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- change to MIT license

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- thread local image reader instances
- add keywords and categories
- add python dependencies
- README
This commit is contained in:
Wim Pomp
2025-02-17 19:53:34 +01:00
parent e5c6361086
commit 2247a994be
8 changed files with 243 additions and 727 deletions
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8
Cargo.toml
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@@ -1,13 +1,16 @@
[package] [package]
name = "ndbioimage" name = "ndbioimage"
version = "2025.2.1" version = "2025.2.2"
edition = "2021" edition = "2021"
rust-version = "1.78.0"
authors = ["Wim Pomp <w.pomp@nki.nl>"] authors = ["Wim Pomp <w.pomp@nki.nl>"]
license = "GPL-3.0-or-later" license = "MIT"
description = "Read bio image formats using the bio-formats java package." description = "Read bio image formats using the bio-formats java package."
homepage = "https://github.com/wimpomp/ndbioimage/tree/rs" homepage = "https://github.com/wimpomp/ndbioimage/tree/rs"
repository = "https://github.com/wimpomp/ndbioimage/tree/rs" repository = "https://github.com/wimpomp/ndbioimage/tree/rs"
readme = "README.md" readme = "README.md"
keywords = ["bioformats", "imread", "ndarray", "metadata"]
categories = ["multimedia::images", "science"]
exclude = ["/tests"] exclude = ["/tests"]
# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
@@ -21,6 +24,7 @@ j4rs = "0.22.0"
ndarray = "0.16.1" ndarray = "0.16.1"
num = "0.4.3" num = "0.4.3"
numpy = { version = "0.23.0", optional = true } numpy = { version = "0.23.0", optional = true }
thread_local = "1.1.8"
[dependencies.pyo3] [dependencies.pyo3]
version = "0.23.4" version = "0.23.4"

693
LICENSE
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@@ -1,674 +1,19 @@
GNU GENERAL PUBLIC LICENSE Copyright (c) 2025 Wim Pomp
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EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
SUCH DAMAGES.
17. Interpretation of Sections 15 and 16.
If the disclaimer of warranty and limitation of liability provided
above cannot be given local legal effect according to their terms,
reviewing courts shall apply local law that most closely approximates
an absolute waiver of all civil liability in connection with the
Program, unless a warranty or assumption of liability accompanies a
copy of the Program in return for a fee.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
state the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
<one line to give the program's name and a brief idea of what it does.>
Copyright (C) <year> <name of author>
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <https://www.gnu.org/licenses/>.
Also add information on how to contact you by electronic and paper mail.
If the program does terminal interaction, make it output a short
notice like this when it starts in an interactive mode:
<program> Copyright (C) <year> <name of author>
This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, your program's commands
might be different; for a GUI interface, you would use an "about box".
You should also get your employer (if you work as a programmer) or school,
if any, to sign a "copyright disclaimer" for the program, if necessary.
For more information on this, and how to apply and follow the GNU GPL, see
<https://www.gnu.org/licenses/>.
The GNU General Public License does not permit incorporating your program
into proprietary programs. If your program is a subroutine library, you
may consider it more useful to permit linking proprietary applications with
the library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License. But first, please read
<https://www.gnu.org/licenses/why-not-lgpl.html>.

113
README.md
View File

@@ -1,4 +1,115 @@
# ndbioimage # ndbioimage
[![Pytest](https://github.com/wimpomp/ndbioimage/actions/workflows/pytest.yml/badge.svg)](https://github.com/wimpomp/ndbioimage/actions/workflows/pytest.yml)
## Work in progress ## Work in progress
Rust rewrite of python version. Read bio image formats using the bio-formats java package. 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/) [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
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.
## Installation
```
pip install ndbioimage
```
### Installation with option to write mp4 or mkv:
Work in progress! Make sure ffmpeg is installed.
```
pip install ndbioimage[write]
```
## Usage
### Python
- Reading an image file and plotting the frame at channel=2, time=1
```
import matplotlib.pyplot as plt
from ndbioimage import Imread
with Imread('image_file.tif', axes='ctyx', dtype=int) as im:
plt.imshow(im[2, 1])
```
- Showing some image metadata
```
from ndbioimage import Imread
from pprint import pprint
with Imread('image_file.tif') as im:
pprint(im)
```
- Slicing the image without loading the image into memory
```
from ndbioimage import Imread
with Imread('image_file.tif', axes='cztyx') as im:
sliced_im = im[1, :, :, 100:200, 100:200]
```
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
```
from ndbioimage import Imread
import numpy as np
with Imread('image_file.tif', axes='cztyx') as im:
array = np.asarray(im[0, 0])
```
### Rust
```
use ndarray::Array2;
use ndbioimage::Reader;
let path = "/path/to/file";
let reader = Reader::new(&path, 0).unwrap();
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>");
}
let xml = reader.get_ome_xml().unwrap();
println!("{}", xml);
```
### 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
## Adding more formats
Readers for image formats subclass AbstractReader. When an image reader is imported, Imread will
automatically recognize it and use it to open the appropriate file format. Image readers
are required to implement the following methods:
- staticmethod _can_open(path): return True if path can be opened by this reader
- \_\_frame__(self, c, z, t): return the frame at channel=c, z-slice=z, time=t from the file
Optional methods:
- get_ome: reads metadata from file and adds them to an OME object imported
from the ome-types library
- open(self): maybe open some file handle
- close(self): close any file handles
Optional fields:
- priority (int): Imread will try readers with a lower number first, default: 99
- do_not_pickle (strings): any attributes that should not be included when the object is pickled,
for example: any file handles
# TODO
- more image formats

2
py/ndbioimage/__init__.py
View File

@@ -968,7 +968,7 @@ class Imread(np.lib.mixins.NDArrayOperatorsMixin, ABC):
@staticmethod @staticmethod
def kill_vm() -> None: def kill_vm() -> None:
JVM().kill_vm() pass
def new(self, *args: Any, **kwargs: Any) -> View: def new(self, *args: Any, **kwargs: Any) -> View:
warnings.warn('Imread.new has been deprecated, use Imread.view instead.', DeprecationWarning, 2) warnings.warn('Imread.new has been deprecated, use Imread.view instead.', DeprecationWarning, 2)

46
pyproject.toml
View File

@@ -1,16 +1,56 @@
[build-system] [build-system]
requires = ["maturin>=1.8.2"] requires = ["maturin>=1.8,<2.0"]
build-backend = "maturin" build-backend = "maturin"
[project] [project]
name = "ndbioimage" name = "ndbioimage"
description = "Bio image reading, metadata and some affine registration."
authors = [
{ name = "W. Pomp", email = "w.pomp@nki.nl" }
]
license = "MIT"
readme = "README.md"
keywords = ["bioformats", "imread", "numpy", "metadata"]
requires-python = ">=3.10" requires-python = ">=3.10"
classifiers = [ classifiers = [
"License :: OSI Approved :: MIT License",
"Programming Language :: Rust", "Programming Language :: Rust",
"Programming Language :: Python :: Implementation :: CPython", "Programming Language :: Python",
"Programming Language :: Python :: Implementation :: PyPy", "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"] dynamic = ["version"]
dependencies = [
"numpy",
"pandas",
"tiffwrite",
"ome-types",
"pint",
"tqdm",
"lxml",
"pyyaml",
"parfor",
"SimpleITK-SimpleElastix",
"scikit-image",
]
[project.optional-dependencies]
test = ["pytest"]
write = ["matplotlib", "scikit-video"]
[project.urls]
Repository = "https://github.com/wimpomp/ndbioimage/tree/rs"
[project.scripts]
ndbioimage = "ndbioimage:main"
[tool.pytest.ini_options]
filterwarnings = ["ignore:::(colorcet)"]
[tool.maturin] [tool.maturin]
python-source = "py" python-source = "py"

12
src/bioformats.rs
View File

@@ -71,6 +71,7 @@ macro_rules! method_arg {
macro_rules! method { macro_rules! method {
($name:ident, $method:expr $(,[$($n:tt: $t:ty$(|$p:tt)?),*])? $(=> $tt:ty$(|$c:tt)?)?) => { ($name:ident, $method:expr $(,[$($n:tt: $t:ty$(|$p:tt)?),*])? $(=> $tt:ty$(|$c:tt)?)?) => {
#[allow(dead_code)]
pub(crate) fn $name(&self, $($($n: $t),*)?) -> method_return!($($tt)?) { pub(crate) fn $name(&self, $($($n: $t),*)?) -> method_return!($($tt)?) {
let args: Vec<InvocationArg> = vec![$($( method_arg!($n:$t$(|$p)?) ),*)?]; let args: Vec<InvocationArg> = vec![$($( method_arg!($n:$t$(|$p)?) ),*)?];
let _result = jvm().invoke(&self.0, $method, &args)?; let _result = jvm().invoke(&self.0, $method, &args)?;
@@ -95,10 +96,12 @@ macro_rules! method {
}; };
} }
pub(crate) struct DebugTools; /// Wrapper around bioformats java class loci.common.DebugTools
pub struct DebugTools;
impl DebugTools { impl DebugTools {
pub(crate) fn set_root_level(level: &str) -> Result<()> { /// set debug root level: ERROR, DEBUG, TRACE, INFO, OFF
pub fn set_root_level(level: &str) -> Result<()> {
jvm().invoke_static( jvm().invoke_static(
"loci.common.DebugTools", "loci.common.DebugTools",
"setRootLevel", "setRootLevel",
@@ -108,6 +111,7 @@ impl DebugTools {
} }
} }
/// Wrapper around bioformats java class loci.formats.ChannelSeparator
pub(crate) struct ChannelSeparator(Instance); pub(crate) struct ChannelSeparator(Instance);
impl ChannelSeparator { impl ChannelSeparator {
@@ -129,7 +133,8 @@ impl ChannelSeparator {
method!(get_index, "getIndex", [z: i32|p, c: i32|p, t: i32|p] => i32|c); method!(get_index, "getIndex", [z: i32|p, c: i32|p, t: i32|p] => i32|c);
} }
pub(crate) struct ImageReader(Instance); /// Wrapper around bioformats java class loci.formats.ImageReader
pub struct ImageReader(Instance);
impl Drop for ImageReader { impl Drop for ImageReader {
fn drop(&mut self) { fn drop(&mut self) {
@@ -179,6 +184,7 @@ impl ImageReader {
method!(close, "close"); method!(close, "close");
} }
/// Wrapper around bioformats java class loci.formats.MetadataTools
pub(crate) struct MetadataTools(Instance); pub(crate) struct MetadataTools(Instance);
impl MetadataTools { impl MetadataTools {

83
src/lib.rs
View File

@@ -9,7 +9,9 @@ use ndarray::Array2;
use num::{FromPrimitive, Zero}; use num::{FromPrimitive, Zero};
use std::any::type_name; use std::any::type_name;
use std::fmt::Debug; use std::fmt::Debug;
use std::ops::Deref;
use std::path::{Path, PathBuf}; use std::path::{Path, PathBuf};
use thread_local::ThreadLocal;
/// Pixel types (u)int(8/16/32) or float(32/64) /// Pixel types (u)int(8/16/32) or float(32/64)
#[derive(Clone, Debug)] #[derive(Clone, Debug)]
@@ -141,7 +143,7 @@ where
/// Reader interface to file. Use get_frame to get data. /// Reader interface to file. Use get_frame to get data.
pub struct Reader { pub struct Reader {
image_reader: ImageReader, image_reader: ThreadLocal<ImageReader>,
/// path to file /// path to file
pub path: PathBuf, pub path: PathBuf,
/// which (if more than 1) of the series in the file to open /// which (if more than 1) of the series in the file to open
@@ -161,6 +163,22 @@ pub struct Reader {
little_endian: bool, little_endian: bool,
} }
impl Deref for Reader {
type Target = ImageReader;
fn deref(&self) -> &Self::Target {
self.image_reader.get_or(|| {
let reader = ImageReader::new().unwrap();
let meta_data_tools = MetadataTools::new().unwrap();
let ome_meta = meta_data_tools.create_ome_xml_metadata().unwrap();
reader.set_metadata_store(ome_meta).unwrap();
reader.set_id(self.path.to_str().unwrap()).unwrap();
reader.set_series(self.series).unwrap();
reader
})
}
}
impl Clone for Reader { impl Clone for Reader {
fn clone(&self) -> Self { fn clone(&self) -> Self {
Reader::new(&self.path, self.series).unwrap() Reader::new(&self.path, self.series).unwrap()
@@ -187,36 +205,31 @@ impl Reader {
/// Create new reader for image file at path. /// Create new reader for image file at path.
pub fn new(path: &Path, series: i32) -> Result<Self> { pub fn new(path: &Path, series: i32) -> Result<Self> {
DebugTools::set_root_level("ERROR")?; DebugTools::set_root_level("ERROR")?;
let reader = ImageReader::new()?; let mut reader = Reader {
let meta_data_tools = MetadataTools::new()?; image_reader: ThreadLocal::new(),
let ome_meta = meta_data_tools.create_ome_xml_metadata()?;
reader.set_metadata_store(ome_meta)?;
reader.set_id(path.to_str().unwrap())?;
reader.set_series(series)?;
let size_x = reader.get_size_x()?;
let size_y = reader.get_size_y()?;
let size_c = reader.get_size_c()?;
let size_z = reader.get_size_z()?;
let size_t = reader.get_size_t()?;
let pixel_type = PixelType::try_from(reader.get_pixel_type()?)?;
let little_endian = reader.is_little_endian()?;
Ok(Reader {
image_reader: reader,
path: PathBuf::from(path), path: PathBuf::from(path),
series, series,
size_x: size_x as usize, size_x: 0,
size_y: size_y as usize, size_y: 0,
size_c: size_c as usize, size_c: 0,
size_z: size_z as usize, size_z: 0,
size_t: size_t as usize, size_t: 0,
pixel_type, pixel_type: PixelType::INT8,
little_endian, little_endian: false,
}) };
reader.size_x = reader.get_size_x()? as usize;
reader.size_y = reader.get_size_y()? as usize;
reader.size_c = reader.get_size_c()? as usize;
reader.size_z = reader.get_size_z()? as usize;
reader.size_t = reader.get_size_t()? as usize;
reader.pixel_type = PixelType::try_from(reader.get_pixel_type()?)?;
reader.little_endian = reader.is_little_endian()?;
Ok(reader)
} }
/// Get ome metadata as xml string /// Get ome metadata as xml string
pub fn get_ome_xml(&self) -> Result<String> { pub fn get_ome_xml(&self) -> Result<String> {
self.image_reader.ome_xml() self.ome_xml()
} }
fn deinterleave(&self, bytes: Vec<u8>, channel: usize) -> Result<Vec<u8>> { fn deinterleave(&self, bytes: Vec<u8>, channel: usize) -> Result<Vec<u8>> {
@@ -240,16 +253,16 @@ impl Reader {
/// Retrieve fame at channel c, slize z and time t. /// Retrieve fame at channel c, slize z and time t.
pub fn get_frame(&self, c: usize, z: usize, t: usize) -> Result<Frame> { pub fn get_frame(&self, c: usize, z: usize, t: usize) -> Result<Frame> {
let bytes = if self.image_reader.is_rgb()? & self.image_reader.is_interleaved()? { let bytes = if self.is_rgb()? & self.is_interleaved()? {
let index = self.image_reader.get_index(z as i32, 0, t as i32)?; let index = self.get_index(z as i32, 0, t as i32)?;
self.deinterleave(self.image_reader.open_bytes(index)?, c)? self.deinterleave(self.open_bytes(index)?, c)?
} else if self.image_reader.get_rgb_channel_count()? > 1 { } else if self.get_rgb_channel_count()? > 1 {
let channel_separator = bioformats::ChannelSeparator::new(&self.image_reader)?; let channel_separator = bioformats::ChannelSeparator::new(self)?;
let index = channel_separator.get_index(z as i32, c as i32, t as i32)?; let index = channel_separator.get_index(z as i32, c as i32, t as i32)?;
channel_separator.open_bytes(index)? channel_separator.open_bytes(index)?
} else if self.image_reader.is_indexed()? { } else if self.is_indexed()? {
let index = self.image_reader.get_index(z as i32, 0, t as i32)?; let index = self.get_index(z as i32, 0, t as i32)?;
self.image_reader.open_bytes(index)? self.open_bytes(index)?
// TODO: apply LUT // TODO: apply LUT
// let _bytes_lut = match self.pixel_type { // let _bytes_lut = match self.pixel_type {
// PixelType::INT8 | PixelType::UINT8 => { // PixelType::INT8 | PixelType::UINT8 => {
@@ -261,8 +274,8 @@ impl Reader {
// _ => {} // _ => {}
// }; // };
} else { } else {
let index = self.image_reader.get_index(z as i32, c as i32, t as i32)?; let index = self.get_index(z as i32, c as i32, t as i32)?;
self.image_reader.open_bytes(index)? self.open_bytes(index)?
}; };
self.bytes_to_frame(bytes) self.bytes_to_frame(bytes)
} }

13
src/py.rs
View File

@@ -8,17 +8,16 @@ use std::path::PathBuf;
#[pyo3(name = "Reader")] #[pyo3(name = "Reader")]
#[derive(Debug)] #[derive(Debug)]
struct PyReader { struct PyReader {
path: PathBuf, reader: Reader,
series: i32,
} }
#[pymethods] #[pymethods]
impl PyReader { impl PyReader {
#[new] #[new]
fn new(path: &str, series: usize) -> PyResult<Self> { fn new(path: &str, series: usize) -> PyResult<Self> {
let path = PathBuf::from(path);
Ok(PyReader { Ok(PyReader {
path: PathBuf::from(path), reader: Reader::new(&path, series as i32)?,
series: series as i32,
}) })
} }
@@ -29,8 +28,7 @@ impl PyReader {
z: usize, z: usize,
t: usize, t: usize,
) -> PyResult<Bound<'py, PyAny>> { ) -> PyResult<Bound<'py, PyAny>> {
let reader = Reader::new(&self.path, self.series)?; // TODO: prevent making a new Reader each time Ok(match self.reader.get_frame(c, z, t)? {
Ok(match reader.get_frame(c, z, t)? {
Frame::INT8(arr) => arr.to_pyarray(py).into_any(), Frame::INT8(arr) => arr.to_pyarray(py).into_any(),
Frame::UINT8(arr) => arr.to_pyarray(py).into_any(), Frame::UINT8(arr) => arr.to_pyarray(py).into_any(),
Frame::INT16(arr) => arr.to_pyarray(py).into_any(), Frame::INT16(arr) => arr.to_pyarray(py).into_any(),
@@ -43,8 +41,7 @@ impl PyReader {
} }
fn get_ome_xml(&self) -> PyResult<String> { fn get_ome_xml(&self) -> PyResult<String> {
let reader = Reader::new(&self.path, self.series)?; // TODO: prevent making a new Reader each time Ok(self.reader.get_ome_xml()?)
Ok(reader.get_ome_xml()?)
} }
} }