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- replace anyhow with thiserror

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w.pomp
2025-09-26 18:14:18 +02:00
parent 7ea0d1c093
commit 56680d88f4
6 changed files with 225 additions and 25 deletions
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11
Cargo.toml
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@@ -1,13 +1,14 @@
[package]
name = "tiffwrite"
version = "2025.8.1"
version = "2025.9.0"
edition = "2024"
rust-version = "1.85.1"
authors = ["Wim Pomp <w.pomp@nki.nl>"]
license = "MIT"
license = "MIT OR Apache-2.0"
description = "Write BioFormats/ImageJ compatible tiffs with zstd compression in parallel."
homepage = "https://github.com/wimpomp/tiffwrite"
repository = "https://github.com/wimpomp/tiffwrite"
documentation = "https://docs.rs/tiffwrite"
readme = "README.md"
keywords = ["bioformats", "tiff", "ndarray", "zstd", "fiji"]
categories = ["multimedia::images", "science"]
@@ -17,7 +18,6 @@ name = "tiffwrite"
crate-type = ["cdylib", "rlib"]
[dependencies]
anyhow = "1.0.98"
colorcet = "0.2.1"
colorgrad = "0.7.2"
chrono = "0.4.41"
@@ -25,9 +25,10 @@ css-color = "0.2.8"
flate2 = "1.1.1"
ndarray = "0.16.1"
num = "0.4.3"
rayon = "1.10.0"
zstd = "0.13.3"
numpy = { version = "0.25.0", optional = true }
rayon = "1.10.0"
thiserror = "2.0.16"
zstd = "0.13.3"
[dependencies.pyo3]
version = "0.25.1"

176
LICENSE-APACHE Normal file
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@@ -0,0 +1,176 @@
Apache License
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http://www.apache.org/licenses/
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0
LICENSE → LICENSE-MIT
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14
src/error.rs Normal file
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@@ -0,0 +1,14 @@
use thiserror::Error;
#[derive(Debug, Error)]
pub enum Error {
#[error("io error: {0}")]
IO(#[from] std::io::Error),
#[error("could not parse color: {0}")]
ColorParse(String),
#[error("colorcet error: {0}")]
ColorCet(#[from] colorcet::ColorcetError),
#[error("could not covert ColorMap into LinearGradient")]
Conversion
}

43
src/lib.rs
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@@ -1,7 +1,7 @@
#[cfg(feature = "python")]
mod py;
mod error;
use anyhow::{Result, anyhow};
use chrono::Utc;
use colorcet::ColorMap;
use colorgrad::{Gradient, LinearGradient};
@@ -23,6 +23,7 @@ use std::{
};
use zstd::zstd_safe::CompressionLevel;
use zstd::{DEFAULT_COMPRESSION_LEVEL, stream::Encoder};
use crate::error::Error;
const TAG_SIZE: usize = 20;
const OFFSET_SIZE: usize = 8;
@@ -59,7 +60,7 @@ impl IFD {
}
}
fn write(&mut self, ijtifffile: &mut IJTiffFile, where_to_write_offset: u64) -> Result<u64> {
fn write(&mut self, ijtifffile: &mut IJTiffFile, where_to_write_offset: u64) -> Result<u64, Error> {
let mut tags = self.tags.drain().collect::<Vec<_>>();
tags.sort();
ijtifffile.file.seek(SeekFrom::End(0))?;
@@ -322,7 +323,7 @@ impl Tag {
c as u64
}
fn write_tag(&mut self, ijtifffile: &mut IJTiffFile) -> Result<()> {
fn write_tag(&mut self, ijtifffile: &mut IJTiffFile) -> Result<(), Error> {
self.offset = ijtifffile.file.stream_position()?;
ijtifffile.file.write_all(&self.code.to_le_bytes())?;
ijtifffile.file.write_all(&self.ttype.to_le_bytes())?;
@@ -338,7 +339,7 @@ impl Tag {
Ok(())
}
fn write_data(&self, ijtifffile: &mut IJTiffFile) -> Result<()> {
fn write_data(&self, ijtifffile: &mut IJTiffFile) -> Result<(), Error> {
if self.bytes.len() > OFFSET_SIZE {
ijtifffile.file.seek(SeekFrom::End(0))?;
let offset = ijtifffile.write(&self.bytes)?;
@@ -493,7 +494,7 @@ impl CompressedFrame {
slice: (usize, usize, usize, usize),
tile_width: usize,
tile_length: usize,
) -> Result<W>
) -> Result<W, Error>
where
W: Write,
T: Bytes,
@@ -524,7 +525,7 @@ impl CompressedFrame {
slice: (usize, usize, usize, usize),
tile_width: usize,
tile_length: usize,
) -> Result<Vec<u8>>
) -> Result<Vec<u8>, Error>
where
T: Bytes,
{
@@ -539,7 +540,7 @@ impl CompressedFrame {
tile_width: usize,
tile_length: usize,
compression_level: i32,
) -> Result<Vec<u8>>
) -> Result<Vec<u8>, Error>
where
T: Bytes,
{
@@ -678,7 +679,7 @@ impl Drop for IJTiffFile {
impl IJTiffFile {
/// create new tifffile from path, use it's 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> {
pub fn new<P: AsRef<Path>>(path: P) -> Result<Self, Error> {
let mut file = OpenOptions::new()
.create(true)
.truncate(true)
@@ -711,7 +712,8 @@ impl IJTiffFile {
}
/// set colors from css color names and #C01085
pub fn set_colors<S: AsRef<str>>(&mut self, colors: &[S]) -> Result<()> {
/// (see [css_color](https://crates.io/crates/css-color))
pub fn set_colors<S: AsRef<str>>(&mut self, colors: &[S]) -> Result<(), Error> {
self.colors = Colors::Colors(
colors
.iter()
@@ -735,17 +737,18 @@ impl IJTiffFile {
(255.0 * c.green).round() as u8,
(255.0 * c.blue).round() as u8,
]),
Err(_) => Err(anyhow!("could not parse color: {}", c)),
Err(_) => Err(Error::ColorParse(c.to_string())),
}
})
.collect::<Result<Vec<_>>>()?,
.collect::<Result<Vec<_>, Error>>()?,
);
Ok(())
}
pub fn set_colormap<S: AsRef<str>>(&mut self, name: S) -> Result<()> {
/// set colormap from named colormap (see [colorcet](https://crates.io/crates/colorcet))
pub fn set_colormap<S: AsRef<str>>(&mut self, name: S) -> Result<(), Error> {
let name = name.as_ref();
let colormap: LinearGradient = name.parse::<ColorMap>()?.try_into()?;
let colormap: LinearGradient = name.parse::<ColorMap>()?.try_into().map_err(|_| Error::Conversion)?;
let mut colormap = colormap
.colors(256)
.into_iter()
@@ -832,7 +835,7 @@ impl IJTiffFile {
hasher.finish()
}
fn hash_check(&mut self, bytes: &Vec<u8>, offset: u64) -> Result<bool> {
fn hash_check(&mut self, bytes: &Vec<u8>, offset: u64) -> Result<bool, Error> {
let current_offset = self.file.stream_position()?;
self.file.seek(SeekFrom::Start(offset))?;
let mut buffer = vec![0; bytes.len()];
@@ -842,7 +845,7 @@ impl IJTiffFile {
Ok(same)
}
fn write(&mut self, bytes: &Vec<u8>) -> Result<u64> {
fn write(&mut self, bytes: &Vec<u8>) -> Result<u64, Error> {
let hash = IJTiffFile::hash(&bytes);
if self.hashes.contains_key(&hash)
&& self.hash_check(bytes, *self.hashes.get(&hash).unwrap())?
@@ -860,7 +863,7 @@ impl IJTiffFile {
}
/// save a 2d array to the tiff file at channel c, slice z, and time t
pub fn save<'a, A, T>(&mut self, frame: A, c: usize, z: usize, t: usize) -> Result<()>
pub fn save<'a, A, T>(&mut self, frame: A, c: usize, z: usize, t: usize) -> Result<(), Error>
where
A: AsArray<'a, T, Ix2>,
T: Bytes + Clone + Send + Sync + 'static,
@@ -882,7 +885,7 @@ impl IJTiffFile {
Ok(())
}
fn collect_threads(&mut self, block: bool) -> Result<()> {
fn collect_threads(&mut self, block: bool) -> Result<(), Error> {
for (c, z, t) in self.threads.keys().cloned().collect::<Vec<_>>() {
if block || self.threads[&(c, z, t)].is_finished() {
if let Some(thread) = self.threads.remove(&(c, z, t)) {
@@ -893,7 +896,7 @@ impl IJTiffFile {
Ok(())
}
fn write_frame(&mut self, frame: CompressedFrame, c: usize, z: usize, t: usize) -> Result<()> {
fn write_frame(&mut self, frame: CompressedFrame, c: usize, z: usize, t: usize) -> Result<(), Error> {
let mut offsets = Vec::new();
let mut bytecounts = Vec::new();
for tile in frame.bytes {
@@ -940,7 +943,7 @@ impl IJTiffFile {
c
}
fn close(&mut self) -> Result<()> {
fn close(&mut self) -> Result<(), Error> {
self.collect_threads(true)?;
let mut c_size = 1;
let mut z_size = 1;
@@ -1074,7 +1077,7 @@ mod tests {
#[test]
/// An example of generating julia fractals.
fn julia_test() -> Result<()> {
fn julia_test() -> Result<(), Error> {
let imgx = 800;
let imgy = 600;

6
src/py.rs
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@@ -4,6 +4,12 @@ use numpy::PyReadonlyArray2;
use pyo3::exceptions::PyValueError;
use pyo3::prelude::*;
impl From<crate::error::Error> for PyErr {
fn from(err: crate::error::Error) -> PyErr {
PyErr::new::<PyValueError, _>(err.to_string())
}
}
#[pyclass(subclass)]
#[pyo3(name = "Tag")]
#[derive(Clone, Debug)]