- replace anyhow with thiserror
This commit is contained in:
11
Cargo.toml
11
Cargo.toml
@@ -1,13 +1,14 @@
|
|||||||
[package]
|
[package]
|
||||||
name = "tiffwrite"
|
name = "tiffwrite"
|
||||||
version = "2025.8.1"
|
version = "2025.9.0"
|
||||||
edition = "2024"
|
edition = "2024"
|
||||||
rust-version = "1.85.1"
|
rust-version = "1.85.1"
|
||||||
authors = ["Wim Pomp <w.pomp@nki.nl>"]
|
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."
|
description = "Write BioFormats/ImageJ compatible tiffs with zstd compression in parallel."
|
||||||
homepage = "https://github.com/wimpomp/tiffwrite"
|
homepage = "https://github.com/wimpomp/tiffwrite"
|
||||||
repository = "https://github.com/wimpomp/tiffwrite"
|
repository = "https://github.com/wimpomp/tiffwrite"
|
||||||
|
documentation = "https://docs.rs/tiffwrite"
|
||||||
readme = "README.md"
|
readme = "README.md"
|
||||||
keywords = ["bioformats", "tiff", "ndarray", "zstd", "fiji"]
|
keywords = ["bioformats", "tiff", "ndarray", "zstd", "fiji"]
|
||||||
categories = ["multimedia::images", "science"]
|
categories = ["multimedia::images", "science"]
|
||||||
@@ -17,7 +18,6 @@ name = "tiffwrite"
|
|||||||
crate-type = ["cdylib", "rlib"]
|
crate-type = ["cdylib", "rlib"]
|
||||||
|
|
||||||
[dependencies]
|
[dependencies]
|
||||||
anyhow = "1.0.98"
|
|
||||||
colorcet = "0.2.1"
|
colorcet = "0.2.1"
|
||||||
colorgrad = "0.7.2"
|
colorgrad = "0.7.2"
|
||||||
chrono = "0.4.41"
|
chrono = "0.4.41"
|
||||||
@@ -25,9 +25,10 @@ css-color = "0.2.8"
|
|||||||
flate2 = "1.1.1"
|
flate2 = "1.1.1"
|
||||||
ndarray = "0.16.1"
|
ndarray = "0.16.1"
|
||||||
num = "0.4.3"
|
num = "0.4.3"
|
||||||
rayon = "1.10.0"
|
|
||||||
zstd = "0.13.3"
|
|
||||||
numpy = { version = "0.25.0", optional = true }
|
numpy = { version = "0.25.0", optional = true }
|
||||||
|
rayon = "1.10.0"
|
||||||
|
thiserror = "2.0.16"
|
||||||
|
zstd = "0.13.3"
|
||||||
|
|
||||||
[dependencies.pyo3]
|
[dependencies.pyo3]
|
||||||
version = "0.25.1"
|
version = "0.25.1"
|
||||||
|
|||||||
176
LICENSE-APACHE
Normal file
176
LICENSE-APACHE
Normal file
@@ -0,0 +1,176 @@
|
|||||||
|
Apache License
|
||||||
|
Version 2.0, January 2004
|
||||||
|
http://www.apache.org/licenses/
|
||||||
|
|
||||||
|
TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
|
||||||
|
|
||||||
|
1. Definitions.
|
||||||
|
|
||||||
|
"License" shall mean the terms and conditions for use, reproduction,
|
||||||
|
and distribution as defined by Sections 1 through 9 of this document.
|
||||||
|
|
||||||
|
"Licensor" shall mean the copyright owner or entity authorized by
|
||||||
|
the copyright owner that is granting the License.
|
||||||
|
|
||||||
|
"Legal Entity" shall mean the union of the acting entity and all
|
||||||
|
other entities that control, are controlled by, or are under common
|
||||||
|
control with that entity. For the purposes of this definition,
|
||||||
|
"control" means (i) the power, direct or indirect, to cause the
|
||||||
|
direction or management of such entity, whether by contract or
|
||||||
|
otherwise, or (ii) ownership of fifty percent (50%) or more of the
|
||||||
|
outstanding shares, or (iii) beneficial ownership of such entity.
|
||||||
|
|
||||||
|
"You" (or "Your") shall mean an individual or Legal Entity
|
||||||
|
exercising permissions granted by this License.
|
||||||
|
|
||||||
|
"Source" form shall mean the preferred form for making modifications,
|
||||||
|
including but not limited to software source code, documentation
|
||||||
|
source, and configuration files.
|
||||||
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|
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|
"Object" form shall mean any form resulting from mechanical
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|
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|
||||||
|
not limited to compiled object code, generated documentation,
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|
and conversions to other media types.
|
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|
"Work" shall mean the work of authorship, whether in Source or
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|
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|
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|
copyright notice that is included in or attached to the work
|
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|
(an example is provided in the Appendix below).
|
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|
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|
"Derivative Works" shall mean any work, whether in Source or Object
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|
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|
||||||
|
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|
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|
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"Contribution" shall mean any work of authorship, including
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|
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2. Grant of Copyright License. Subject to the terms and conditions of
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or a Contribution incorporated within the Work constitutes direct
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or contributory patent infringement, then any patent licenses
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as of the date such litigation is filed.
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4. Redistribution. You may reproduce and distribute copies of the
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meet the following conditions:
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|
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|
(a) You must give any other recipients of the Work or
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|
(b) You must cause any modified files to carry prominent notices
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|
stating that You changed the files; and
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|
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|
(c) You must retain, in the Source form of any Derivative Works
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excluding those notices that do not pertain to any part of
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|
(d) If the Work includes a "NOTICE" text file as part of its
|
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|
distribution, then any Derivative Works that You distribute must
|
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|
include a readable copy of the attribution notices contained
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|
within such NOTICE file, excluding those notices that do not
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|
pertain to any part of the Derivative Works, in at least one
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of the following places: within a NOTICE text file distributed
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within a display generated by the Derivative Works, if and
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wherever such third-party notices normally appear. The contents
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of the NOTICE file are for informational purposes only and
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|
do not modify the License. You may add Your own attribution
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|
notices within Derivative Works that You distribute, alongside
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or as an addendum to the NOTICE text from the Work, provided
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that such additional attribution notices cannot be construed
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as modifying the License.
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|
You may add Your own copyright statement to Your modifications and
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may provide additional or different license terms and conditions
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for use, reproduction, or distribution of Your modifications, or
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the conditions stated in this License.
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5. Submission of Contributions. Unless You explicitly state otherwise,
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any Contribution intentionally submitted for inclusion in the Work
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|
Notwithstanding the above, nothing herein shall supersede or modify
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|
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6. Trademarks. This License does not grant permission to use the trade
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7. Disclaimer of Warranty. Unless required by applicable law or
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has been advised of the possibility of such damages.
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9. Accepting Warranty or Additional Liability. While redistributing
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and charge a fee for, acceptance of support, warranty, indemnity,
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defend, and hold each Contributor harmless for any liability
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incurred by, or claims asserted against, such Contributor by reason
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of your accepting any such warranty or additional liability.
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|
END OF TERMS AND CONDITIONS
|
||||||
14
src/error.rs
Normal file
14
src/error.rs
Normal file
@@ -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
43
src/lib.rs
@@ -1,7 +1,7 @@
|
|||||||
#[cfg(feature = "python")]
|
#[cfg(feature = "python")]
|
||||||
mod py;
|
mod py;
|
||||||
|
mod error;
|
||||||
|
|
||||||
use anyhow::{Result, anyhow};
|
|
||||||
use chrono::Utc;
|
use chrono::Utc;
|
||||||
use colorcet::ColorMap;
|
use colorcet::ColorMap;
|
||||||
use colorgrad::{Gradient, LinearGradient};
|
use colorgrad::{Gradient, LinearGradient};
|
||||||
@@ -23,6 +23,7 @@ use std::{
|
|||||||
};
|
};
|
||||||
use zstd::zstd_safe::CompressionLevel;
|
use zstd::zstd_safe::CompressionLevel;
|
||||||
use zstd::{DEFAULT_COMPRESSION_LEVEL, stream::Encoder};
|
use zstd::{DEFAULT_COMPRESSION_LEVEL, stream::Encoder};
|
||||||
|
use crate::error::Error;
|
||||||
|
|
||||||
const TAG_SIZE: usize = 20;
|
const TAG_SIZE: usize = 20;
|
||||||
const OFFSET_SIZE: usize = 8;
|
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<_>>();
|
let mut tags = self.tags.drain().collect::<Vec<_>>();
|
||||||
tags.sort();
|
tags.sort();
|
||||||
ijtifffile.file.seek(SeekFrom::End(0))?;
|
ijtifffile.file.seek(SeekFrom::End(0))?;
|
||||||
@@ -322,7 +323,7 @@ impl Tag {
|
|||||||
c as u64
|
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()?;
|
self.offset = ijtifffile.file.stream_position()?;
|
||||||
ijtifffile.file.write_all(&self.code.to_le_bytes())?;
|
ijtifffile.file.write_all(&self.code.to_le_bytes())?;
|
||||||
ijtifffile.file.write_all(&self.ttype.to_le_bytes())?;
|
ijtifffile.file.write_all(&self.ttype.to_le_bytes())?;
|
||||||
@@ -338,7 +339,7 @@ impl Tag {
|
|||||||
Ok(())
|
Ok(())
|
||||||
}
|
}
|
||||||
|
|
||||||
fn write_data(&self, ijtifffile: &mut IJTiffFile) -> Result<()> {
|
fn write_data(&self, ijtifffile: &mut IJTiffFile) -> Result<(), Error> {
|
||||||
if self.bytes.len() > OFFSET_SIZE {
|
if self.bytes.len() > OFFSET_SIZE {
|
||||||
ijtifffile.file.seek(SeekFrom::End(0))?;
|
ijtifffile.file.seek(SeekFrom::End(0))?;
|
||||||
let offset = ijtifffile.write(&self.bytes)?;
|
let offset = ijtifffile.write(&self.bytes)?;
|
||||||
@@ -493,7 +494,7 @@ impl CompressedFrame {
|
|||||||
slice: (usize, usize, usize, usize),
|
slice: (usize, usize, usize, usize),
|
||||||
tile_width: usize,
|
tile_width: usize,
|
||||||
tile_length: usize,
|
tile_length: usize,
|
||||||
) -> Result<W>
|
) -> Result<W, Error>
|
||||||
where
|
where
|
||||||
W: Write,
|
W: Write,
|
||||||
T: Bytes,
|
T: Bytes,
|
||||||
@@ -524,7 +525,7 @@ impl CompressedFrame {
|
|||||||
slice: (usize, usize, usize, usize),
|
slice: (usize, usize, usize, usize),
|
||||||
tile_width: usize,
|
tile_width: usize,
|
||||||
tile_length: usize,
|
tile_length: usize,
|
||||||
) -> Result<Vec<u8>>
|
) -> Result<Vec<u8>, Error>
|
||||||
where
|
where
|
||||||
T: Bytes,
|
T: Bytes,
|
||||||
{
|
{
|
||||||
@@ -539,7 +540,7 @@ impl CompressedFrame {
|
|||||||
tile_width: usize,
|
tile_width: usize,
|
||||||
tile_length: usize,
|
tile_length: usize,
|
||||||
compression_level: i32,
|
compression_level: i32,
|
||||||
) -> Result<Vec<u8>>
|
) -> Result<Vec<u8>, Error>
|
||||||
where
|
where
|
||||||
T: Bytes,
|
T: Bytes,
|
||||||
{
|
{
|
||||||
@@ -678,7 +679,7 @@ impl Drop for IJTiffFile {
|
|||||||
impl IJTiffFile {
|
impl IJTiffFile {
|
||||||
/// create new tifffile from path, use it's save() method to save frames
|
/// create new tifffile from path, use it's save() method to save frames
|
||||||
/// the file is finalized when it goes out of scope
|
/// 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()
|
let mut file = OpenOptions::new()
|
||||||
.create(true)
|
.create(true)
|
||||||
.truncate(true)
|
.truncate(true)
|
||||||
@@ -711,7 +712,8 @@ impl IJTiffFile {
|
|||||||
}
|
}
|
||||||
|
|
||||||
/// set colors from css color names and #C01085
|
/// 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(
|
self.colors = Colors::Colors(
|
||||||
colors
|
colors
|
||||||
.iter()
|
.iter()
|
||||||
@@ -735,17 +737,18 @@ impl IJTiffFile {
|
|||||||
(255.0 * c.green).round() as u8,
|
(255.0 * c.green).round() as u8,
|
||||||
(255.0 * c.blue).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(())
|
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 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
|
let mut colormap = colormap
|
||||||
.colors(256)
|
.colors(256)
|
||||||
.into_iter()
|
.into_iter()
|
||||||
@@ -832,7 +835,7 @@ impl IJTiffFile {
|
|||||||
hasher.finish()
|
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()?;
|
let current_offset = self.file.stream_position()?;
|
||||||
self.file.seek(SeekFrom::Start(offset))?;
|
self.file.seek(SeekFrom::Start(offset))?;
|
||||||
let mut buffer = vec![0; bytes.len()];
|
let mut buffer = vec![0; bytes.len()];
|
||||||
@@ -842,7 +845,7 @@ impl IJTiffFile {
|
|||||||
Ok(same)
|
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);
|
let hash = IJTiffFile::hash(&bytes);
|
||||||
if self.hashes.contains_key(&hash)
|
if self.hashes.contains_key(&hash)
|
||||||
&& self.hash_check(bytes, *self.hashes.get(&hash).unwrap())?
|
&& 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
|
/// 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
|
where
|
||||||
A: AsArray<'a, T, Ix2>,
|
A: AsArray<'a, T, Ix2>,
|
||||||
T: Bytes + Clone + Send + Sync + 'static,
|
T: Bytes + Clone + Send + Sync + 'static,
|
||||||
@@ -882,7 +885,7 @@ impl IJTiffFile {
|
|||||||
Ok(())
|
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<_>>() {
|
for (c, z, t) in self.threads.keys().cloned().collect::<Vec<_>>() {
|
||||||
if block || 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)) {
|
if let Some(thread) = self.threads.remove(&(c, z, t)) {
|
||||||
@@ -893,7 +896,7 @@ impl IJTiffFile {
|
|||||||
Ok(())
|
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 offsets = Vec::new();
|
||||||
let mut bytecounts = Vec::new();
|
let mut bytecounts = Vec::new();
|
||||||
for tile in frame.bytes {
|
for tile in frame.bytes {
|
||||||
@@ -940,7 +943,7 @@ impl IJTiffFile {
|
|||||||
c
|
c
|
||||||
}
|
}
|
||||||
|
|
||||||
fn close(&mut self) -> Result<()> {
|
fn close(&mut self) -> Result<(), Error> {
|
||||||
self.collect_threads(true)?;
|
self.collect_threads(true)?;
|
||||||
let mut c_size = 1;
|
let mut c_size = 1;
|
||||||
let mut z_size = 1;
|
let mut z_size = 1;
|
||||||
@@ -1074,7 +1077,7 @@ mod tests {
|
|||||||
|
|
||||||
#[test]
|
#[test]
|
||||||
/// An example of generating julia fractals.
|
/// An example of generating julia fractals.
|
||||||
fn julia_test() -> Result<()> {
|
fn julia_test() -> Result<(), Error> {
|
||||||
let imgx = 800;
|
let imgx = 800;
|
||||||
let imgy = 600;
|
let imgy = 600;
|
||||||
|
|
||||||
|
|||||||
@@ -4,6 +4,12 @@ use numpy::PyReadonlyArray2;
|
|||||||
use pyo3::exceptions::PyValueError;
|
use pyo3::exceptions::PyValueError;
|
||||||
use pyo3::prelude::*;
|
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)]
|
#[pyclass(subclass)]
|
||||||
#[pyo3(name = "Tag")]
|
#[pyo3(name = "Tag")]
|
||||||
#[derive(Clone, Debug)]
|
#[derive(Clone, Debug)]
|
||||||
|
|||||||
Reference in New Issue
Block a user