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

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- Rust: more derives
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w.pomp
2026-06-22 18:08:58 +02:00
parent 034b879e3f
commit 5ecc5c6cb4
38 changed files with 7582 additions and 3435 deletions
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.github/workflows/publish.yml
-171
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@@ -1,171 +0,0 @@
name: Publish
on: [push, pull_request, workflow_call]
permissions:
contents: read
jobs:
linux:
runs-on: ${{ matrix.platform.runner }}
strategy:
matrix:
platform:
- runner: ubuntu-latest
target: x86_64
- runner: ubuntu-latest
target: x86
- runner: ubuntu-latest
target: aarch64
- runner: ubuntu-latest
target: armv7
- runner: ubuntu-latest
target: s390x
- runner: ubuntu-latest
target: ppc64le
steps:
- uses: actions/checkout@v6
- uses: actions/setup-python@v6
with:
python-version: '3.12'
- name: Build wheels
uses: PyO3/maturin-action@v1
with:
target: ${{ matrix.platform.target }}
args: --release --out dist
sccache: 'true'
manylinux: auto
- name: Upload wheels
uses: actions/upload-artifact@v6
with:
name: wheels-linux-${{ matrix.platform.target }}
path: dist
windows:
runs-on: ${{ matrix.platform.runner }}
strategy:
matrix:
platform:
- runner: windows-latest
target: x64
# - runner: windows-11-arm
# target: aarch64
steps:
- uses: actions/checkout@v6
- uses: actions/setup-python@v6
with:
python-version: '3.12'
architecture: ${{ matrix.platform.target }}
- name: Build wheels
uses: PyO3/maturin-action@v1
with:
target: ${{ matrix.platform.target }}
args: --release --out dist
sccache: 'true'
- name: Upload wheels
uses: actions/upload-artifact@v6
with:
name: wheels-windows-${{ matrix.platform.target }}
path: dist
macos:
runs-on: ${{ matrix.platform.runner }}
strategy:
matrix:
platform:
- runner: macos-latest
target: x86_64
- runner: macos-14
target: aarch64
steps:
- uses: actions/checkout@v6
- uses: actions/setup-python@v6
with:
python-version: '3.12'
- name: Build wheels
uses: PyO3/maturin-action@v1
with:
target: ${{ matrix.platform.target }}
args: --release --out dist
sccache: 'true'
- name: Upload wheels
uses: actions/upload-artifact@v6
with:
name: wheels-macos-${{ matrix.platform.target }}
path: dist
sdist:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v6
- name: Build sdist
uses: PyO3/maturin-action@v1
with:
command: sdist
args: --out dist
- name: Upload sdist
uses: actions/upload-artifact@v6
with:
name: wheels-sdist
path: dist
release:
name: Release
runs-on: ubuntu-latest
needs: [linux, windows, macos, sdist]
steps:
- uses: actions/download-artifact@v7
- name: Publish to PyPI
uses: PyO3/maturin-action@v1
env:
MATURIN_PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
with:
command: upload
args: --non-interactive --skip-existing wheels-*/*
crates_io_publish:
name: Publish (crates.io)
runs-on: ubuntu-latest
timeout-minutes: 25
steps:
- uses: actions/checkout@v6
- uses: dtolnay/rust-toolchain@stable
- name: cargo-release Cache
id: cargo_release_cache
uses: actions/cache@v5
with:
path: ~/.cargo/bin/cargo-release
key: ${{ runner.os }}-cargo-release
- run: cargo install cargo-release
if: steps.cargo_release_cache.outputs.cache-hit != 'true'
- name: cargo login
run: cargo login ${{ secrets.CRATES_IO_API_TOKEN }}
# allow-branch HEAD is because GitHub actions switches
# to the tag while building, which is a detached head
# Publishing is currently messy, because:
#
# * `peace_rt_model_core` exports `NativeError` or `WebError` depending on the target.
# * `peace_rt_model_web` fails to build when publishing the workspace for a native target.
# * `peace_rt_model_web` still needs its dependencies to be published before it can be
# published.
# * `peace_rt_model_hack` needs `peace_rt_model_web` to be published before it can be
# published.
#
# We *could* pass through `--no-verify` so `cargo` doesn't build the crate before publishing,
# which is reasonable, since this job only runs after the Linux, Windows, and WASM builds
# have passed.
- name: "cargo release publish"
run: |-
cargo release \
publish \
--workspace \
--all-features \
--allow-branch "main" \
--no-confirm \
--no-verify \
--execute
.github/workflows/publish_crates.yml
+66
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@@ -0,0 +1,66 @@
name: Publish
on: [workflow_dispatch]
permissions:
contents: read
jobs:
crates_io_publish:
name: Publish (crates.io)
runs-on: ubuntu-latest
timeout-minutes: 25
steps:
- uses: actions/checkout@v6
- name: Restore cache
uses: actions/cache/restore@v4
with:
path: |
~/.cargo
key: cache-ubuntu-cargo-publish
- name: Install Rust
run: |-
export PATH="$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 ${{ secrets.CRATES_IO_API_TOKEN }}
cargo release \
publish \
--workspace \
--all-features \
--allow-branch "main" \
--no-confirm \
--no-verify \
--execute
- name: Store cache
uses: actions/cache/save@v4
with:
path: |
~/.cargo
key: cache-ubuntu-cargo-publish
.github/workflows/publish_pypi.yml
+115
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@@ -0,0 +1,115 @@
name: CI
on: [workflow_dispatch]
permissions:
contents: read
jobs:
pypi_publish:
name: Publish (pypi.org)
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v6
- uses: actions/setup-python@v5
with:
python-version: 3.x
- name: Restore cache
uses: actions/cache/restore@v4
with:
path: |
~/.cache/pip
~/.cache/pip-wheel
~/.cache/sccache
~/.cache/cargo-xwin
~/.cargo
~/.osxcross
key: cache-ubuntu-maturin-cross-compile
- name: Install llvm
run: |
if ! command -v llvm-dlltool >/dev/null 2>&1; then
sudo apt update
sudo apt install -y llvm
fi
shell: bash
- name: Install Rust
run: |
export PATH="$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
.gitignore
+4 -2
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@@ -70,5 +70,7 @@ docs/_build/
# Pyenv
.python-version
/Cargo.lock
/tests/om/
Cargo.lock
target/
.agentbridge
Cargo.toml
+10 -28
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@@ -1,34 +1,16 @@
[package]
name = "ome-metadata"
version = "0.4.0"
[workspace]
resolver = "3"
members = ["ome-metadata", "ome-metadata-derive"]
[workspace.package]
version = "0.5.0"
edition = "2024"
rust-version = "1.85.1"
rust-version = "1.88.0"
authors = ["Wim Pomp <w.pomp@nki.nl>"]
license = "MIT"
license = "MIT OR Apache-2.0"
description = "Ome metadata as a rust/python structure."
homepage = "https://github.com/wimpomp/ome-metadata"
repository = "https://github.com/wimpomp/ome-metadata"
documentation = "https://docs.rs/ome-metadata"
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"]
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]
enum-utils = "0.1"
serde = { version = "1", features = ["derive"] }
thiserror = "2"
quick-xml = { version = "0.38", features = ["serialize"] }
[dependencies.pyo3]
version = "0.27"
features = ["extension-module", "abi3-py310", "generate-import-lib", "anyhow"]
optional = true
[features]
python = ["dep:pyo3"]
LICENSE
-19
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@@ -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
+2 -2
View File
@@ -9,7 +9,7 @@ use ome_metadata::Ome;
let xml = read_to_string($file)?;
let ome: Ome = xml.parse()?;
let image = &ome.image.unwrap()[0];
let image = &ome.image[0];
println!("acquisition date: {:#?}", image.acquisition_date);
```
@@ -22,4 +22,4 @@ with open($file) as f:
ome = Ome.from_xml(xml)
image = ome.image[0]
print(f"acquisition date: {image.acquisition_date}")
```
```
ome-metadata-derive/Cargo.toml
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@@ -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
+201
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@@ -0,0 +1,201 @@
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ome-metadata-derive/LICENSE-MIT
+27
View File
@@ -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
+1
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@@ -0,0 +1 @@
# Derive macros for ome-metadata
ome-metadata-derive/src/lib.rs
+297
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@@ -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
+32
View File
@@ -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
+201
View File
@@ -0,0 +1,201 @@
Apache License
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http://www.apache.org/licenses/
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APPENDIX: How to apply the Apache License to your work.
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boilerplate notice, with the fields enclosed by brackets "[]"
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you may not use this file except in compliance with the License.
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Unless required by applicable law or agreed to in writing, software
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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
+27
View File
@@ -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
+25
View File
@@ -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.xsd → ome-metadata/ome.xsd
View File
ome-metadata/pyproject.toml
+33
View File
@@ -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
src/error.rs → ome-metadata/src/error.rs
+3 -1
View File
@@ -5,7 +5,9 @@ pub enum Error {
#[error(transparent)]
IO(#[from] std::io::Error),
#[error(transparent)]
SerdeXml(#[from] quick_xml::DeError),
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")]
src/lib.rs → ome-metadata/src/lib.rs
+5 -14
View File
@@ -3,24 +3,14 @@ pub mod ome;
pub mod error;
#[cfg(feature = "python")]
mod py;
pub mod py;
use crate::error::Error;
pub use ome::Ome;
use quick_xml::de::from_str;
use std::str::FromStr;
impl FromStr for Ome {
type Err = Error;
fn from_str(s: &str) -> Result<Self, Error> {
Ok(from_str(s)?)
}
}
#[cfg(test)]
mod tests {
use super::*;
use crate::Ome;
use crate::error::Error;
use std::fs::read_to_string;
macro_rules! test_read {
@@ -29,7 +19,8 @@ mod tests {
#[test]
fn $name() -> Result<(), Error> {
let file = read_to_string(format!("tests/{}.xml", $file))?;
let _ome: Ome = file.parse()?;
let ome = Ome::from_xml(file)?;
let _xml = ome.to_xml()?;
Ok(())
}
)*
ome-metadata/src/ome.rs
+6035
View File
File diff suppressed because it is too large Load Diff
ome-metadata/src/py.rs
+487
View File
@@ -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(())
}
}
tests/1xp53-01-AP1.xml → ome-metadata/tests/1xp53-01-AP1.xml
View File
tests/20230511-p53-4x-CMV-1min-4h-01-Airyscan Processing-01.xml → ome-metadata/tests/20230511-p53-4x-CMV-1min-4h-01-Airyscan Processing-01.xml
View File
tests/4-Pos_001_002.xml → ome-metadata/tests/4-Pos_001_002.xml
View File
tests/Experiment-2029.xml → ome-metadata/tests/Experiment-2029.xml
View File
tests/MK022_cE9_1-01-Airyscan Processing-01-Scene-2-P1.xml → ome-metadata/tests/MK022_cE9_1-01-Airyscan Processing-01-Scene-2-P1.xml
View File
tests/YTL1841B2-2-1_1hr_DMSO_galinduction_1.xml → ome-metadata/tests/YTL1841B2-2-1_1hr_DMSO_galinduction_1.xml
View File
tests/YTL1849A111_2023_05_04__14_46_19_cellnr_1_track.xml → ome-metadata/tests/YTL1849A111_2023_05_04__14_46_19_cellnr_1_track.xml
View File
tests/YTL1849A131_2023_05_04__13_36_36.xml → ome-metadata/tests/YTL1849A131_2023_05_04__13_36_36.xml
View File
tests/YTL378_JF552.xml → ome-metadata/tests/YTL378_JF552.xml
View File
tests/beads_2023_05_04__19_00_22.xml → ome-metadata/tests/beads_2023_05_04__19_00_22.xml
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tests/multi-channel.ome.xml → ome-metadata/tests/multi-channel.ome.xml
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tests/test.xml → ome-metadata/tests/test.xml
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py/ome_metadata/__init__.py
-45
View File
@@ -1,45 +0,0 @@
from __future__ import annotations
from collections import UserDict, UserList
from . import ome_metadata_rs as rs # noqa
class Ome(UserDict):
@staticmethod
def from_xml(xml: str) -> Ome:
"""Create the OME structure from an XML string"""
new = Ome()
new.update(rs.ome(str(xml)))
return new
def __dir__(self) -> list[str]:
return list(self.keys()) + list(super().__dir__())
def __getattr__(self, key: str) -> Ome | OmeList | int | float | str:
try:
new = self.__getitem__(key)
except KeyError:
raise AttributeError(f"'Ome' object has no attribute '{key}'")
if isinstance(new, dict):
return Ome(**new)
elif isinstance(new, list):
return OmeList(new)
else:
return new
def __getstate__(self) -> dict[str, Any]:
return self.data
def __setstate__(self, state: dict[str, Any]) -> None:
self.data = state
class OmeList(UserList):
def __getitem__(self, item: int) -> Ome | OmeList | int | float | str:
new = super().__getitem__(item)
if isinstance(new, dict):
return Ome(**new)
elif isinstance(new, list):
return OmeList(new)
else:
return new
pyproject.toml
-32
View File
@@ -1,32 +0,0 @@
[build-system]
requires = ["maturin>=1.8,<2.0"]
build-backend = "maturin"
[project]
name = "ome-metadata"
keywords = ["bioformats", "imread", "ome", "metadata"]
requires-python = ">=3.10"
classifiers = [
"License :: OSI Approved :: MIT License",
"Programming Language :: Rust",
"Programming Language :: Python",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3 :: Only",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: 3.13",
"Programming Language :: Python :: 3.14",
]
dynamic = ["version", "description", "authors", "license", "readme"]
[project.urls]
Repository = "https://github.com/wimpomp/ome-metadata"
[tool.maturin]
python-source = "py"
features = ["pyo3/extension-module", "python"]
module-name = "ome_metadata.ome_metadata_rs"
[tool.isort]
line_length = 119
src/ome.rs
-3022
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File diff suppressed because it is too large Load Diff
src/py.rs
-99
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@@ -1,99 +0,0 @@
use crate::Ome;
use crate::ome::{
Convert, UnitsElectricPotential, UnitsFrequency, UnitsLength, UnitsPower, UnitsPressure,
UnitsTemperature, UnitsTime,
};
use pyo3::exceptions::PyValueError;
use pyo3::prelude::*;
impl From<crate::error::Error> for PyErr {
fn from(err: crate::error::Error) -> PyErr {
PyErr::new::<PyValueError, _>(err.to_string())
}
}
macro_rules! impl_enum_into_py_object {
($($s:ident: $t:ty $(,)?)*) => {
$(
#[pyclass(module = "ome_metadata.ome_metadata_rs")]
pub struct $s {
inner: $t,
}
#[pymethods]
impl $s {
#[new]
fn new(unit: &str) -> PyResult<Self> {
match unit.parse() {
Ok(unit) => Ok(Self { inner: unit }),
Err(_) => Err(PyErr::new::<PyValueError, _>(format!("Invalid unit: {}", unit)))
}
}
/// convert a value between units
fn convert(&self, unit: &str, value: f64) -> PyResult<f64> {
match unit.parse() {
Ok(unit) => Ok(self.inner.convert(&unit, value)?),
Err(_) => Err(PyErr::new::<PyValueError, _>(format!("Invalid unit: {}", unit)))
}
}
/// all possible variants of this enum that can be constructed or converted into
#[staticmethod]
fn variants() -> Vec<String> {
<$t>::variants().iter().map(|v| format!("{:?}", v)).collect()
}
fn __repr__(&self) -> String {
format!("{:?}", self.inner)
}
fn __str__(&self) -> String {
format!("{:?}", self.inner)
}
fn __getnewargs__(&self) -> (String,) {
(format!("{:?}", self.inner),)
}
}
impl<'py> IntoPyObject<'py> for $t {
type Target = $s;
type Output = Bound<'py, Self::Target>;
type Error = PyErr;
fn into_pyobject(self, py: Python<'py>) -> PyResult<Self::Output> {
Bound::new(py, $s { inner: self })
}
}
)*
};
}
impl_enum_into_py_object! {
ElectricPotential: UnitsElectricPotential
Frequency: UnitsFrequency
Length: UnitsLength
Power: UnitsPower
Pressure: UnitsPressure
Temperature: UnitsTemperature
Time: UnitsTime
}
#[pyfunction]
fn ome(text: &str) -> PyResult<Ome> {
Ok(text.parse()?)
}
#[pymodule]
#[pyo3(name = "ome_metadata_rs")]
fn ome_metadata_rs(m: &Bound<'_, PyModule>) -> PyResult<()> {
m.add_class::<ElectricPotential>()?;
m.add_class::<Frequency>()?;
m.add_class::<Length>()?;
m.add_class::<Power>()?;
m.add_class::<Pressure>()?;
m.add_class::<Temperature>()?;
m.add_class::<Time>()?;
m.add_function(wrap_pyfunction!(ome, m)?)?;
Ok(())
}