wim/ndbioimage
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

- bump bioformats to 8.3.0

Browse Source 
- rust: command line binary, save as mp4, save as tiff, ome metadata, more methods for View, bugfixes, less unsafe code
- python: ome as dict
This commit is contained in:
Wim Pomp
2025-08-21 19:45:02 +02:00
parent 24af64ac7e
commit 3dc8e6af04
17 changed files with 2317 additions and 1261 deletions
Download Patch File Download Diff File Expand all files Collapse all files

375
src/py.rs
View File

@@ -1,16 +1,21 @@
use crate::axes::Axis;
use crate::bioformats::download_bioformats;
use crate::metadata::Metadata;
use crate::reader::{PixelType, Reader};
use crate::view::{Item, View};
use anyhow::{anyhow, Result};
use anyhow::{Result, anyhow};
use itertools::Itertools;
use ndarray::{Ix0, IxDyn, SliceInfoElem};
use numpy::IntoPyArray;
use ome_metadata::Ome;
use pyo3::IntoPyObjectExt;
use pyo3::exceptions::PyNotImplementedError;
use pyo3::prelude::*;
use pyo3::types::{PyEllipsis, PyInt, PyList, PySlice, PySliceMethods, PyString, PyTuple};
use pyo3::IntoPyObjectExt;
use serde::{Deserialize, Serialize};
use serde_json::{from_str, to_string};
use std::path::PathBuf;
use std::sync::Arc;
#[pyclass(module = "ndbioimage.ndbioimage_rs")]
struct ViewConstructor;
@@ -22,12 +27,10 @@ impl ViewConstructor {
Self
}
fn __getstate__(&self) -> (u8,) {
(0,)
fn __getnewargs__<'py>(&self, py: Python<'py>) -> Bound<'py, PyTuple> {
PyTuple::empty(py)
}
fn __setstate__(&self, _state: (u8,)) {}
#[staticmethod]
fn __call__(state: String) -> PyResult<PyView> {
if let Ok(new) = from_str(&state) {
@@ -40,32 +43,122 @@ impl ViewConstructor {
#[pyclass(subclass, module = "ndbioimage.ndbioimage_rs")]
#[pyo3(name = "View")]
#[derive(Debug, Serialize, Deserialize)]
#[derive(Clone, Debug, Serialize, Deserialize)]
struct PyView {
view: View<IxDyn>,
dtype: PixelType,
ome: Arc<Ome>,
}
#[pymethods]
impl PyView {
#[new]
#[pyo3(signature = (path, series = 0, dtype = "uint16"))]
/// new view on a file at path, open series #, open as dtype: (u)int(8/16/32) or float(32/64)
fn new(path: &str, series: usize, dtype: &str) -> PyResult<Self> {
let mut path = PathBuf::from(path);
if path.is_dir() {
for file in path.read_dir()?.flatten() {
let p = file.path();
if file.path().is_file() & (p.extension() == Some("tif".as_ref())) {
path = p;
break;
#[new]
#[pyo3(signature = (path, series = 0, dtype = "uint16", axes = "cztyx"))]
fn new(path: Bound<'_, PyAny>, series: usize, dtype: &str, axes: &str) -> PyResult<Self> {
if path.is_instance_of::<Self>() {
Ok(path.downcast_into::<Self>()?.extract::<Self>()?)
} else {
let mut path = PathBuf::from(path.downcast_into::<PyString>()?.extract::<String>()?);
if path.is_dir() {
for file in path.read_dir()?.flatten() {
let p = file.path();
if file.path().is_file() && (p.extension() == Some("tif".as_ref())) {
path = p;
break;
}
}
}
let axes = axes
.chars()
.map(|a| a.to_string().parse())
.collect::<Result<Vec<Axis>>>()?;
let reader = Reader::new(&path, series)?;
let view = View::new_with_axes(Arc::new(reader), axes)?;
let dtype = dtype.parse()?;
let ome = Arc::new(view.get_ome()?);
Ok(Self { view, dtype, ome })
}
}
fn squeeze<'py>(&self, py: Python<'py>) -> PyResult<Bound<'py, PyAny>> {
let view = self.view.squeeze()?;
if view.ndim() == 0 {
Ok(match self.dtype {
PixelType::I8 => view
.into_dimensionality::<Ix0>()?
.item::<i8>()?
.into_pyobject(py)?
.into_any(),
PixelType::U8 => view
.into_dimensionality::<Ix0>()?
.item::<u8>()?
.into_pyobject(py)?
.into_any(),
PixelType::I16 => view
.into_dimensionality::<Ix0>()?
.item::<i16>()?
.into_pyobject(py)?
.into_any(),
PixelType::U16 => view
.into_dimensionality::<Ix0>()?
.item::<u16>()?
.into_pyobject(py)?
.into_any(),
PixelType::I32 => view
.into_dimensionality::<Ix0>()?
.item::<i32>()?
.into_pyobject(py)?
.into_any(),
PixelType::U32 => view
.into_dimensionality::<Ix0>()?
.item::<u32>()?
.into_pyobject(py)?
.into_any(),
PixelType::I64 => view
.into_dimensionality::<Ix0>()?
.item::<i64>()?
.into_pyobject(py)?
.into_any(),
PixelType::U64 => view
.into_dimensionality::<Ix0>()?
.item::<u64>()?
.into_pyobject(py)?
.into_any(),
PixelType::I128 => view
.into_dimensionality::<Ix0>()?
.item::<i64>()?
.into_pyobject(py)?
.into_any(),
PixelType::U128 => view
.into_dimensionality::<Ix0>()?
.item::<u64>()?
.into_pyobject(py)?
.into_any(),
PixelType::F32 => view
.into_dimensionality::<Ix0>()?
.item::<f32>()?
.into_pyobject(py)?
.into_any(),
PixelType::F64 => view
.into_dimensionality::<Ix0>()?
.item::<f64>()?
.into_pyobject(py)?
.into_any(),
PixelType::F128 => view
.into_dimensionality::<Ix0>()?
.item::<f64>()?
.into_pyobject(py)?
.into_any(),
})
} else {
PyView {
view,
dtype: self.dtype.clone(),
ome: self.ome.clone(),
}
.into_bound_py_any(py)
}
Ok(Self {
view: Reader::new(&path, series as i32)?.view().into_dyn(),
dtype: dtype.parse()?,
})
}
/// close the file: does nothing as this is handled automatically
@@ -73,11 +166,18 @@ impl PyView {
Ok(())
}
fn copy(&self) -> PyView {
PyView {
/// change the data type of the view: (u)int(8/16/32) or float(32/64)
fn as_type(&self, dtype: &str) -> PyResult<PyView> {
Ok(PyView {
view: self.view.clone(),
dtype: self.dtype.clone(),
}
dtype: dtype.parse()?,
ome: self.ome.clone(),
})
}
/// change the data type of the view: (u)int(8/16/32) or float(32/64)
fn astype(&self, dtype: &str) -> PyResult<PyView> {
self.as_type(dtype)
}
/// slice the view and return a new view or a single number
@@ -216,11 +316,33 @@ impl PyView {
PyView {
view,
dtype: self.dtype.clone(),
ome: self.ome.clone(),
}
.into_bound_py_any(py)
}
}
#[pyo3(signature = (dtype = None))]
fn __array__<'py>(&self, py: Python<'py>, dtype: Option<&str>) -> PyResult<Bound<'py, PyAny>> {
if let Some(dtype) = dtype {
self.as_type(dtype)?.as_array(py)
} else {
self.as_array(py)
}
}
fn __contains__(&self, _item: Bound<'_, PyAny>) -> PyResult<bool> {
Err(PyNotImplementedError::new_err("contains not implemented"))
}
fn __enter__<'p>(slf: PyRef<'p, Self>, _py: Python<'p>) -> PyResult<PyRef<'p, Self>> {
Ok(slf)
}
fn __exit__(&self) -> PyResult<()> {
self.close()
}
fn __reduce__(&self) -> PyResult<(ViewConstructor, (String,))> {
if let Ok(s) = to_string(self) {
Ok((ViewConstructor, (s,)))
@@ -229,6 +351,34 @@ impl PyView {
}
}
fn __copy__(&self) -> Self {
Self {
view: self.view.clone(),
dtype: self.dtype.clone(),
ome: self.ome.clone(),
}
}
fn copy(&self) -> Self {
Self {
view: self.view.clone(),
dtype: self.dtype.clone(),
ome: self.ome.clone(),
}
}
fn __len__(&self) -> PyResult<usize> {
Ok(self.view.len())
}
fn __repr__(&self) -> PyResult<String> {
Ok(self.view.summary()?)
}
fn __str__(&self) -> PyResult<String> {
Ok(self.view.path.display().to_string())
}
/// retrieve a single frame at czt, sliced accordingly
fn get_frame<'py>(
&self,
@@ -240,73 +390,113 @@ impl PyView {
Ok(match self.dtype {
PixelType::I8 => self
.view
.get_frame::<i8>(c, z, t)?
.get_frame::<i8, _>(c, z, t)?
.into_pyarray(py)
.into_any(),
PixelType::U8 => self
.view
.get_frame::<u8>(c, z, t)?
.get_frame::<u8, _>(c, z, t)?
.into_pyarray(py)
.into_any(),
PixelType::I16 => self
.view
.get_frame::<i16>(c, z, t)?
.get_frame::<i16, _>(c, z, t)?
.into_pyarray(py)
.into_any(),
PixelType::U16 => self
.view
.get_frame::<u16>(c, z, t)?
.get_frame::<u16, _>(c, z, t)?
.into_pyarray(py)
.into_any(),
PixelType::I32 => self
.view
.get_frame::<i32>(c, z, t)?
.get_frame::<i32, _>(c, z, t)?
.into_pyarray(py)
.into_any(),
PixelType::U32 => self
.view
.get_frame::<u32>(c, z, t)?
.get_frame::<u32, _>(c, z, t)?
.into_pyarray(py)
.into_any(),
PixelType::F32 => self
.view
.get_frame::<f32>(c, z, t)?
.get_frame::<f32, _>(c, z, t)?
.into_pyarray(py)
.into_any(),
PixelType::F64 => self
.view
.get_frame::<f64>(c, z, t)?
.get_frame::<f64, _>(c, z, t)?
.into_pyarray(py)
.into_any(),
PixelType::I64 => self
.view
.get_frame::<i64>(c, z, t)?
.get_frame::<i64, _>(c, z, t)?
.into_pyarray(py)
.into_any(),
PixelType::U64 => self
.view
.get_frame::<u64>(c, z, t)?
.get_frame::<u64, _>(c, z, t)?
.into_pyarray(py)
.into_any(),
PixelType::I128 => self
.view
.get_frame::<i64>(c, z, t)?
.get_frame::<i64, _>(c, z, t)?
.into_pyarray(py)
.into_any(),
PixelType::U128 => self
.view
.get_frame::<u64>(c, z, t)?
.get_frame::<u64, _>(c, z, t)?
.into_pyarray(py)
.into_any(),
PixelType::F128 => self
.view
.get_frame::<f64>(c, z, t)?
.get_frame::<f64, _>(c, z, t)?
.into_pyarray(py)
.into_any(),
})
}
/// retrieve the ome metadata as an xml string
fn flatten<'py>(&self, py: Python<'py>) -> PyResult<Bound<'py, PyAny>> {
Ok(match self.dtype {
PixelType::I8 => self.view.flatten::<i8>()?.into_pyarray(py).into_any(),
PixelType::U8 => self.view.flatten::<u8>()?.into_pyarray(py).into_any(),
PixelType::I16 => self.view.flatten::<i16>()?.into_pyarray(py).into_any(),
PixelType::U16 => self.view.flatten::<u16>()?.into_pyarray(py).into_any(),
PixelType::I32 => self.view.flatten::<i32>()?.into_pyarray(py).into_any(),
PixelType::U32 => self.view.flatten::<u32>()?.into_pyarray(py).into_any(),
PixelType::F32 => self.view.flatten::<f32>()?.into_pyarray(py).into_any(),
PixelType::F64 => self.view.flatten::<f64>()?.into_pyarray(py).into_any(),
PixelType::I64 => self.view.flatten::<i64>()?.into_pyarray(py).into_any(),
PixelType::U64 => self.view.flatten::<u64>()?.into_pyarray(py).into_any(),
PixelType::I128 => self.view.flatten::<i64>()?.into_pyarray(py).into_any(),
PixelType::U128 => self.view.flatten::<u64>()?.into_pyarray(py).into_any(),
PixelType::F128 => self.view.flatten::<f64>()?.into_pyarray(py).into_any(),
})
}
fn to_bytes(&self) -> PyResult<Vec<u8>> {
Ok(match self.dtype {
PixelType::I8 => self.view.to_bytes::<i8>()?,
PixelType::U8 => self.view.to_bytes::<u8>()?,
PixelType::I16 => self.view.to_bytes::<i16>()?,
PixelType::U16 => self.view.to_bytes::<u16>()?,
PixelType::I32 => self.view.to_bytes::<i32>()?,
PixelType::U32 => self.view.to_bytes::<u32>()?,
PixelType::F32 => self.view.to_bytes::<f32>()?,
PixelType::F64 => self.view.to_bytes::<f64>()?,
PixelType::I64 => self.view.to_bytes::<i64>()?,
PixelType::U64 => self.view.to_bytes::<u64>()?,
PixelType::I128 => self.view.to_bytes::<i64>()?,
PixelType::U128 => self.view.to_bytes::<u64>()?,
PixelType::F128 => self.view.to_bytes::<f64>()?,
})
}
fn tobytes(&self) -> PyResult<Vec<u8>> {
self.to_bytes()
}
/// retrieve the ome metadata as an XML string
fn get_ome_xml(&self) -> PyResult<String> {
Ok(self.view.get_ome_xml()?)
}
@@ -319,18 +509,14 @@ impl PyView {
/// the series in the file
#[getter]
fn series(&self) -> PyResult<i32> {
fn series(&self) -> PyResult<usize> {
Ok(self.view.series)
}
/// the axes in the view
#[getter]
fn axes(&self) -> Vec<String> {
self.view
.axes()
.iter()
.map(|a| format!("{:?}", a))
.collect()
fn axes(&self) -> String {
self.view.axes().iter().map(|a| format!("{:?}", a)).join("")
}
/// the shape of the view
@@ -391,6 +577,7 @@ impl PyView {
Ok(PyView {
view,
dtype: self.dtype.clone(),
ome: self.ome.clone(),
})
}
@@ -409,9 +596,16 @@ impl PyView {
Ok(PyView {
view,
dtype: self.dtype.clone(),
ome: self.ome.clone(),
})
}
#[allow(non_snake_case)]
#[getter]
fn T(&self) -> PyResult<Self> {
self.transpose(None)
}
/// collect data into a numpy array
fn as_array<'py>(&self, py: Python<'py>) -> PyResult<Bound<'py, PyAny>> {
Ok(match self.dtype {
@@ -431,14 +625,6 @@ impl PyView {
})
}
/// change the data type of the view: (u)int(8/16/32) or float(32/64)
fn as_type(&self, dtype: String) -> PyResult<Self> {
Ok(PyView {
view: self.view.clone(),
dtype: dtype.parse()?,
})
}
#[getter]
fn get_dtype(&self) -> PyResult<&str> {
Ok(match self.dtype {
@@ -475,6 +661,7 @@ impl PyView {
PyView {
dtype: self.dtype.clone(),
view: self.view.max_proj(self.get_ax(axis)?)?,
ome: self.ome.clone(),
}
.into_bound_py_any(py)
} else {
@@ -507,6 +694,7 @@ impl PyView {
PyView {
dtype: self.dtype.clone(),
view: self.view.min_proj(self.get_ax(axis)?)?,
ome: self.ome.clone(),
}
.into_bound_py_any(py)
} else {
@@ -544,6 +732,7 @@ impl PyView {
PyView {
dtype,
view: self.view.mean_proj(self.get_ax(axis)?)?,
ome: self.ome.clone(),
}
.into_bound_py_any(py)
} else {
@@ -580,6 +769,7 @@ impl PyView {
PyView {
dtype,
view: self.view.sum_proj(self.get_ax(axis)?)?,
ome: self.ome.clone(),
}
.into_bound_py_any(py)
} else {
@@ -595,6 +785,83 @@ impl PyView {
})
}
}
#[getter]
fn z_stack(&self) -> PyResult<bool> {
if let Some(s) = self.view.size_ax(Axis::Z) {
Ok(s > 1)
} else {
Ok(false)
}
}
#[getter]
fn time_series(&self) -> PyResult<bool> {
if let Some(s) = self.view.size_ax(Axis::T) {
Ok(s > 1)
} else {
Ok(false)
}
}
#[getter]
fn pixel_size(&self) -> PyResult<Option<f64>> {
Ok(self.ome.pixel_size()?)
}
#[getter]
fn delta_z(&self) -> PyResult<Option<f64>> {
Ok(self.ome.delta_z()?)
}
#[getter]
fn time_interval(&self) -> PyResult<Option<f64>> {
Ok(self.ome.time_interval()?)
}
fn exposure_time(&self, channel: usize) -> PyResult<Option<f64>> {
Ok(self.ome.exposure_time(channel)?)
}
fn binning(&self, channel: usize) -> Option<usize> {
self.ome.binning(channel)
}
fn laser_wavelengths(&self, channel: usize) -> PyResult<Option<f64>> {
Ok(self.ome.laser_wavelengths(channel)?)
}
fn laser_power(&self, channel: usize) -> PyResult<Option<f64>> {
Ok(self.ome.laser_powers(channel)?)
}
#[getter]
fn objective_name(&self) -> Option<String> {
self.ome.objective_name()
}
#[getter]
fn magnification(&self) -> Option<f64> {
self.ome.magnification()
}
#[getter]
fn tube_lens_name(&self) -> Option<String> {
self.ome.tube_lens_name()
}
fn filter_set_name(&self, channel: usize) -> Option<String> {
self.ome.filter_set_name(channel)
}
fn gain(&self, channel: usize) -> Option<f64> {
self.ome.gain(channel)
}
/// gives a helpful summary of the recorded experiment
fn summary(&self) -> PyResult<String> {
Ok(self.view.summary()?)
}
}
pub(crate) fn ndbioimage_file() -> anyhow::Result<PathBuf> {