- some warnings

- better color(map) support
- make python module optional in rust
- max 48 threads

.github/workflows/publish.yml

@@ -0,0 +1,24 @@
+name: Publish
+
+on: workflow_dispatch
+
+jobs:
+  publish_wheels:
+    uses: ./.github/workflows/wheels.yml
+  publish:
+    name: publish
+    needs: publish_wheels
+    runs-on: ubuntu-latest
+    environment: pypi
+    steps:
+      - uses: actions/download-artifact@v4
+        with:
+          # unpacks all tiffwrite artifacts into dist/
+          pattern: tiffwrite-*
+          path: dist
+          merge-multiple: true
+      - name: Publish package to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}
+          repository-url: https://upload.pypi.org/legacy/

.github/workflows/pytest.yml

@@ -1,6 +1,6 @@
 name: PyTest
 
-on: [push, pull_request]
+on: [workflow_call, push, pull_request]
 
 jobs:
   pytest:

.github/workflows/wheels.yml

@@ -0,0 +1,42 @@
+name: Wheels
+
+on: workflow_call
+
+jobs:
+  wheels_pytest:
+    uses: ./.github/workflows/pytest.yml
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    needs: [ wheels_pytest ]
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ ubuntu-latest, windows-latest, macos-13, macos-latest ]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v2.21.2
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: tiffwrite-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: ./wheelhouse/*.whl
+
+  build_sdist:
+    name: Build source distribution
+    needs: [ wheels_pytest ]
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build sdist
+        run: |
+          pip install build
+          python -m build --sdist
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: tiffwrite-sdist
+          path: dist/*.tar.gz

Cargo.toml

@@ -3,20 +3,23 @@ name = "tiffwrite"
 version = "2024.10.2"
 edition = "2021"
 
-# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
 [lib]
 name = "tiffwrite"
 crate-type = ["cdylib", "rlib"]
 
 [dependencies]
-pyo3 = { version = "0.21.2", features = ["extension-module", "abi3-py310", "generate-import-lib", "anyhow", "multiple-pymethods"] }
 anyhow = "1.0.89"
-rayon = "1.10.0"
-num = "0.4.3"
-ndarray = "0.15.6"
 chrono = "0.4.38"
-numpy = "0.21.0"
+ndarray = "0.15.6"
+num = "0.4.3"
+rayon = "1.10.0"
 zstd = "0.13.2"
+numpy = { version = "0.22.0", optional = true }
+
+[dependencies.pyo3]
+version = "0.22.2"
+features = ["extension-module", "abi3-py310", "generate-import-lib", "anyhow", "multiple-pymethods"]
+optional = true
 
 [features]
-nopython = []
+python = ["dep:pyo3", "dep:numpy"]

README.md

@@ -1,23 +1,26 @@
-[![mypy](https://github.com/wimpomp/tiffwrite/actions/workflows/mypy.yml/badge.svg)](https://github.com/wimpomp/tiffwrite/actions/workflows/mypy.yml)
 [![pytest](https://github.com/wimpomp/tiffwrite/actions/workflows/pytest.yml/badge.svg)](https://github.com/wimpomp/tiffwrite/actions/workflows/pytest.yml)
 
 # Tiffwrite
-Exploiting [tifffile](https://pypi.org/project/tifffile/) in parallel to write BioFormats/ImageJ compatible tiffs with
+Write BioFormats/ImageJ compatible tiffs with zstd compression in parallel using Rust.
-good compression.
 
 ## Features
 - Writes bigtiff files that open in ImageJ as hyperstack with correct dimensions.
 - Parallel compression.
 - Write individual frames in random order.
 - Compresses even more by referencing tag or image data which otherwise would have been saved several times.
-For example empty frames, or a long string tag on every frame.
+For example empty frames, or a long string tag on every frame. Editing tiffs becomes mostly impossible, but compression
+makes that very hard anyway.
 - Enables memory efficient scripts by saving frames whenever they're ready to be saved, not waiting for the whole stack.
-- Colormaps, extra tags, globally or frame dependent.
+- Colormaps
+- Extra tags, globally or frame dependent.
 
 ## Installation
     pip install tiffwrite
 or
 
+- install [rust](https://rustup.rs/)     
+
+    
     pip install tiffwrite@git+https://github.com/wimpomp/tiffwrite
 
 # Usage
@@ -67,11 +70,10 @@ or
     from tiffwrite import IJTiffFile
     import numpy as np
 
-    shape = (3, 5, 10)  # channels, z, time
+    with IJTiffFile('file.tif', pxsize=0.09707) as tif:
-    with IJTiffFile('file.tif', shape, pxsize=0.09707) as tif:
+        for c in range(3):
-        for c in range(shape[0]):
+            for z in range(5):
-            for z in range(shape[1]):
+                for t in range(10):
-                for t in range(shape[2]):
                     tif.save(np.random.randint(0, 10, (32, 32)), c, z, t)
 
 ## Saving multiple tiffs simultaneously
@@ -79,7 +81,7 @@ or
     import numpy as np
     
     shape = (3, 5, 10)  # channels, z, time
-    with IJTiffFile('fileA.tif', shape) as tif_a, IJTiffFile('fileB.tif', shape) as tif_b:
+    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]):

py/tiffwrite/__init__.py

@@ -3,8 +3,10 @@ from __future__ import annotations
 from itertools import product
 from pathlib import Path
 from typing import Any, Sequence
+from warnings import warn
 
 import colorcet
+import matplotlib
 import numpy as np
 from matplotlib import colors as mpl_colors
 from numpy.typing import ArrayLike, DTypeLike
@@ -12,13 +14,13 @@ from tqdm.auto import tqdm
 
 from . import tiffwrite_rs as rs  # noqa
 
-
 __all__ = ['Header', 'IJTiffFile', 'IFD', 'FrameInfo', 'Tag', 'Strip', 'tiffwrite']
 
 
 class Header:
     pass
 
+
 class IFD(dict):
     pass
 
@@ -32,38 +34,60 @@ CZT = tuple[int, int, int]
 FrameInfo = tuple[np.ndarray, None, CZT]
 
 
+class TiffWriteWarning(UserWarning):
+    pass
+
+
 class IJTiffFile(rs.IJTiffFile):
-    def __new__(cls, path: str | Path, shape: tuple[int, int, int] = None, dtype: DTypeLike = 'uint16',
+    """ Writes a tiff file in a format that the BioFormats reader in Fiji understands.
+        file:           filename of the new tiff file
+        shape:          not used anymore
+        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
+        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',
                  colors: Sequence[str] = None, colormap: str = None, pxsize: float = None,
                  deltaz: float = None, timeinterval: float = None, compression: int = None, comment: str = None,
-                **extratags: Tag) -> IJTiffFile:
+                 extratags: Sequence[Tag] = None) -> None:
-        new = super().__new__(cls, str(path))
+        self.path = Path(path)
+        self.shape = shape
+        self.dtype = np.dtype(dtype)
         if compression is not None:
             if isinstance(compression, Sequence):
                 compression = compression[-1]
-            new.set_compression_level(compression)
+            self.set_compression_level(compression)
         if colors is not None:
-            new.colors = np.array([get_color(color) for color in colors])
+            self.colors = np.array([get_color(color) for color in colors])
         if colormap is not None:
-            new.colormap = get_colormap(colormap)
+            self.colormap = get_colormap(colormap)
         if pxsize is not None:
-            new.px_size = float(pxsize)
+            self.px_size = float(pxsize)
         if deltaz is not None:
-            new.delta_z = float(deltaz)
+            self.delta_z = float(deltaz)
         if timeinterval is not None:
-            new.time_interval = float(timeinterval)
+            self.time_interval = float(timeinterval)
         if comment is not None:
-            new.comment = comment
+            self.comment = comment
+        if extratags is not None:
             for extra_tag in extratags:
-            new.append_extra_tag(extra_tag, None)
+                self.append_extra_tag(extra_tag, None)
-        return new
+        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.',
-    def __init__(self, path: str | Path, shape: tuple[int, int, int] = None, dtype: DTypeLike = 'uint16',  # noqa
+                 TiffWriteWarning, stacklevel=2)
-                 colors: Sequence[str] = None, colormap: str = None, pxsize: float = None,  # noqa
+        if shape is not None:
-                 deltaz: float = None, timeinterval: float = None, comment: str = None,  # noqa
+            warn('Providing shape is not needed anymore, the argument will be removed in the future.',
-                 **extratags:  Tag.Value | Tag) -> None:  # noqa
+                 DeprecationWarning, stacklevel=2)
-        self.path = Path(path)
+        if colors is not None and colormap is not None:
-        self.dtype = np.dtype(dtype)
+            warn('Cannot have colors and colormap simultaneously.', TiffWriteWarning, stacklevel=2)
 
     def __enter__(self) -> IJTiffFile:
         return self
@@ -71,7 +95,8 @@ class IJTiffFile(rs.IJTiffFile):
     def __exit__(self, exc_type, exc_val, exc_tb):
         self.close()
 
-    def save(self, frame: ArrayLike, c: int, z: int, t: int) -> None:
+    def save(self, frame: ArrayLike, c: int, z: int, t: int, extratags: Sequence[Tag] = None) -> None:
+        """ save a 2d numpy array to the tiff at channel=c, slice=z, time=t, with optional extra tif tags """
         for frame, _, (cn, zn, tn) in self.compress_frame(frame):
             frame = np.asarray(frame).astype(self.dtype)
             match self.dtype:
@@ -97,15 +122,36 @@ class IJTiffFile(rs.IJTiffFile):
                     self.save_f64(frame, c + cn, z + zn, t + tn)
                 case _:
                     raise TypeError(f'Cannot save type {self.dtype}')
+            if extratags is not None:
+                for extra_tag in extratags:
+                    self.append_extra_tag(extra_tag, (c, z, t))
 
     def compress_frame(self, frame: ArrayLike) -> tuple[FrameInfo]:  # noqa
+        """ backwards compatibility """
         return (frame, None, (0, 0, 0)),
 
+
 def get_colormap(colormap: str) -> np.ndarray:
-    colormap = getattr(colorcet, colormap)
+    if hasattr(colorcet, colormap.rstrip('_r')):
-    colormap[0] = '#ffffff'
+        cm = np.array([[int(''.join(i), 16) for i in zip(*[iter(s[1:])] * 2)]
-    colormap[-1] = '#000000'
+                        for s in getattr(colorcet, colormap.rstrip('_r'))]).astype('uint8')
-    return np.array([[int(''.join(i), 16) for i in zip(*[iter(s[1:])] * 2)] for s in colormap]).astype('uint8')
+        if colormap.endswith('_r'):
+            cm = cm[::-1]
+        if colormap.startswith('glasbey') or colormap.endswith('glasbey'):
+            cm[0] = 0, 0, 0
+            cm[-1] = 255, 255, 255
+    else:
+        cmap = matplotlib.colormaps.get_cmap(colormap)
+        if cmap.N < 256:
+            cm = (255 * np.vstack(((0, 0, 0),
+                                   matplotlib.cm.ScalarMappable(matplotlib.colors.Normalize(1, 254),
+                                                                cmap).to_rgba(np.arange(1, 254))[:, :3],
+                                   (1, 1, 1)))).astype('uint8')
+        else:
+            cm = (255 * matplotlib.cm.ScalarMappable(matplotlib.colors.Normalize(0, 255), cmap)
+                  .to_rgba(np.arange(256))[:, :3]).astype('uint8')
+    return cm
+
 
 def get_color(color: str) -> np.ndarray:
     return np.array([int(''.join(i), 16) for i in zip(*[iter(mpl_colors.to_hex(color)[1:])] * 2)]).astype('uint8')
@@ -131,10 +177,7 @@ def tiffwrite(file: str | Path, data: np.ndarray, axes: str = 'TZCXY', dtype: DT
             data = np.expand_dims(data, axis)
 
     shape = data.shape[:3]
-    with IJTiffFile(file, shape, data.dtype if dtype is None else dtype, *args, **kwargs) as f:  # type: ignore
+    with IJTiffFile(file, dtype=data.dtype if dtype is None else dtype, *args, **kwargs) as f:
-        at_least_one = False
         for n in tqdm(product(*[range(i) for i in shape]), total=np.prod(shape),  # type: ignore
                       desc='Saving tiff', disable=not bar):
-            if np.any(data[n]) or not at_least_one:
             f.save(data[n], *n)
-                at_least_one = True

pyproject.toml

@@ -15,11 +15,11 @@ classifiers = [
 dependencies = ["colorcet", "matplotlib", "numpy", "tqdm"]
 
 [project.optional-dependencies]
-test = ["pytest", "tifffile"]
+test = ["pytest", "tifffile", "imagecodecs"]
 
 [tool.maturin]
 python-source = "py"
-features = ["pyo3/extension-module"]
+features = ["pyo3/extension-module", "python"]
 module-name = "tiffwrite.tiffwrite_rs"
 
 [tool.isort]

src/lib.rs

@@ -1,4 +1,4 @@
-#[cfg(not(feature = "nopython"))]
+#[cfg(feature = "python")]
 mod py;
 
 use anyhow::Result;
@@ -6,26 +6,30 @@ use chrono::Utc;
 use ndarray::{s, Array2};
 use num::{traits::ToBytes, Complex, FromPrimitive, Rational32, Zero};
 use rayon::prelude::*;
-use std::{cmp::Ordering, collections::HashMap};
 use std::fs::{File, OpenOptions};
 use std::hash::{DefaultHasher, Hash, Hasher};
 use std::io::{copy, Read, Seek, SeekFrom, Write};
-use std::{thread, thread::JoinHandle};
+use std::time::Duration;
-use zstd::{DEFAULT_COMPRESSION_LEVEL, stream::Encoder};
+use std::{cmp::Ordering, collections::HashMap};
+use std::{
+    thread,
+    thread::{sleep, JoinHandle},
+};
+use zstd::{stream::Encoder, DEFAULT_COMPRESSION_LEVEL};
 
 const TAG_SIZE: usize = 20;
 const OFFSET_SIZE: usize = 8;
 const OFFSET: u64 = 16;
 const COMPRESSION: u16 = 50000;
 
-pub fn encode_all(source: Vec<u8>, level: i32) -> Result<Vec<u8>> {
+fn encode_all(source: Vec<u8>, level: i32) -> Result<Vec<u8>> {
     let mut result = Vec::<u8>::new();
     copy_encode(&*source, &mut result, level, source.len() as u64)?;
     Ok(result)
 }
 
 /// copy_encode from zstd crate, but let it include the content size in the zstd block header
-pub fn copy_encode<R, W>(mut source: R, destination: W, level: i32, length: u64) -> Result<()>
+fn copy_encode<R, W>(mut source: R, destination: W, level: i32, length: u64) -> Result<()>
 where
     R: Read,
     W: Write,
@@ -518,7 +522,7 @@ impl IJTiffFile {
     }
 
     pub fn set_compression_level(&mut self, compression_level: i32) {
-        self.compression_level = compression_level;
+        self.compression_level = compression_level.max(-7).min(22);
     }
 
     pub fn description(&self, c_size: usize, z_size: usize, t_size: usize) -> String {
@@ -644,10 +648,17 @@ impl IJTiffFile {
                 .into_iter()
                 .map(|tile| tile.map(|x| x.bytes()).into_iter().flatten().collect())
                 .collect();
-            let bytes = byte_tiles
+            let bytes = if byte_tiles.len() > 4 {
+                byte_tiles
                     .into_par_iter()
                     .map(|x| encode_all(x, compression_level).unwrap())
-                .collect::<Vec<_>>();
+                    .collect::<Vec<_>>()
+            } else {
+                byte_tiles
+                    .into_iter()
+                    .map(|x| encode_all(x, compression_level).unwrap())
+                    .collect::<Vec<_>>()
+            };
             CompressedFrame {
                 bytes,
                 image_width,
@@ -657,22 +668,24 @@ impl IJTiffFile {
                 sample_format: T::SAMPLE_FORMAT,
             }
         }
+        loop {
+            self.collect_threads(false)?;
+            if self.threads.len() < 48 {
+                break;
+            }
+            sleep(Duration::from_millis(100));
+        }
         let compression_level = self.compression_level;
         self.threads.insert(
             (c, z, t),
             thread::spawn(move || compress(frame, compression_level)),
         );
-        for key in self
+        Ok(())
-            .threads
-            .keys()
-            .cloned()
-            .collect::<Vec<(usize, usize, usize)>>()
-        {
-            if self.threads[&key].is_finished() {}
     }
 
+    fn collect_threads(&mut self, block: bool) -> Result<()> {
         for (c, z, t) in self.threads.keys().cloned().collect::<Vec<_>>() {
-            if self.threads[&(c, z, t)].is_finished() {
+            if block | self.threads[&(c, z, t)].is_finished() {
                 if let Some(thread) = self.threads.remove(&(c, z, t)) {
                     self.write_frame(thread.join().unwrap(), c, z, t)?;
                 }
@@ -739,40 +752,33 @@ impl IJTiffFile {
     }
 
     fn get_colormap(&self, colormap: &Vec<Vec<u8>>, bits_per_sample: u16) -> Vec<u16> {
-        if bits_per_sample == 8 {
+        let mut r = Vec::new();
-            colormap
+        let mut g = Vec::new();
-                .iter()
+        let mut b = Vec::new();
-                .flatten()
+        let n = 2usize.pow(bits_per_sample as u32 - 8);
-                .map(|x| (*x as u16) * 256)
+        for color in colormap {
-                .collect()
+            r.extend(vec![(color[0] as u16) * 257; n]);
-        } else {
+            g.extend(vec![(color[1] as u16) * 257; n]);
-            colormap
+            b.extend(vec![(color[2] as u16) * 257; n]);
-                .iter()
-                .map(|x| vec![x; 256])
-                .flatten()
-                .flatten()
-                .map(|x| (*x as u16) * 256)
-                .collect()
         }
+        r.extend(g);
+        r.extend(b);
+        r
     }
 
-    fn get_color(&self, colors: &Vec<u8>, bits_per_sample: u16) -> Result<Vec<u16>> {
+    fn get_color(&self, colors: &Vec<u8>, bits_per_sample: u16) -> Vec<u16> {
         let mut c = Vec::new();
-        let lvl = if bits_per_sample == 8 { 255 } else { 65535 };
+        let n = 2usize.pow(bits_per_sample as u32 - 8);
-        for i in 0..=lvl {
+        for color in colors {
-            c.push(i * (colors[0] as u16) / 255);
+            for i in 0..256 {
-            c.push(i * (colors[1] as u16) / 255);
+                c.extend(vec![i * (*color as u16) / 255 * 257; n])
-            c.push(i * (colors[2] as u16) / 255);
             }
-        Ok(c)
+        }
+        c
     }
 
     fn close(&mut self) -> Result<()> {
-        for (c, z, t) in self.threads.keys().cloned().collect::<Vec<_>>() {
+        self.collect_threads(true)?;
-            if let Some(thread) = self.threads.remove(&(c, z, t)) {
-                self.write_frame(thread.join().unwrap(), c, z, t)?;
-            }
-        }
         let mut c_size = 1;
         let mut z_size = 1;
         let mut t_size = 1;
@@ -812,7 +818,7 @@ impl IJTiffFile {
                 ifd.push_tag(Tag::short(259, &vec![COMPRESSION]));
                 ifd.push_tag(Tag::ascii(270, &self.description(c_size, z_size, t_size)));
                 ifd.push_tag(Tag::short(277, &vec![frame_count as u16]));
-                ifd.push_tag(Tag::ascii(305, "tiffwrite_tllab_NKI"));
+                ifd.push_tag(Tag::ascii(305, "tiffwrite_rs"));
                 ifd.push_tag(Tag::short(322, &vec![frame.tile_width]));
                 ifd.push_tag(Tag::short(323, &vec![frame.tile_length]));
                 ifd.push_tag(Tag::long8(324, &offsets));
@@ -824,7 +830,6 @@ impl IJTiffFile {
                     let r = vec![Rational32::from_f64(px_size).unwrap()];
                     ifd.push_tag(Tag::rational(282, &r));
                     ifd.push_tag(Tag::rational(283, &r));
-                    ifd.push_tag(Tag::short(296, &vec![1]));
                 }
                 if let Colors::Colormap(_) = &self.colors {
                     ifd.push_tag(Tag::short(262, &vec![3]));
@@ -839,11 +844,11 @@ impl IJTiffFile {
                         ));
                     }
                 }
-                if frame_number < samples_per_pixel as usize {
+                if frame_number < c_size {
                     if let Colors::Colors(colors) = &self.colors {
                         ifd.push_tag(Tag::short(
                             320,
-                            &self.get_color(&colors[frame_number], frame.bits_per_sample)?,
+                            &self.get_color(&colors[frame_number], frame.bits_per_sample),
                         ));
                         ifd.push_tag(Tag::short(262, &vec![3]));
                     }

tests/test_single.py

@@ -10,7 +10,7 @@ from tiffwrite import IJTiffFile
 @pytest.mark.parametrize('dtype', ('uint8', 'uint16', 'uint32', 'uint64',
                                    'int8', 'int16', 'int32', 'int64', 'float32', 'float64'))
 def test_single(tmp_path: Path, dtype) -> None:
-    with IJTiffFile(tmp_path / 'test.tif', dtype=dtype) as tif:
+    with IJTiffFile(tmp_path / 'test.tif', dtype=dtype, pxsize=0.1, deltaz=0.5, timeinterval=6.5) as tif:
         a0, b0 = np.meshgrid(range(100), range(100))
         a0[::2, :] = 0
         b0[:, ::2] = 1