- work around a bioformats issue

.github/workflows/cargo_test.yml

@@ -1,9 +1,10 @@
-name: PyTest
+name: Cargo Test
 
 on: [push, pull_request, workflow_call]
 
 jobs:
-  pytest:
+  cargo_test:
+    name: Cargo Test
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v6

.gitignore

@@ -9,3 +9,4 @@
 *.tif
 *.so
 __pycache__
+.agentbridge/

Cargo.toml

@@ -1,13 +1,13 @@
 [package]
 name = "tiffwrite"
-version = "2026.5.1"
+version = "2026.6.0"
 edition = "2024"
 rust-version = "1.88.0"
 authors = ["Wim Pomp <w.pomp@nki.nl>"]
 license = "MIT OR Apache-2.0"
 description = "Write BioFormats/ImageJ compatible tiffs with zstd compression in parallel."
-homepage = "https://git.wimpomp.nl/wim/tiffwrite"
+homepage = "https://git.pomppervova.nl/wim/tiffwrite"
-repository = "https://git.wimpomp.nl/wim/tiffwrite"
+repository = "https://git.pomppervova.nl/wim/tiffwrite"
 documentation = "https://docs.rs/tiffwrite"
 readme = "README.md"
 keywords = ["bioformats", "tiff", "ndarray", "zstd", "fiji"]
@@ -28,7 +28,7 @@ lazy_static = "1"
 ndarray = "0.17"
 num = "0.4"
 numpy = { version = "0.28", optional = true }
-pyo3 = { version = "0.28", features = ["abi3-py310", "eyre", "generate-import-lib", "multiple-pymethods"], optional = true }
+pyo3 = { version = "0.28", features = ["abi3-py310", "eyre", "multiple-pymethods"], optional = true }
 pyo3-stub-gen = { version = "0.22", optional = true }
 rayon = "1"
 thiserror = "2"

README.md

@@ -1,5 +1,5 @@
-[![pytest](https://git.wimpomp.nl/wim/tiffwrite/actions/workflows/pytest.yml/badge.svg)](https://git.wimpomp.nl/wim/tiffwrite/actions?workflow=pytest.yml)
+[![pytest](https://git.pomppervova.nl/wim/tiffwrite/actions/workflows/pytest.yml/badge.svg)](https://git.pomppervova.nl/wim/tiffwrite/actions?workflow=pytest.yml)
-[![cargo test](https://git.wimpomp.nl/wim/tiffwrite/actions/workflows/cargo_test.yml/badge.svg)](https://git.wimpomp.nl/wim/tiffwrite/actions?workflow=cargo_test.yml)
+[![cargo test](https://git.pomppervova.nl/wim/tiffwrite/actions/workflows/cargo_test.yml/badge.svg)](https://git.pomppervova.nl/wim/tiffwrite/actions?workflow=cargo_test.yml)
 
 # Tiffwrite
 Write BioFormats/ImageJ compatible tiffs with zstd compression in parallel using Rust.
@@ -22,7 +22,7 @@ makes that very hard anyway.
 or
 
 - install [rust](https://rustup.rs/)
-- ``` pip install tiffwrite@git+https://git.wimpomp.nl/wim/tiffwrite ```
+- ``` pip install tiffwrite@git+https://git.pomppervova.nl/wim/tiffwrite ```
 
 ## Usage
 ### Write an image stack

py/tiffwrite/__init__.py

@@ -57,7 +57,7 @@ class IJTiffFile(rs.IJTiffFile):
 
     def __init__(
         self,
-        path: str | Path,
+        path: str | Path,  # noqa
         *,
         dtype: DTypeLike = "uint16",
         colors: Sequence[str] = None,
@@ -79,7 +79,6 @@ class IJTiffFile(rs.IJTiffFile):
         if colors is not None and colormap is not None:
             warn("Cannot have colors and colormap simultaneously.", TiffWriteWarning, stacklevel=2)
 
-        self.path = Path(path)
         self.dtype = np.dtype(dtype)
         if compression is not None:
             if isinstance(compression, tuple):
@@ -140,7 +139,7 @@ class IJTiffFile(rs.IJTiffFile):
             case np.float64:
                 self.save_f64(frame, c, z, t)
             case _:
-                raise TypeError(f"Cannot save type {self.dtype}")
+                raise TypeError(f"Cannot save type {self.dtype}")  # noqa
         if extratags is not None:
             for extra_tag in extratags:
                 self.append_extra_tag(extra_tag, (c, z, t))

py/tiffwrite/tiffwrite_rs.pyi

@@ -2,6 +2,7 @@
 # ruff: noqa: E501, F401, F403, F405
 
 import builtins
+import pathlib
 import typing
 
 import numpy
@@ -13,6 +14,8 @@ __all__ = [
 ]
 
 class IJTiffFile:
+    @property
+    def path(self) -> typing.Optional[pathlib.Path]: ...
     @property
     def colors(self) -> typing.Optional[builtins.list[builtins.list[builtins.int]]]: ...
     @colors.setter
@@ -49,16 +52,16 @@ class IJTiffFile:
         self, czt: typing.Optional[tuple[builtins.int, builtins.int, builtins.int]] = None
     ) -> builtins.list[Tag]: ...
     def close(self) -> None: ...
-    def save_f64(self, frame: numpy.typing.ArrayLike, c: builtins.int, t: builtins.int, z: builtins.int) -> None: ...
-    def save_u32(self, frame: numpy.typing.ArrayLike, c: builtins.int, t: builtins.int, z: builtins.int) -> None: ...
-    def save_u16(self, frame: numpy.typing.ArrayLike, c: builtins.int, t: builtins.int, z: builtins.int) -> None: ...
-    def save_i64(self, frame: numpy.typing.ArrayLike, c: builtins.int, t: builtins.int, z: builtins.int) -> None: ...
     def save_f32(self, frame: numpy.typing.ArrayLike, c: builtins.int, t: builtins.int, z: builtins.int) -> None: ...
+    def save_f64(self, frame: numpy.typing.ArrayLike, c: builtins.int, t: builtins.int, z: builtins.int) -> None: ...
+    def save_i64(self, frame: numpy.typing.ArrayLike, c: builtins.int, t: builtins.int, z: builtins.int) -> None: ...
+    def save_u16(self, frame: numpy.typing.ArrayLike, c: builtins.int, t: builtins.int, z: builtins.int) -> None: ...
+    def save_u32(self, frame: numpy.typing.ArrayLike, c: builtins.int, t: builtins.int, z: builtins.int) -> None: ...
     def save_u8(self, frame: numpy.typing.ArrayLike, c: builtins.int, t: builtins.int, z: builtins.int) -> None: ...
-    def save_i32(self, frame: numpy.typing.ArrayLike, c: builtins.int, t: builtins.int, z: builtins.int) -> None: ...
-    def save_u64(self, frame: numpy.typing.ArrayLike, c: builtins.int, t: builtins.int, z: builtins.int) -> None: ...
-    def save_i16(self, frame: numpy.typing.ArrayLike, c: builtins.int, t: builtins.int, z: builtins.int) -> None: ...
     def save_i8(self, frame: numpy.typing.ArrayLike, c: builtins.int, t: builtins.int, z: builtins.int) -> None: ...
+    def save_u64(self, frame: numpy.typing.ArrayLike, c: builtins.int, t: builtins.int, z: builtins.int) -> None: ...
+    def save_i32(self, frame: numpy.typing.ArrayLike, c: builtins.int, t: builtins.int, z: builtins.int) -> None: ...
+    def save_i16(self, frame: numpy.typing.ArrayLike, c: builtins.int, t: builtins.int, z: builtins.int) -> None: ...
 
 class Tag:
     @staticmethod

pyproject.toml

@@ -34,7 +34,7 @@ tiffwrite_generate_stub = "tiffwrite:tiffwrite_generate_stub"
 
 [tool.maturin]
 python-source = "py"
-features = ["pyo3/extension-module", "python"]
+features = ["python"]
 module-name = "tiffwrite.tiffwrite_rs"
 
 [tool.isort]

src/lib.rs

@@ -16,7 +16,7 @@ use std::collections::HashSet;
 use std::fs::{File, OpenOptions};
 use std::hash::{DefaultHasher, Hash, Hasher};
 use std::io::{BufWriter, Read, Seek, SeekFrom, Write};
-use std::path::Path;
+use std::path::{Path, PathBuf};
 use std::sync::{Arc, Mutex};
 use std::thread::available_parallelism;
 use std::{cmp::Ordering, collections::HashMap};
@@ -356,9 +356,6 @@ impl Tag {
                 self.offset + (TAG_SIZE - OFFSET_SIZE) as u64,
             ))?;
             file.write_all(&offset.to_le_bytes())?;
-            if file.stream_position()? % 2 == 1 {
-                file.write_all(&[0])?;
-            }
         }
         Ok(())
     }
@@ -560,9 +557,20 @@ impl Frame {
         let bytes_per_sample = (T::BITS_PER_SAMPLE / 8) as usize;
         encoder.include_contentsize(true)?;
         encoder.set_pledged_src_size(Some((bytes_per_sample * tile_width * tile_length) as u64))?;
-        encoder.include_checksum(false)?;
+        encoder.include_checksum(true)?;
         encoder = Frame::encode(encoder, frame, slice, tile_width, tile_length)?;
         encoder.finish()?;
+        // work around https://github.com/ome/bioformats/issues/4442
+        if dest.len() == frame.len() {
+            dest.clear();
+            let mut encoder = Encoder::new(&mut dest, compression_level)?;
+            encoder.include_contentsize(true)?;
+            encoder
+                .set_pledged_src_size(Some((bytes_per_sample * tile_width * tile_length) as u64))?;
+            encoder.include_checksum(false)?;
+            encoder = Frame::encode(encoder, frame, slice, tile_width, tile_length)?;
+            encoder.finish()?;
+        }
         Ok(dest)
     }
 }
@@ -669,6 +677,7 @@ pub struct IJTiffFile {
     frames: HashMap<(usize, usize, usize), Frame>,
     hashes: Arc<Mutex<HashMap<u64, u64>>>,
     threads: HashMap<(usize, usize, usize), JoinHandle<Result<Frame, Error>>>,
+    path: PathBuf,
     /// zstd: -7 ..= 22
     pub compression: Compression,
     pub colors: Colors,
@@ -695,6 +704,7 @@ impl IJTiffFile {
     /// create new tifffile from path, use its save() method to save frames
     /// the file is finalized when it goes out of scope
     pub fn new<P: AsRef<Path>>(path: P) -> Result<Self, Error> {
+        let path = path.as_ref();
         let mut file = OpenOptions::new()
             .create(true)
             .truncate(true)
@@ -711,6 +721,7 @@ impl IJTiffFile {
             frames: HashMap::new(),
             hashes: Arc::new(Mutex::new(HashMap::new())),
             threads: HashMap::new(),
+            path: path.to_owned(),
             compression: Compression::Zstd(DEFAULT_COMPRESSION_LEVEL),
             colors: Colors::None,
             comment: None,
@@ -854,6 +865,7 @@ impl IJTiffFile {
     }
 
     fn hash_check(f: &mut BufWriter<File>, bytes: &Vec<u8>, offset: u64) -> Result<bool, Error> {
+        f.flush()?;
         let current_offset = f.stream_position()?;
         f.seek(SeekFrom::Start(offset))?;
         let mut buffer = vec![0; bytes.len()];
@@ -1054,7 +1066,10 @@ impl IJTiffFile {
                 warn.push((frame_number, 0));
             }
             if !warn.is_empty() {
-                println!("The following frames were not added to the tif file:");
+                println!(
+                    "The following frames were not added to the tif file: {}",
+                    self.path.display()
+                );
                 for (frame_number, channel) in &warn {
                     let (c, z, t) = self.get_czt(*frame_number, *channel, c_size, z_size);
                     println!("c: {c}, z: {z}, t: {t}")

src/py.rs

@@ -184,6 +184,11 @@ impl PyIJTiffFile {
         })
     }
 
+    #[getter]
+    fn get_path(&self) -> PyResult<Option<PathBuf>> {
+        Ok(self.ijtifffile.as_ref().map(|f| f.path.clone()))
+    }
+
     /// set zstd compression level: -7 ..= 22
     fn set_compression(&mut self, compression: i32, level: i32) -> PyResult<()> {
         let c = match compression {
@@ -240,11 +245,7 @@ impl PyIJTiffFile {
 
     #[getter]
     fn get_px_size(&self) -> PyResult<Option<f64>> {
-        if let Some(ijtifffile) = &self.ijtifffile {
+        Ok(self.ijtifffile.as_ref().and_then(|f| f.px_size))
-            Ok(ijtifffile.px_size)
-        } else {
-            Ok(None)
-        }
     }
 
     #[setter]
@@ -257,11 +258,7 @@ impl PyIJTiffFile {
 
     #[getter]
     fn get_delta_z(&self) -> PyResult<Option<f64>> {
-        if let Some(ijtifffile) = &self.ijtifffile {
+        Ok(self.ijtifffile.as_ref().and_then(|f| f.delta_z))
-            Ok(ijtifffile.delta_z)
-        } else {
-            Ok(None)
-        }
     }
 
     #[setter]
@@ -274,11 +271,7 @@ impl PyIJTiffFile {
 
     #[getter]
     fn get_time_interval(&self) -> PyResult<Option<f64>> {
-        if let Some(ijtifffile) = &self.ijtifffile {
+        Ok(self.ijtifffile.as_ref().and_then(|f| f.time_interval))
-            Ok(ijtifffile.time_interval)
-        } else {
-            Ok(None)
-        }
     }
 
     #[setter]
@@ -291,11 +284,7 @@ impl PyIJTiffFile {
 
     #[getter]
     fn get_comment(&self) -> PyResult<Option<String>> {
-        if let Some(ijtifffile) = &self.ijtifffile {
+        Ok(self.ijtifffile.as_ref().and_then(|f| f.comment.clone()))
-            Ok(ijtifffile.comment.clone())
-        } else {
-            Ok(None)
-        }
     }
 
     #[setter]
@@ -308,10 +297,8 @@ impl PyIJTiffFile {
 
     #[pyo3(signature = (tag, czt=None))]
     fn append_extra_tag(&mut self, tag: PyTag, czt: Option<(usize, usize, usize)>) {
-        if let Some(ijtifffile) = self.ijtifffile.as_mut()
+        if let Some(ijtifffile) = self.ijtifffile.as_mut() {
-            && let Some(extra_tags) = ijtifffile.extra_tags.get_mut(&czt)
+            ijtifffile.extra_tags.entry(czt).or_default().push(tag.tag);
-        {
-            extra_tags.push(tag.tag)
         }
     }