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- various fixes

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This commit is contained in:
w.pomp
2026-08-07 15:14:16 +02:00
parent e4de76f26c
commit a0d2359e55
13 changed files with 191 additions and 97 deletions
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Cargo.toml
+2 -2
View File
@@ -28,7 +28,7 @@ itertools = "0.15"
indexmap = { version = "2", features = ["serde"] }
indicatif = { version = "0.18", features = ["rayon"], optional = true }
j4rs = { version = "0.25", optional = true }
libczirw-sys = { path = "../libczirw-sys", optional = true }
libczirw-sys = { version = "0.5", optional = true }
ndarray = { version = "0.17", features = ["serde"] }
num = "0.4"
numpy = { version = "0.29", optional = true }
@@ -76,7 +76,7 @@ tiff = ["dep:tiff", "dep:thread_local"]
movie = ["dep:ffmpeg-sidecar", "dep:tokio", "dep:ordered-float", "dep:indicatif", "dep:console"]
[package.metadata.docs.rs]
features = ["bioformats_java", "gpl-formats", "czi", "tiff", "movie"]
features = ["bioformats_java", "czi", "tiff", "tiffseq", "movie", "tiffwrite", "movie"]
[profile.test]
inherits = "release"
README.md
+39 -27
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@@ -1,12 +1,14 @@
# ndbioimage
[![Pytest](https://github.com/pomppervova/ndbioimage/actions/workflows/pytest.yml/badge.svg)](https://github.com/pomppervova/ndbioimage/actions/workflows/pytest.yml)
## Work in progress
Rust rewrite of python version. Read bio image formats using the bio-formats java package.
[https://www.openmicroscopy.org/bio-formats/](https://www.openmicroscopy.org/bio-formats/)
Exposes (bio) images as a numpy ndarray-like object, but without loading the whole
image into memory, reading from the file only when needed. Some metadata is read
Exposes (bio) images as a numpy ndarray-like object (Python) or a struct that can be sliced like an ndarray Array
(Rust), but without loading the whole image into memory, reading from the file only when needed. Some metadata is read
and stored in an [ome](https://genomebiology.biomedcentral.com/articles/10.1186/gb-2005-6-5-r47) structure.
Additionally, it can automatically calculate an affine transform that corrects for chromatic aberrations etc. and apply
it on the fly to the image.
@@ -23,6 +25,7 @@ pip install ndbioimage
```
### Installation with option to write mp4 or mkv:
Work in progress! Make sure ffmpeg is installed.
```
@@ -30,6 +33,7 @@ pip install ndbioimage[write]
```
## Usage
### Python
- Reading an image file and plotting the frame at channel=2, time=1
@@ -60,7 +64,6 @@ with Imread('image_file.tif', axes='cztyx') as im:
sliced_im is an instance of Imread which will load any image data from file only when needed
- Converting (part) of the image to a numpy ndarray
```
@@ -71,36 +74,45 @@ with Imread('image_file.tif', axes='cztyx') as im:
```
### Rust
```
use ndarray::Array2;
use ndbioimage::Reader;
let path = "/path/to/file";
let reader = Reader::new(&path, 0)?;
println!("size: {}, {}", reader.size_y, reader.size_y);
let frame = reader.get_frame(0, 0, 0).unwrap();
if let Ok(arr) = <Frame as TryInto<Array2<i8>>>::try_into(frame) {
println!("{:?}", arr);
} else {
println!("could not convert Frame to Array<i8>");
```rust
use ndarray::Array2;
use ndbioimage::{DynReader, Frame, Reader};
fn main() -> Result<(), ndbioimage::error::Error> {
let path = "/path/to/file";
let reader = DynReader::new(&path, 0, 0)?;
println!("shape: {}", reader.shape());
let frame = reader.get_frame(0, 0, 0)?;
if let Ok(arr) = <Frame as TryInto<Array2<i8>>>::try_into(frame) {
println!("{:?}", arr);
} else {
println!("could not convert Frame to Array<i8>");
}
let xml = reader.metadata()?.to_xml()?;
println!("{}", xml);
Ok(())
}
let xml = reader.get_ome_xml().unwrap();
println!("{}", xml);
```
```
use ndarray::Array2;
use ndbioimage::Reader;
```rust
use ndbioimage::{DynReader, Reader};
let path = "/path/to/file";
let reader = Reader::new(&path, 0)?;
let view = reader.view();
let view = view.max_proj(3)?;
let array = view.as_array::<u16>()?
fn main() -> Result<(), ndbioimage::error::Error> {
let path = "/path/to/file";
let reader = DynReader::new(&path, 0, 0)?;
let view = reader.view();
let view = view.max_proj(3)?;
let array = view.as_array::<u16>()?;
println!("{:?}", array.shape());
Ok(())
}
```
### Command line
```ndbioimage --help```: show help
```ndbioimage image```: show metadata about image
```ndbioimage image -w {name}.tif -r```: copy image into image.tif (replacing {name} with image), while registering channels
```ndbioimage image -w image.mp4 -C cyan lime red``` copy image into image.mp4 (z will be max projected), make channel colors cyan lime and red
```ndbioimage info image```: show metadata about image
```ndbioimage tiff image image.tif -r```: copy image into image.tif, while registering channels
```ndbioimage movie image image.mp4 -C cyan lime red``` copy image into image.mp4 (z will be max projected), make channel
colors cyan lime and red
pyproject.toml
+1 -1
View File
@@ -4,7 +4,7 @@ build-backend = "maturin"
[project]
name = "ndbioimage"
version = "2027.0.2"
version = "2027.0.3"
requires-python = ">=3.10"
classifiers = [
"License :: OSI Approved :: MIT License",
src/lib.rs
+47 -3
View File
@@ -1,4 +1,47 @@
#![cfg_attr(docsrs, feature(doc_cfg))]
//! The ndbioimage crate exposes (bio) images a struct that can be sliced like an ndarray Array
//! (Rust), but without loading the whole image into memory, reading from the file only when needed.
//! Some metadata is read
//! and stored in an [ome](https://genomebiology.biomedcentral.com/articles/10.1186/gb-2005-6-5-r47)
//! structure. Additionally, it can automatically calculate an affine transform that corrects for
//! chromatic aberrations etc. and apply it on the fly to the image.
//!
//! Currently, it supports imagej tif files, czi files, micromanager tif sequences and anything
//! [bioformats](https://www.openmicroscopy.org/bio-formats/) can handle.
//!
//! ```rust,no_run
//! use ndarray::Array2;
//! use ndbioimage::readers::{DynReader, Frame, Reader};
//!
//! # fn main() -> Result<(), ndbioimage::error::Error> {
//! let path = "/path/to/file";
//! let reader = DynReader::new(&path, 0, 0)?;
//! println!("shape: {}", reader.shape());
//! let frame = reader.get_frame(0, 0, 0)?;
//! if let Ok(arr) = <Frame as TryInto<Array2<i8>>>::try_into(frame) {
//! println!("{:?}", arr);
//! } else {
//! println!("could not convert Frame to Array<i8>");
//! }
//! let xml = reader.metadata()?.to_xml()?;
//! println!("{}", xml);
//! # Ok(())
//! # }
//! ```
//!
//! ```rust,no_run
//! use ndbioimage::readers::{DynReader, Reader};
//!
//! # fn main() -> Result<(), ndbioimage::error::Error> {
//! let path = "/path/to/file";
//! let reader = DynReader::new(&path, 0, 0)?;
//! let view = reader.view();
//! let view = view.max_proj(3)?;
//! let array = view.as_array::<u16>()?;
//! println!("{:?}", array.shape());
//! # Ok(())
//! # }
//! ```
pub mod axes;
#[cfg(feature = "python")]
@@ -14,7 +57,7 @@ pub mod movie;
pub mod readers;
#[cfg(feature = "tiffwrite")]
pub mod tiffwrite;
// mod cache;
mod utils;
pub mod main {
#[cfg(feature = "tiffwrite")]
@@ -30,7 +73,8 @@ pub mod main {
use std::path::PathBuf;
#[derive(Parser)]
#[command(arg_required_else_help = true, version, about, long_about = None, propagate_version = true)]
#[command(arg_required_else_help = true, version, about, long_about = None, propagate_version = true
)]
struct Cli {
#[command(subcommand)]
command: Commands,
@@ -162,7 +206,7 @@ pub mod main {
output,
} => {
let options = crate::tiffwrite::TiffOptions::new(
Some(crate::tiffwrite::get_bar(
Some(crate::utils::progress::get_bar(
Some(0),
Some("writing tiff file".to_string()),
)),
src/movie.rs
+6 -19
View File
@@ -2,18 +2,16 @@ use crate::axes::Axis;
use crate::colors::Color;
use crate::error::Error;
use crate::readers::{PixelType, Reader};
use crate::utils::progress::get_bar;
use crate::view::View;
use console::Term;
use ffmpeg_sidecar::command::FfmpegCommand;
use ffmpeg_sidecar::download::auto_download;
use ffmpeg_sidecar::event::{FfmpegEvent, LogLevel};
use indicatif::{ProgressBar, ProgressDrawTarget, ProgressStyle};
use itertools::Itertools;
use ndarray::{Array2, Array3, Dimension, IxDyn, s, stack};
use ordered_float::OrderedFloat;
use std::io::Write;
use std::path::Path;
use std::time::Duration;
pub struct MovieOptions {
velocity: f64,
@@ -138,20 +136,6 @@ fn cframe(frame: Array2<f64>, color: &[u8], a: f64, b: f64) -> Array3<f64> {
stack(ndarray::Axis(2), &view).unwrap()
}
/// a progress bar with an ok style that when py::detach is used also works in jupyter
pub fn get_bar(count: Option<usize>) -> ProgressBar {
let style = ProgressStyle::with_template(
"{spinner:.green} {percent}% [{wide_bar:.green/lime}] {pos:>7}/{len:7} [{elapsed}/{eta}, {per_sec:<5}]",
).expect("template should be working").progress_chars("#>-");
let bar = ProgressBar::with_draw_target(
count.map(|i| i as u64),
ProgressDrawTarget::term_like_with_hz(Box::new(Term::buffered_stdout()), 20),
)
.with_style(style);
bar.enable_steady_tick(Duration::from_millis(100));
bar
}
impl<D, R> View<D, R>
where
D: Dimension,
@@ -252,7 +236,10 @@ where
};
let rt = tokio::runtime::Runtime::new()?;
let bar = get_bar(Some(size_t));
let bar = get_bar(
Some(size_t),
Some("autoscaling movie brightness".to_string()),
);
let rt_bar = bar.clone();
let write_task = rt.spawn(async move {
for t in 0..size_t {
@@ -275,7 +262,7 @@ where
});
bar.finish();
let bar = get_bar(Some(size_t));
let bar = get_bar(Some(size_t), Some("saving movie".to_string()));
let rt_bar = bar.clone();
let progress_task = rt.spawn(async move {
for event in movie.iter().map_err(|e| Error::Ffmpeg(e.to_string()))? {
src/py.rs
+11 -2
View File
@@ -1741,7 +1741,7 @@ impl PyView {
bar: bool,
) -> PyResult<()> {
let bar = if bar {
Some(crate::tiffwrite::get_bar(
Some(crate::utils::progress::get_bar(
Some(0),
Some("writing tiff file".to_string()),
))
@@ -1991,7 +1991,16 @@ impl PyShape {
false,
)
} else if idx.is_instance_of::<PyInt>() {
(vec![idx.cast::<PyInt>()?.extract::<usize>()?], true)
let i = idx.cast::<PyInt>()?.extract::<isize>()?;
let len = self.inner.order.len() as isize;
let i = if i < 0 { i + len } else { i };
if i < 0 || i >= len {
return Err(PyIndexError::new_err(format!(
"index {} is out of bounds for size {}",
i, len
)));
}
(vec![i as usize], true)
} else {
return Err(PyErr::new::<PyTypeError, _>(format!(
"Unknown type: {:?}",
src/readers.rs
+1 -1
View File
@@ -136,7 +136,7 @@ pub enum ArrayT<D: Dimension> {
F128(Array<f64, D>), // f128 is nightly
}
pub(crate) type Frame = ArrayT<Ix2>;
pub type Frame = ArrayT<Ix2>;
pub trait Reader: Clone + Sized + Debug + Send + Hash + Into<DynReader> {
fn new<P>(path: P, series: usize, position: usize) -> Result<Self, Error>
src/readers/bioformats_java.rs
+13 -6
View File
@@ -5,10 +5,9 @@ use serde::{Deserialize, Serialize};
use std::fmt::Debug;
use std::path::{Path, PathBuf};
pub use crate::readers::{ArrayT, PixelType, Reader};
use crate::readers::{DynReader, Frame, Shape};
use crate::readers::{ArrayT, DynReader, Frame, PixelType, Reader, Shape};
use itertools::Itertools;
use j4rs::{Instance, InvocationArg, Jvm, JvmBuilder};
use j4rs::{Instance, InvocationArg, JavaOpt, Jvm, JvmBuilder};
use std::cell::OnceCell;
use std::collections::HashSet;
use std::hash::{Hash, Hasher};
@@ -109,8 +108,16 @@ fn jvm() -> Rc<Jvm> {
let j = JvmBuilder::new()
.skip_setting_native_lib()
.with_base_path(class_path.to_str().unwrap())
.build()
.expect("Failed to build JVM");
.java_opt(JavaOpt::new("--enable-native-access=ALL-UNNAMED"))
.build();
let j = match j {
Ok(j) => j,
Err(_) => JvmBuilder::new()
.skip_setting_native_lib()
.with_base_path(class_path.to_str().unwrap())
.build()
.expect("Failed to build JVM"),
};
if let Ok(e) = InvocationArg::try_from("ERROR") {
let _ = j.invoke_static(
"loci.common.DebugTools",
@@ -122,7 +129,7 @@ fn jvm() -> Rc<Jvm> {
})
}
})
.clone()
.clone()
})
}
src/readers/tiff.rs
+1 -1
View File
@@ -331,7 +331,7 @@ impl Reader for TiffReader {
fn get_frame(&self, c: usize, z: usize, t: usize) -> Result<Frame, Error> {
let (page_idx, offset, stride) = if self.p_ndim == 3 {
(z * self.shape.t + t, c, self.n_samples)
(t * self.shape.z + z, c, self.n_samples)
} else {
(c + z * self.shape.c + t * self.shape.c * self.shape.z, 0, 1)
};
src/tiffwrite.rs
+19 -26
View File
@@ -4,15 +4,14 @@ use crate::error::Error;
use crate::metadata::Metadata;
use crate::readers::{DynReader, PixelType, Reader};
use crate::stats::MinMax;
use crate::utils::progress::get_bar;
use crate::view::{Number, View};
use console::Term;
use indicatif::{ProgressBar, ProgressDrawTarget, ProgressStyle};
use indicatif::ProgressBar;
use itertools::iproduct;
use ndarray::{Array0, Array1, Array2, ArrayD, Dimension};
use rayon::prelude::*;
use std::path::{Path, PathBuf};
use std::sync::{Arc, Condvar, Mutex};
use std::time::Duration;
use tiffwrite::{Bytes, Colors, Compression, IJTiffFile};
#[derive(Debug, Clone)]
@@ -34,23 +33,6 @@ impl Default for TiffOptions {
}
}
/// a progress bar with an ok style that when py::detach is used also works in jupyter
pub fn get_bar(count: Option<usize>, message: Option<String>) -> ProgressBar {
let style = ProgressStyle::with_template(
"{spinner:.green} {percent}% [{wide_bar:.green/lime}] {pos:>7}/{len:7} [{elapsed}/{eta}, {per_sec:<5}]",
).expect("template should be working").progress_chars("#>-");
let bar = ProgressBar::with_draw_target(
count.map(|i| i as u64),
ProgressDrawTarget::term_like_with_hz(Box::new(Term::buffered_stdout()), 20),
)
.with_style(style);
if let Some(message) = message {
bar.set_message(message);
}
bar.enable_steady_tick(Duration::from_millis(100));
bar
}
impl TiffOptions {
pub fn new(
bar: Option<ProgressBar>,
@@ -258,14 +240,25 @@ mod tests {
use std::fs::create_dir_all;
use std::path::PathBuf;
#[cfg(any(
feature = "czi",
feature = "tiffseq",
feature = "tiff",
feature = "bioformats_java"
))]
#[test]
fn tiff() -> Result<(), Error> {
#[cfg(any(feature = "czi", feature = "bioformats_java"))]
let file = "czi/1xp53-01-AP1.czi";
#[cfg(feature = "tiff")]
let file = "tiff/20251014_20-Pos_000_000_loc_results_Cy3.tif";
#[cfg(feature = "tiffseq")]
let file = "tiffseq/20-Pos_005_005";
let file = if cfg!(any(feature = "czi", feature = "bioformats_java")) {
"czi/1xp53-01-AP1.czi"
} else if cfg!(feature = "tiff") {
"tiff/20251014_20-Pos_000_000_loc_results_Cy3.tif"
} else if cfg!(feature = "tiffseq") {
"tiffseq/20-Pos_005_005"
} else {
unreachable!(
"need to enable one of these features: czi, bioformats_java, tiff, tiffseq"
);
};
let path = std::env::current_dir()?
.join("tests")
.join("files")
src/utils.rs
+32
View File
@@ -0,0 +1,32 @@
#[cfg(any(feature = "tiffwrite", feature = "movie"))]
pub(crate) mod progress {
use console::Term;
use indicatif::{ProgressBar, ProgressDrawTarget, ProgressState, ProgressStyle};
use std::time::Duration;
/// a progress bar with an ok style that when py::detach is used also works in jupyter
pub fn get_bar(count: Option<usize>, message: Option<String>) -> ProgressBar {
let style = ProgressStyle::with_template(
"{spinner:.green} {msg} {percent}% [{wide_bar:.green/lime}] {pos:>7}/{len:7} [{elapsed}/{eta}, {rate}]",
)
.expect("could not build progress bar style")
.with_key("rate", |state: &ProgressState, w: &mut dyn std::fmt::Write| {
if state.per_sec() < 1.0 {
write!(w, "{:>4.2} s", 1.0 / state.per_sec()).expect("could not write to progress bar");
} else {
write!(w, "{:>4.2}/s", state.per_sec()).expect("could not write to progress bar");
}
})
.progress_chars("#>-");
let bar = ProgressBar::with_draw_target(
count.map(|i| i as u64),
ProgressDrawTarget::term_like_with_hz(Box::new(Term::buffered_stdout()), 20),
)
.with_style(style);
if let Some(message) = message {
bar.set_message(message);
}
bar.enable_steady_tick(Duration::from_millis(100));
bar
}
}
src/view.rs
+17 -8
View File
@@ -1197,14 +1197,23 @@ impl<D: Dimension, R: Reader> View<D, R> {
let _ = out.insert(a);
}
}
let mut n = 1;
for (ax, size) in self.shape().to_hashmap().into_iter() {
if ((ax == Axis::C) || (ax == Axis::Z) || (ax == Axis::T))
&& let Some(Operation::Mean) = self.operations.get(&ax)
{
n *= size;
}
}
let n = if let Some((&ax, op)) = op_czt.first()
&& *op == Operation::Mean
{
self.axes
.iter()
.zip(self.slice.iter())
.find(|(a, _)| **a == ax)
.and_then(|(_, s)| match s {
SliceInfoElem::Slice { start, end, step } => {
end.map(|e| (((e - start).max(0) / step) as usize).max(1))
}
_ => Some(1),
})
.unwrap_or(1)
} else {
1
};
let array = if n == 1 {
out.take().unwrap()
} else {
tests/test_ufuncs.py
+2 -1
View File
@@ -14,10 +14,11 @@ def array():
return np.random.randint(0, 255, (64, 64, 2, 3, 4), "uint16")
@pytest.fixture()
@pytest.fixture
def image(array):
with tempfile.TemporaryDirectory() as folder:
file = Path(folder) / "tiff" / "test.tif"
file.parent.mkdir(parents=True)
tiffwrite(file, array, "yxczt")
with Imread(file, axes="yxczt") as im:
yield im