topozarr-core 0.1.0__tar.gz

topozarr_core-0.1.0/Cargo.lock

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topozarr_core-0.1.0/Cargo.toml

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+[package]
+name = "topozarr-core"
+version = "0.1.0"
+edition = "2021"
+license = "MIT"
+description = "Block-reduction kernel for topozarr pyramid generation"
+readme = "README.md"
+
+[lib]
+name = "topozarr_core"
+crate-type = ["cdylib"]
+
+[dependencies]
+pyo3 = { version = "0.28", features = ["extension-module", "abi3-py312"] }
+numpy = "0.28"
+ndarray = { version = "0.17", features = ["rayon"] }
+
+[profile.release]
+lto = true

topozarr_core-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: topozarr-core
+Version: 0.1.0
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Programming Language :: Rust
+Classifier: Topic :: Scientific/Engineering
+Requires-Dist: numpy
+Summary: Block-reduction kernel for topozarr pyramid generation
+License-Expression: MIT
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+Project-URL: Repository, https://github.com/carbonplan/topozarr
+
+# topozarr-core
+
+Rust block-reduction kernel for [topozarr](https://github.com/carbonplan/topozarr) pyramid generation.
+
+This package provides the low-level numeric kernel only. Install
+[`topozarr`](https://pypi.org/project/topozarr/) for the user-facing API.
+

topozarr_core-0.1.0/README.md

@@ -0,0 +1,6 @@
+# topozarr-core
+
+Rust block-reduction kernel for [topozarr](https://github.com/carbonplan/topozarr) pyramid generation.
+
+This package provides the low-level numeric kernel only. Install
+[`topozarr`](https://pypi.org/project/topozarr/) for the user-facing API.

topozarr_core-0.1.0/pyproject.toml

@@ -0,0 +1,26 @@
+[project]
+name = "topozarr-core"
+version = "0.1.0"
+description = "Block-reduction kernel for topozarr pyramid generation"
+readme = "README.md"
+requires-python = ">=3.12"
+dependencies = ["numpy"]
+license = "MIT"
+classifiers = [
+    "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Programming Language :: Rust",
+    "Topic :: Scientific/Engineering",
+]
+
+[project.urls]
+Repository = "https://github.com/carbonplan/topozarr"
+
+[build-system]
+requires = ["maturin>=1.7,<2"]
+build-backend = "maturin"
+
+[tool.maturin]
+module-name = "topozarr_core"
+features = ["pyo3/extension-module"]

topozarr_core-0.1.0/src/lib.rs

@@ -0,0 +1,230 @@
+use ndarray::{ArrayD, ArrayViewD, IxDyn, Zip};
+use numpy::{
+    IntoPyArray, PyArrayDescrMethods, PyArrayDyn, PyArrayMethods, PyUntypedArray,
+    PyUntypedArrayMethods,
+};
+use pyo3::exceptions::{PyTypeError, PyValueError};
+use pyo3::prelude::*;
+
+#[derive(Clone, Copy, PartialEq)]
+enum Method {
+    Mean,
+    Max,
+    Min,
+    Sum,
+}
+
+impl Method {
+    fn parse(s: &str) -> PyResult<Self> {
+        match s {
+            "mean" => Ok(Method::Mean),
+            "max" => Ok(Method::Max),
+            "min" => Ok(Method::Min),
+            "sum" => Ok(Method::Sum),
+            _ => Err(PyValueError::new_err(format!(
+                "method must be one of 'mean', 'max', 'min', 'sum'; got {s:?}"
+            ))),
+        }
+    }
+}
+
+/// Element types the kernel dispatches over. `nan()` is `None` for integers.
+trait Element: Copy + Send + Sync + PartialOrd + 'static {
+    const ZERO: Self;
+    fn to_f64(self) -> f64;
+    fn from_f64(v: f64) -> Self;
+    fn is_nan(self) -> bool;
+    fn nan() -> Option<Self>;
+}
+
+macro_rules! impl_element_int {
+    ($($t:ty),*) => {$(
+        impl Element for $t {
+            const ZERO: Self = 0;
+            fn to_f64(self) -> f64 { self as f64 }
+            fn from_f64(v: f64) -> Self { v as $t }
+            fn is_nan(self) -> bool { false }
+            fn nan() -> Option<Self> { None }
+        }
+    )*};
+}
+
+macro_rules! impl_element_float {
+    ($($t:ty),*) => {$(
+        impl Element for $t {
+            const ZERO: Self = 0.0;
+            fn to_f64(self) -> f64 { self as f64 }
+            fn from_f64(v: f64) -> Self { v as $t }
+            fn is_nan(self) -> bool { self.is_nan() }
+            fn nan() -> Option<Self> { Some(<$t>::NAN) }
+        }
+    )*};
+}
+
+impl_element_int!(u8, u16, i16, i32, i64);
+impl_element_float!(f32, f64);
+
+#[inline]
+fn is_missing<T: Element>(v: T, fill: Option<T>) -> bool {
+    v.is_nan() || fill.is_some_and(|f| v == f)
+}
+
+/// Value emitted for a window with zero valid elements.
+/// Unreachable for integer dtypes without a fill value (nothing can be missing).
+#[inline]
+fn all_missing_result<T: Element>(fill: Option<T>) -> T {
+    fill.or_else(T::nan).unwrap_or(T::ZERO)
+}
+
+fn reduce_window<T: Element>(
+    w: &ArrayViewD<T>,
+    method: Method,
+    fill: Option<T>,
+    skipna: bool,
+) -> T {
+    match method {
+        Method::Mean | Method::Sum => {
+            let mut acc = 0.0f64;
+            let mut count = 0usize;
+            for &v in w.iter() {
+                if skipna && is_missing(v, fill) {
+                    continue;
+                }
+                acc += v.to_f64();
+                count += 1;
+            }
+            if count == 0 {
+                // sum over an all-missing window is 0, matching numpy nansum
+                // and xarray's skipna sum; mean is fill/NaN
+                return match method {
+                    Method::Sum => T::ZERO,
+                    _ => all_missing_result(fill),
+                };
+            }
+            if method == Method::Mean {
+                acc /= count as f64;
+            }
+            T::from_f64(acc)
+        }
+        Method::Max | Method::Min => {
+            let mut best: Option<T> = None;
+            for &v in w.iter() {
+                if skipna {
+                    if is_missing(v, fill) {
+                        continue;
+                    }
+                } else if v.is_nan() {
+                    return v;
+                }
+                best = Some(match best {
+                    None => v,
+                    Some(b) => {
+                        let take = if method == Method::Max { v > b } else { v < b };
+                        if take {
+                            v
+                        } else {
+                            b
+                        }
+                    }
+                });
+            }
+            best.unwrap_or_else(|| all_missing_result(fill))
+        }
+    }
+}
+
+fn reduce<T: Element>(
+    a: ArrayViewD<T>,
+    stride: &[usize],
+    method: Method,
+    fill: Option<T>,
+    skipna: bool,
+) -> ArrayD<T> {
+    // Output: max(n // s, 1) per axis. Windows are min(s, n) wide so an axis
+    // smaller than its stride still yields one window; exact_chunks drops
+    // trailing partial windows, reproducing coarsen(boundary="trim").
+    let out_shape: Vec<usize> = a
+        .shape()
+        .iter()
+        .zip(stride)
+        .map(|(&n, &s)| (n / s).max(1))
+        .collect();
+    let window: Vec<usize> = a
+        .shape()
+        .iter()
+        .zip(stride)
+        .map(|(&n, &s)| s.min(n).max(1))
+        .collect();
+
+    let mut out = ArrayD::<T>::from_elem(IxDyn(&out_shape), T::ZERO);
+    Zip::from(&mut out)
+        .and(a.exact_chunks(IxDyn(&window)))
+        .par_for_each(|o, w| *o = reduce_window(&w.into_dyn(), method, fill, skipna));
+    out
+}
+
+#[pyfunction]
+#[pyo3(signature = (a, stride, method, fill_value=None, skipna=true))]
+fn block_reduce<'py>(
+    py: Python<'py>,
+    a: &Bound<'py, PyUntypedArray>,
+    stride: Vec<usize>,
+    method: &str,
+    fill_value: Option<f64>,
+    skipna: bool,
+) -> PyResult<Bound<'py, PyAny>> {
+    let method = Method::parse(method)?;
+    let ndim = a.ndim();
+    if ndim == 0 || ndim > 4 {
+        return Err(PyValueError::new_err(format!(
+            "array must have 1-4 dimensions, got {ndim}"
+        )));
+    }
+    if stride.len() != ndim {
+        return Err(PyValueError::new_err(format!(
+            "stride length {} does not match array ndim {ndim}",
+            stride.len()
+        )));
+    }
+    if stride.contains(&0) {
+        return Err(PyValueError::new_err("stride entries must be >= 1"));
+    }
+
+    macro_rules! dispatch {
+        ($t:ty) => {{
+            let arr = a.cast::<PyArrayDyn<$t>>()?;
+            let ro = arr.readonly();
+            let view = ro.as_array();
+            let fill = fill_value.map(<$t as Element>::from_f64);
+            let out = py.detach(|| reduce(view, &stride, method, fill, skipna));
+            Ok(out.into_pyarray(py).into_any())
+        }};
+    }
+
+    let dtype = a.dtype();
+    if dtype.is_equiv_to(&numpy::dtype::<f32>(py)) {
+        dispatch!(f32)
+    } else if dtype.is_equiv_to(&numpy::dtype::<f64>(py)) {
+        dispatch!(f64)
+    } else if dtype.is_equiv_to(&numpy::dtype::<i16>(py)) {
+        dispatch!(i16)
+    } else if dtype.is_equiv_to(&numpy::dtype::<i32>(py)) {
+        dispatch!(i32)
+    } else if dtype.is_equiv_to(&numpy::dtype::<i64>(py)) {
+        dispatch!(i64)
+    } else if dtype.is_equiv_to(&numpy::dtype::<u8>(py)) {
+        dispatch!(u8)
+    } else if dtype.is_equiv_to(&numpy::dtype::<u16>(py)) {
+        dispatch!(u16)
+    } else {
+        Err(PyTypeError::new_err(format!(
+            "unsupported dtype {dtype}; expected one of u8, u16, i16, i32, i64, f32, f64"
+        )))
+    }
+}
+
+#[pymodule]
+fn topozarr_core(m: &Bound<'_, PyModule>) -> PyResult<()> {
+    m.add_function(wrap_pyfunction!(block_reduce, m)?)?;
+    Ok(())
+}