try:
-    parfor.__doc__ = pmap.__doc__ = gmap.__doc__
-    pmap.__annotations__ = gmap.__annotations__ | pmap.__annotations__
-    parfor.__annotations__ = {key: value for key, value in pmap.__annotations__.items() if key != "fun"}
-except AttributeError:
-    pass

parfor/pickler.py

@@ -1,119 +0,0 @@
-from __future__ import annotations
-
-import copyreg
-from io import BytesIO
-from pickle import PicklingError
-from typing import Any, Callable
-
-import dill
-
-loads = dill.loads
-
-
-class CouldNotBePickled:
-    def __init__(self, class_name: str) -> None:
-        self.class_name = class_name
-
-    def __repr__(self) -> str:
-        return f"Item of type '{self.class_name}' could not be pickled and was omitted."
-
-    @classmethod
-    def reduce(cls, item: Any) -> tuple[Callable[[str], CouldNotBePickled], tuple[str]]:
-        return cls, (type(item).__name__,)
-
-
-class Pickler(dill.Pickler):
-    """Overload dill to ignore unpicklable parts of objects.
-    You probably didn't want to use these parts anyhow.
-    However, if you did, you'll have to find some way to make them picklable.
-    """
-
-    def save(self, obj: Any, save_persistent_id: bool = True) -> None:
-        """Copied from pickle and amended."""
-        self.framer.commit_frame()
-
-        # Check for persistent id (defined by a subclass)
-        pid = self.persistent_id(obj)
-        if pid is not None and save_persistent_id:
-            self.save_pers(pid)
-            return
-
-        # Check the memo
-        x = self.memo.get(id(obj))
-        if x is not None:
-            self.write(self.get(x[0]))
-            return
-
-        rv = NotImplemented
-        reduce = getattr(self, "reducer_override", None)
-        if reduce is not None:
-            rv = reduce(obj)
-
-        if rv is NotImplemented:
-            # Check the type dispatch table
-            t = type(obj)
-            f = self.dispatch.get(t)
-            if f is not None:
-                f(self, obj)  # Call unbound method with explicit self
-                return
-
-            # Check private dispatch table if any, or else
-            # copyreg.dispatch_table
-            reduce = getattr(self, "dispatch_table", copyreg.dispatch_table).get(t)
-            if reduce is not None:
-                rv = reduce(obj)
-            else:
-                # Check for a class with a custom metaclass; treat as regular
-                # class
-                if issubclass(t, type):
-                    self.save_global(obj)
-                    return
-
-                # Check for a __reduce_ex__ method, fall back to __reduce__
-                reduce = getattr(obj, "__reduce_ex__", None)
-                try:
-                    if reduce is not None:
-                        rv = reduce(self.proto)
-                    else:
-                        reduce = getattr(obj, "__reduce__", None)
-                        if reduce is not None:
-                            rv = reduce()
-                        else:
-                            raise PicklingError("Can't pickle %r object: %r" % (t.__name__, obj))
-                except Exception:  # noqa
-                    rv = CouldNotBePickled.reduce(obj)
-
-        # Check for string returned by reduce(), meaning "save as global"
-        if isinstance(rv, str):
-            try:
-                self.save_global(obj, rv)
-            except Exception:  # noqa
-                self.save_global(obj, CouldNotBePickled.reduce(obj))
-            return
-
-        # Assert that reduce() returned a tuple
-        if not isinstance(rv, tuple):
-            raise PicklingError("%s must return string or tuple" % reduce)
-
-        # Assert that it returned an appropriately sized tuple
-        length = len(rv)
-        if not (2 <= length <= 6):
-            raise PicklingError("Tuple returned by %s must have two to six elements" % reduce)
-
-        # Save the reduce() output and finally memoize the object
-        try:
-            self.save_reduce(obj=obj, *rv)
-        except Exception:  # noqa
-            self.save_reduce(obj=obj, *CouldNotBePickled.reduce(obj))
-
-
-def dumps(
-    obj: Any, protocol: str = None, byref: bool = None, fmode: str = None, recurse: bool = True, **kwds: Any
-) -> bytes:
-    """pickle an object to a string"""
-    protocol = dill.settings["protocol"] if protocol is None else int(protocol)
-    _kwds = kwds.copy()
-    _kwds.update(dict(byref=byref, fmode=fmode, recurse=recurse))
-    with BytesIO() as file:
-        Pickler(file, protocol, **_kwds).dump(obj)
-        return file.getvalue()

pyproject.toml

@@ -1,30 +0,0 @@
-[project]
-name = "parfor"
-version = "2026.5.0"
-description = "A package to mimic the use of parfor as done in Matlab."
-authors = [
-    { name = "Wim Pomp-Pervova", email = "wimpomp@gmail.com" }
-]
-license = { text = "MIT" }
-readme = "README.md"
-keywords = ["parfor", "concurrency", "multiprocessing", "parallel"]
-requires-python = ">=3.10"
-dependencies = [
-    "dill >= 0.3.0",
-    "numpy",
-    "tqdm >= 4.50.0",
-    "ray",
-]
-
-[project.urls]
-repository = "https://git.wimpomp.nl/wim/parfor"
-
-[project.optional-dependencies]
-test = ["pytest"]
-
-[tool.ruff]
-line-length = 119
-indent-width = 4
-
-[tool.isort]
-line_length = 119

tests/test_parfor.py

@@ -1,174 +0,0 @@
-from __future__ import annotations
-
-from dataclasses import dataclass
-from os import getpid
-from time import sleep
-from typing import Any, Iterator, Optional, Sequence
-
-import numpy as np
-import pytest
-
-from parfor import Chunks, ParPool, SharedArray, parfor, pmap
-
-
-class SequenceIterator:
-    def __init__(self, sequence: Sequence) -> None:
-        self._sequence = sequence
-        self._index = 0
-
-    def __iter__(self) -> SequenceIterator:
-        return self
-
-    def __next__(self) -> Any:
-        if self._index < len(self._sequence):
-            item = self._sequence[self._index]
-            self._index += 1
-            return item
-        else:
-            raise StopIteration
-
-    def __len__(self) -> int:
-        return len(self._sequence)
-
-
-class Iterable:
-    def __init__(self, sequence: Sequence) -> None:
-        self.sequence = sequence
-
-    def __iter__(self) -> SequenceIterator:
-        return SequenceIterator(self.sequence)
-
-
-def iterators() -> tuple[Iterator, Optional[int]]:
-    yield range(10), None
-    yield list(range(10)), None
-    yield (i for i in range(10)), 10
-    yield SequenceIterator(range(10)), None
-    yield Iterable(range(10)), 10
-
-
-@pytest.mark.parametrize("iterator", iterators())
-def test_chunks(iterator: tuple[Iterator, Optional[int]]) -> None:
-    chunks = Chunks(iterator[0], size=2, length=iterator[1])
-    assert list(chunks) == [[0, 1], [2, 3], [4, 5], [6, 7], [8, 9]]
-
-
-def test_parpool() -> None:
-    def fun(i, j, k) -> int:  # noqa
-        return i * j * k
-
-    with ParPool(fun, (3,), {"k": 2}) as pool:  # noqa
-        for i in range(10):
-            pool[i] = i
-
-        assert [pool[i] for i in range(10)] == [0, 6, 12, 18, 24, 30, 36, 42, 48, 54]
-
-
-def test_parfor() -> None:
-    @parfor(range(10), (3,), {"k": 2})
-    def fun(i, j, k):
-        return i * j * k
-
-    assert fun == [0, 6, 12, 18, 24, 30, 36, 42, 48, 54]
-
-
-@pytest.mark.parametrize("serial", (True, False))
-def test_pmap(serial) -> None:
-    def fun(i, j, k):
-        return i * j * k
-
-    assert pmap(fun, range(10), (3,), {"k": 2}, serial=serial) == [
-        0,
-        6,
-        12,
-        18,
-        24,
-        30,
-        36,
-        42,
-        48,
-        54,
-    ]
-
-
-@pytest.mark.parametrize("serial", (True, False))
-def test_pmap_with_idx(serial) -> None:
-    def fun(i, j, k):
-        return i * j * k
-
-    assert pmap(fun, range(10), (3,), {"k": 2}, serial=serial, yield_index=True) == [
-        (0, 0),
-        (1, 6),
-        (2, 12),
-        (3, 18),
-        (4, 24),
-        (5, 30),
-        (6, 36),
-        (7, 42),
-        (8, 48),
-        (9, 54),
-    ]
-
-
-@pytest.mark.parametrize("serial", (True, False))
-def test_pmap_chunks(serial) -> None:
-    def fun(i, j, k):
-        return [i_ * j * k for i_ in i]
-
-    chunks = Chunks(range(10), size=2)
-    assert pmap(fun, chunks, (3,), {"k": 2}, serial=serial) == [
-        [0, 6],
-        [12, 18],
-        [24, 30],
-        [36, 42],
-        [48, 54],
-    ]
-
-
-def test_id_reuse() -> None:
-    def fun(i):
-        return i[0].a
-
-    @dataclass
-    class T:
-        a: int = 3
-
-    def gen(total):
-        for i in range(total):
-            t = T(i)
-            yield t
-            del t
-
-    a = pmap(fun, Chunks(gen(1000), size=1, length=1000), total=1000)  # noqa
-    assert all([i == j for i, j in enumerate(a)])
-
-
-@pytest.mark.parametrize("n_processes", (2, 4, 6))
-def test_n_processes(n_processes) -> None:
-    @parfor(range(12), n_processes=n_processes)
-    def fun(i):  # noqa
-        sleep(0.25)
-        return getpid()
-
-    assert len(set(fun)) <= n_processes
-
-
-def test_shared_array() -> None:
-    def fun(i, a):
-        a[i] = i
-
-    with SharedArray(100, int) as arr:
-        pmap(fun, range(len(arr)), (arr,))
-        b = np.array(arr)
-
-    assert np.all(b == np.arange(len(arr)))
-
-
-def test_nesting() -> None:
-    def a(i):
-        return i**2
-
-    def b(i):
-        return pmap(a, range(i, i + 50))
-
-    assert pmap(b, range(10)) == [[i**2 for i in range(j, j + 50)] for j in range(10)]