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- python: remove deprecated shape argument

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- rust: make frame argument to save more generic
This commit is contained in:
Wim Pomp
2024-10-17 13:45:32 +02:00
parent 76046b762e
commit 19c17a798d
6 changed files with 128 additions and 66 deletions
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60
.github/workflows/wheels.yml → .github/workflows/publish.yml vendored
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@@ -1,4 +1,4 @@
name: Wheels
name: Publish
on: [push, pull_request, workflow_call]
@@ -6,10 +6,10 @@ permissions:
contents: read
jobs:
wheels_pytest:
publish_pytest:
uses: ./.github/workflows/pytest.yml
linux:
needs: [ wheels_pytest ]
needs: [ publish_pytest ]
runs-on: ${{ matrix.platform.runner }}
strategy:
matrix:
@@ -45,7 +45,7 @@ jobs:
path: dist
windows:
needs: [ wheels_pytest ]
needs: [ publish_pytest ]
runs-on: ${{ matrix.platform.runner }}
strategy:
matrix:
@@ -73,7 +73,7 @@ jobs:
path: dist
macos:
needs: [ wheels_pytest ]
needs: [ publish_pytest ]
runs-on: ${{ matrix.platform.runner }}
strategy:
matrix:
@@ -100,7 +100,7 @@ jobs:
path: dist
sdist:
needs: [ wheels_pytest ]
needs: [ publish_pytest ]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
@@ -128,3 +128,51 @@ jobs:
with:
command: upload
args: --non-interactive --skip-existing wheels-*/*
crates_io_publish:
name: Publish (crates.io)
needs: [ publish_pytest ]
runs-on: ubuntu-latest
timeout-minutes: 25
steps:
- uses: actions/checkout@v4
- uses: dtolnay/rust-toolchain@stable
- name: cargo-release Cache
id: cargo_release_cache
uses: actions/cache@v3
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 HEAD \
--no-confirm \
--no-verify \
--execute

2
Cargo.toml
View File

@@ -1,6 +1,6 @@
[package]
name = "tiffwrite"
version = "2024.10.7"
version = "2024.10.8"
edition = "2021"
authors = ["Wim Pomp <w.pomp@nki.nl>"]
license = "GPL-3.0-or-later"

73
README.md
View File

@@ -14,36 +14,35 @@ makes that very hard anyway.
- Colormaps
- Extra tags, globally or frame dependent.
# Python
## Installation
pip install tiffwrite
```pip install tiffwrite```
or
- install [rust](https://rustup.rs/)
- install [rust](https://rustup.rs/)
- ``` pip install tiffwrite@git+https://github.com/wimpomp/tiffwrite ```
pip install tiffwrite@git+https://github.com/wimpomp/tiffwrite
# Usage
## Write an image stack
## Usage
### Write an image stack
tiffwrite(file, data, axes='TZCXY', dtype=None, bar=False, *args, **kwargs)
- file: string; filename of the new tiff file.
- data: 2 to 5D numpy array in one of these datatypes: (u)int8, (u)int16, float32.
- axes: string; order of dimensions in data, default: TZCXY for 5D, ZCXY for 4D, CXY for 3D, XY for 2D data.
- dtype: string; cast data to dtype before saving, only (u)int8, (u)int16 and float32 are supported.
- bar: bool; whether or not to show a progress bar.
- bar: bool; whether to show a progress bar.
- args, kwargs: arguments to be passed to IJTiffFile, see below.
## Write one frame at a time
with IJTiffFile(file, shape, dtype='uint16', colors=None, colormap=None, pxsize=None, deltaz=None,
### Write one frame at a time
with IJTiffFile(file, dtype='uint16', colors=None, colormap=None, pxsize=None, deltaz=None,
timeinterval=None, **extratags) as tif:
some loop:
tif.save(frame, c, z, t)
- file: string; filename of the new tiff file.
- shape: iterable; shape (C, Z, T) of data to be written in file.
- dtype: string; cast data to dtype before saving, only (u)int8, (u)int16 and float32 are supported.
- path: string; path to the new tiff file.
- dtype: string; cast data to dtype before saving, only (u)int8, (u)int16 and float32 are supported by Fiji.
- colors: iterable of strings; one color per channel, valid colors (also html) are defined in matplotlib.colors.
Without colormap BioFormats will set the colors in this order: rgbwcmy.
Note that the color green is dark, the usual green is named 'lime' here.
@@ -51,22 +50,24 @@ or
- pxsize: float; pixel size im um.
- deltaz: float; z slice interval in um.
- timeinterval: float; time between frames in seconds.
- extratags: other tags to be saved, example: Artist='John Doe', Tag4567=[400, 500] or
Copyright=Tag('ascii', 'Made by me'). See tiff_tag_registry.items().
- compression: int; zstd compression level: -7 to 22.
- comment: str; comment to be saved in tif
- extratags: Sequence\[Tag\]; other tags to be saved, example: Tag.ascii(315, 'John Doe') or Tag.ascii(33432, 'Made by me').
- frame: 2D numpy array with data.
- c, z, t: int; channel, z, time coordinates of the frame.
# Examples
## Write an image stack
## Examples
### Write an image stack
from tiffwrite import tiffwrite
import numpy as np
image = np.random.randint(0, 255, (5, 3, 64, 64), 'uint16')
tiffwrite('file.tif', image, 'TCXY')
## Write one frame at a time
### Write one frame at a time
from tiffwrite import IJTiffFile
import numpy as np
@@ -76,20 +77,34 @@ or
for t in range(10):
tif.save(np.random.randint(0, 10, (32, 32)), c, z, t)
## Saving multiple tiffs simultaneously
### Saving multiple tiffs simultaneously
from tiffwrite import IJTiffFile
import numpy as np
shape = (3, 5, 10) # channels, z, time
with IJTiffFile('fileA.tif') as tif_a, IJTiffFile('fileB.tif') as tif_b:
for c in range(shape[0]):
for z in range(shape[1]):
for t in range(shape[2]):
for c in range(3):
for z in range(5):
for t in range(10):
tif_a.save(np.random.randint(0, 10, (32, 32)), c, z, t)
tif_b.save(np.random.randint(0, 10, (32, 32)), c, z, t)
## Tricks & tips
- The order of feeding frames to IJTiffFile is unimportant, IJTiffFile will order the ifd's such that the file will
be opened as a correctly ordered hyperstack.
- Using the colormap parameter you can make ImageJ open the file and apply the colormap. colormap='glasbey' is very
useful.
# Rust
use ndarray::Array2;
use tiffwrite::IJTiffFile;
{ // f will be closed when f goes out of scope
let mut f = IJTiffFile::new("file.tif")?;
for c in 0..3 {
for z in 0..5 {
for t in 0..10 {
let arr = Array2::<u16>::zeros((100, 100));
f.save(&arr, c, z, t)?;
}
}
}
}
# Tricks & tips
- The order of feeding frames to IJTiffFile is unimportant, IJTiffFile will order the ifd's such that the file will be opened as a correctly ordered hyperstack.
- Using the colormap parameter you can make ImageJ open the file and apply the colormap. colormap='glasbey' is very useful.

13
py/tiffwrite/__init__.py
View File

@@ -36,26 +36,26 @@ class TiffWriteWarning(UserWarning):
class IJTiffFile(rs.IJTiffFile):
""" Writes a tiff file in a format that the BioFormats reader in Fiji understands.
Zstd compression is done in parallel using Rust.
file: filename of the new tiff file
shape: not used anymore
path: path to the new tiff file
dtype: datatype to use when saving to tiff
colors: a tuple with a color per channel, chosen from matplotlib.colors, html colors are also possible
colormap: name of a colormap from colorcet
pxsize: pixel size in um
deltaz: z slice interval in um
timeinterval: time between frames in seconds
compression: zstd compression level: -7 to 22.
comment: comment to be saved in tif
extratags: other tags to be saved, example: (Tag.ascii(315, 'John Doe'), Tag.bytes(4567, [400, 500])
or (Tag.ascii(33432, 'Made by me'),).
"""
def __new__(cls, path: str | Path, *args, **kwargs) -> IJTiffFile:
return super().__new__(cls, str(path))
def __init__(self, path: str | Path, shape: tuple[int, int, int] = None, dtype: DTypeLike = 'uint16',
def __init__(self, path: str | Path, *, dtype: DTypeLike = 'uint16',
colors: Sequence[str] = None, colormap: str = None, pxsize: float = None,
deltaz: float = None, timeinterval: float = None, compression: int = None, comment: str = None,
extratags: Sequence[Tag] = None) -> None:
self.path = Path(path)
self.shape = shape
self.dtype = np.dtype(dtype)
if compression is not None:
if isinstance(compression, Sequence):
@@ -79,9 +79,6 @@ class IJTiffFile(rs.IJTiffFile):
if self.dtype.itemsize == 1 and colors is not None:
warn('Fiji will not interpret colors saved in an (u)int8 tif, save as (u)int16 instead.',
TiffWriteWarning, stacklevel=2)
if shape is not None:
warn('Providing shape is not needed anymore, the argument will be removed in the future.',
DeprecationWarning, stacklevel=2)
if colors is not None and colormap is not None:
warn('Cannot have colors and colormap simultaneously.', TiffWriteWarning, stacklevel=2)
@@ -176,7 +173,7 @@ def tiffwrite(file: str | Path, data: np.ndarray, axes: str = 'TZCXY', dtype: DT
try:
from parfor import ParPool, Task
from abc import abstractmethod, ABCMeta
from abc import ABCMeta, abstractmethod
from functools import wraps

44
src/lib.rs
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@@ -3,7 +3,7 @@ mod py;
use anyhow::Result;
use chrono::Utc;
use ndarray::{s, Array2, ArrayView2};
use ndarray::{s, ArcArray2, Array2, ArrayView2, AsArray, Ix2};
use num::{traits::ToBytes, Complex, FromPrimitive, Rational32, Zero};
use rayon::prelude::*;
use std::collections::HashSet;
@@ -148,7 +148,8 @@ impl Tag {
pub fn long(code: u16, value: &Vec<u32>) -> Self {
Tag::new(
code,
value.into_iter()
value
.into_iter()
.map(|x| x.to_le_bytes())
.flatten()
.collect(),
@@ -253,7 +254,11 @@ impl Tag {
pub fn ifd(code: u16, value: &Vec<u32>) -> Self {
Tag::new(
code,
value.into_iter().map(|x| x.to_le_bytes()).flatten().collect(),
value
.into_iter()
.map(|x| x.to_le_bytes())
.flatten()
.collect(),
13,
)
}
@@ -508,6 +513,8 @@ impl Drop for IJTiffFile {
}
impl IJTiffFile {
/// create new tifffile from path string
pub fn new(path: &str) -> Result<Self> {
let mut file = OpenOptions::new()
.create(true)
@@ -535,10 +542,12 @@ impl IJTiffFile {
})
}
/// set zstd compression level: -7 ..= 22
pub fn set_compression_level(&mut self, compression_level: i32) {
self.compression_level = compression_level.max(-7).min(22);
}
/// to be saved in description tag (270)
pub fn description(&self, c_size: usize, z_size: usize, t_size: usize) -> String {
let mut desc: String = String::from("ImageJ=1.11a");
if let Colors::None = self.colors {
@@ -632,20 +641,12 @@ impl IJTiffFile {
}
}
pub fn save<T>(&mut self, frame: ArrayView2<T>, c: usize, z: usize, t: usize) -> Result<()>
pub fn save<'a, A, T>(&mut self, frame: A, c: usize, z: usize, t: usize) -> Result<()>
where
T: Bytes + Clone + Send + Zero + 'static,
A: AsArray<'a, T, Ix2>,
T: Bytes + Clone + Send + Sync + Zero + 'static,
{
self.compress_frame(frame.reversed_axes(), c, z, t)?;
Ok(())
}
fn compress_frame<T>(&mut self, frame: ArrayView2<T>,
c: usize, z: usize, t: usize) -> Result<()>
where
T: Bytes + Clone + Send + Zero + 'static,
{
fn compress<T>(frame: Array2<T>, compression_level: i32) -> CompressedFrame
fn compress<T>(frame: ArcArray2<T>, compression_level: i32) -> CompressedFrame
where
T: Bytes + Clone + Zero,
{
@@ -658,7 +659,7 @@ impl IJTiffFile {
)
.max(16)
.min(1024);
let tiles = IJTiffFile::tile(frame.view().reversed_axes(), tile_size);
let tiles = IJTiffFile::tile(frame.view(), tile_size);
let byte_tiles: Vec<Vec<u8>> = tiles
.into_iter()
.map(|tile| tile.map(|x| x.bytes()).into_iter().flatten().collect())
@@ -691,7 +692,7 @@ impl IJTiffFile {
sleep(Duration::from_millis(100));
}
let compression_level = self.compression_level;
let frame = frame.to_owned();
let frame = frame.into().to_shared();
self.threads.insert(
(c, z, t),
thread::spawn(move || compress(frame, compression_level)),
@@ -906,12 +907,13 @@ impl IJTiffFile {
let (c, z, t) = self.get_czt(*frame_number, *channel, c_size, z_size);
println!("c: {c}, z: {z}, t: {t}")
}
println!("Either you forgot them, \
or an error occurred and the tif file was closed prematurely.")
println!(
"Either you forgot them, \
or an error occurred and the tif file was closed prematurely."
)
}
}
self.file
.seek(SeekFrom::Start(where_to_write_next_ifd_offset))?;
self.file.seek(SeekFrom::Start(where_to_write_next_ifd_offset))?;
self.file.write(&0u64.to_le_bytes())?;
Ok(())
}

2
src/main.rs
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@@ -18,6 +18,6 @@ fn main() -> Result<()> {
arr.slice_mut(s![64.., ..64]).fill(1);
arr.slice_mut(s![..64, 64..]).fill(2);
arr.slice_mut(s![64.., 64..]).fill(3);
f.save(arr.view(), 1, 0, 0)?;
f.save(&arr, 1, 0, 0)?;
Ok(())
}