- can now save the common types
This commit is contained in:
Wim Pomp
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checksum = "67ce096073ec5405f5ee2b8b31f03a68e02aa10d5d4f565eca04acc41931fa1c"
|
|
||||||
dependencies = [
|
|
||||||
"libc",
|
|
||||||
"pyo3-build-config",
|
|
||||||
]
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "pyo3-macros"
|
|
||||||
version = "0.22.3"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "2440c6d12bc8f3ae39f1e775266fa5122fd0c8891ce7520fa6048e683ad3de28"
|
|
||||||
dependencies = [
|
|
||||||
"proc-macro2",
|
|
||||||
"pyo3-macros-backend",
|
|
||||||
"quote",
|
|
||||||
"syn",
|
|
||||||
]
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "pyo3-macros-backend"
|
|
||||||
version = "0.22.3"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "1be962f0e06da8f8465729ea2cb71a416d2257dff56cbe40a70d3e62a93ae5d1"
|
|
||||||
dependencies = [
|
|
||||||
"heck",
|
|
||||||
"proc-macro2",
|
|
||||||
"pyo3-build-config",
|
|
||||||
"quote",
|
|
||||||
"syn",
|
|
||||||
]
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "python3-dll-a"
|
|
||||||
version = "0.2.10"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "bd0b78171a90d808b319acfad166c4790d9e9759bbc14ac8273fe133673dd41b"
|
|
||||||
dependencies = [
|
|
||||||
"cc",
|
|
||||||
]
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "quote"
|
|
||||||
version = "1.0.37"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "b5b9d34b8991d19d98081b46eacdd8eb58c6f2b201139f7c5f643cc155a633af"
|
|
||||||
dependencies = [
|
|
||||||
"proc-macro2",
|
|
||||||
]
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "rawpointer"
|
|
||||||
version = "0.2.1"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "60a357793950651c4ed0f3f52338f53b2f809f32d83a07f72909fa13e4c6c1e3"
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "rayon"
|
|
||||||
version = "1.10.0"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "b418a60154510ca1a002a752ca9714984e21e4241e804d32555251faf8b78ffa"
|
|
||||||
dependencies = [
|
|
||||||
"either",
|
|
||||||
"rayon-core",
|
|
||||||
]
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "rayon-core"
|
|
||||||
version = "1.12.1"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "1465873a3dfdaa8ae7cb14b4383657caab0b3e8a0aa9ae8e04b044854c8dfce2"
|
|
||||||
dependencies = [
|
|
||||||
"crossbeam-deque",
|
|
||||||
"crossbeam-utils",
|
|
||||||
]
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "shlex"
|
|
||||||
version = "1.3.0"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "0fda2ff0d084019ba4d7c6f371c95d8fd75ce3524c3cb8fb653a3023f6323e64"
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "syn"
|
|
||||||
version = "2.0.79"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "89132cd0bf050864e1d38dc3bbc07a0eb8e7530af26344d3d2bbbef83499f590"
|
|
||||||
dependencies = [
|
|
||||||
"proc-macro2",
|
|
||||||
"quote",
|
|
||||||
"unicode-ident",
|
|
||||||
]
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "target-lexicon"
|
|
||||||
version = "0.12.16"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "61c41af27dd6d1e27b1b16b489db798443478cef1f06a660c96db617ba5de3b1"
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "tiffwrite"
|
|
||||||
version = "2024.10.0"
|
|
||||||
dependencies = [
|
|
||||||
"anyhow",
|
|
||||||
"chrono",
|
|
||||||
"fraction",
|
|
||||||
"ndarray",
|
|
||||||
"num",
|
|
||||||
"pyo3",
|
|
||||||
"rayon",
|
|
||||||
]
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "unicode-ident"
|
|
||||||
version = "1.0.13"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "e91b56cd4cadaeb79bbf1a5645f6b4f8dc5bde8834ad5894a8db35fda9efa1fe"
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "unindent"
|
|
||||||
version = "0.2.3"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "c7de7d73e1754487cb58364ee906a499937a0dfabd86bcb980fa99ec8c8fa2ce"
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "wasm-bindgen"
|
|
||||||
version = "0.2.93"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "a82edfc16a6c469f5f44dc7b571814045d60404b55a0ee849f9bcfa2e63dd9b5"
|
|
||||||
dependencies = [
|
|
||||||
"cfg-if",
|
|
||||||
"once_cell",
|
|
||||||
"wasm-bindgen-macro",
|
|
||||||
]
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "wasm-bindgen-backend"
|
|
||||||
version = "0.2.93"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "9de396da306523044d3302746f1208fa71d7532227f15e347e2d93e4145dd77b"
|
|
||||||
dependencies = [
|
|
||||||
"bumpalo",
|
|
||||||
"log",
|
|
||||||
"once_cell",
|
|
||||||
"proc-macro2",
|
|
||||||
"quote",
|
|
||||||
"syn",
|
|
||||||
"wasm-bindgen-shared",
|
|
||||||
]
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "wasm-bindgen-macro"
|
|
||||||
version = "0.2.93"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "585c4c91a46b072c92e908d99cb1dcdf95c5218eeb6f3bf1efa991ee7a68cccf"
|
|
||||||
dependencies = [
|
|
||||||
"quote",
|
|
||||||
"wasm-bindgen-macro-support",
|
|
||||||
]
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "wasm-bindgen-macro-support"
|
|
||||||
version = "0.2.93"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "afc340c74d9005395cf9dd098506f7f44e38f2b4a21c6aaacf9a105ea5e1e836"
|
|
||||||
dependencies = [
|
|
||||||
"proc-macro2",
|
|
||||||
"quote",
|
|
||||||
"syn",
|
|
||||||
"wasm-bindgen-backend",
|
|
||||||
"wasm-bindgen-shared",
|
|
||||||
]
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "wasm-bindgen-shared"
|
|
||||||
version = "0.2.93"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "c62a0a307cb4a311d3a07867860911ca130c3494e8c2719593806c08bc5d0484"
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "windows-core"
|
|
||||||
version = "0.52.0"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "33ab640c8d7e35bf8ba19b884ba838ceb4fba93a4e8c65a9059d08afcfc683d9"
|
|
||||||
dependencies = [
|
|
||||||
"windows-targets",
|
|
||||||
]
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "windows-targets"
|
|
||||||
version = "0.52.6"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "9b724f72796e036ab90c1021d4780d4d3d648aca59e491e6b98e725b84e99973"
|
|
||||||
dependencies = [
|
|
||||||
"windows_aarch64_gnullvm",
|
|
||||||
"windows_aarch64_msvc",
|
|
||||||
"windows_i686_gnu",
|
|
||||||
"windows_i686_gnullvm",
|
|
||||||
"windows_i686_msvc",
|
|
||||||
"windows_x86_64_gnu",
|
|
||||||
"windows_x86_64_gnullvm",
|
|
||||||
"windows_x86_64_msvc",
|
|
||||||
]
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "windows_aarch64_gnullvm"
|
|
||||||
version = "0.52.6"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "32a4622180e7a0ec044bb555404c800bc9fd9ec262ec147edd5989ccd0c02cd3"
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "windows_aarch64_msvc"
|
|
||||||
version = "0.52.6"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "09ec2a7bb152e2252b53fa7803150007879548bc709c039df7627cabbd05d469"
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "windows_i686_gnu"
|
|
||||||
version = "0.52.6"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "8e9b5ad5ab802e97eb8e295ac6720e509ee4c243f69d781394014ebfe8bbfa0b"
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "windows_i686_gnullvm"
|
|
||||||
version = "0.52.6"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66"
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "windows_i686_msvc"
|
|
||||||
version = "0.52.6"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66"
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "windows_x86_64_gnu"
|
|
||||||
version = "0.52.6"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78"
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "windows_x86_64_gnullvm"
|
|
||||||
version = "0.52.6"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d"
|
|
||||||
|
|
||||||
[[package]]
|
|
||||||
name = "windows_x86_64_msvc"
|
|
||||||
version = "0.52.6"
|
|
||||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
|
||||||
checksum = "589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec"
|
|
||||||
10
Cargo.toml
10
Cargo.toml
@@ -1,21 +1,23 @@
|
|||||||
[package]
|
[package]
|
||||||
name = "tiffwrite"
|
name = "tiffwrite"
|
||||||
version = "2024.10.0"
|
version = "2024.10.1"
|
||||||
edition = "2021"
|
edition = "2021"
|
||||||
|
|
||||||
# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
|
# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
|
||||||
[lib]
|
[lib]
|
||||||
name = "tiffwrite"
|
name = "tiffwrite"
|
||||||
crate-type = ["cdylib"]
|
crate-type = ["cdylib", "rlib"]
|
||||||
|
|
||||||
[dependencies]
|
[dependencies]
|
||||||
pyo3 = { version = "0.22.3", features = ["extension-module", "abi3-py310", "generate-import-lib", "anyhow"] }
|
pyo3 = { version = "0.21.2", features = ["extension-module", "abi3-py310", "generate-import-lib", "anyhow", "multiple-pymethods"] }
|
||||||
anyhow = "1.0.89"
|
anyhow = "1.0.89"
|
||||||
rayon = "1.10.0"
|
rayon = "1.10.0"
|
||||||
fraction = "0.15.3"
|
fraction = "0.15.3"
|
||||||
num = "0.4.3"
|
num = "0.4.3"
|
||||||
ndarray = "0.16.1"
|
ndarray = "0.15.6"
|
||||||
chrono = "0.4.38"
|
chrono = "0.4.38"
|
||||||
|
numpy = "0.21.0"
|
||||||
|
futures = "0.3.31"
|
||||||
|
|
||||||
[features]
|
[features]
|
||||||
nopython = []
|
nopython = []
|
||||||
|
|||||||
105
src/lib.rs
105
src/lib.rs
@@ -1,3 +1,6 @@
|
|||||||
|
#[cfg(not(feature = "nopython"))]
|
||||||
|
mod py;
|
||||||
|
|
||||||
use std::cmp::Ordering;
|
use std::cmp::Ordering;
|
||||||
use std::collections::HashMap;
|
use std::collections::HashMap;
|
||||||
use std::fs::{File, OpenOptions};
|
use std::fs::{File, OpenOptions};
|
||||||
@@ -15,6 +18,7 @@ use chrono::Utc;
|
|||||||
const TAG_SIZE: usize = 20;
|
const TAG_SIZE: usize = 20;
|
||||||
const OFFSET_SIZE: usize = 8;
|
const OFFSET_SIZE: usize = 8;
|
||||||
const OFFSET: u64 = 16;
|
const OFFSET: u64 = 16;
|
||||||
|
const COMPRESSION: u16 = 1;
|
||||||
|
|
||||||
|
|
||||||
#[derive(Clone, Debug)]
|
#[derive(Clone, Debug)]
|
||||||
@@ -238,7 +242,7 @@ struct Frame {
|
|||||||
image_width: u32,
|
image_width: u32,
|
||||||
image_length: u32,
|
image_length: u32,
|
||||||
bits_per_sample: u16,
|
bits_per_sample: u16,
|
||||||
compression: u16,
|
sample_format: u16,
|
||||||
tile_width: u16,
|
tile_width: u16,
|
||||||
tile_length: u16,
|
tile_length: u16,
|
||||||
extra_tags: Vec<Tag>
|
extra_tags: Vec<Tag>
|
||||||
@@ -246,17 +250,63 @@ struct Frame {
|
|||||||
|
|
||||||
impl Frame {
|
impl Frame {
|
||||||
fn new(
|
fn new(
|
||||||
tilebyteoffsets: Vec<u64>, tilebytecounts: Vec<u64>, image_width: u32,
|
tilebyteoffsets: Vec<u64>, tilebytecounts: Vec<u64>, image_width: u32, image_length: u32,
|
||||||
image_length: u32, bits_per_sample: u16, compression: u16, tile_width: u16, tile_length: u16
|
bits_per_sample: u16, sample_format: u16, tile_width: u16, tile_length: u16
|
||||||
) -> Self {
|
) -> Self {
|
||||||
Frame {
|
Frame {
|
||||||
tilebyteoffsets, tilebytecounts, image_width, image_length, bits_per_sample,
|
tilebyteoffsets, tilebytecounts, image_width, image_length, bits_per_sample,
|
||||||
compression, tile_width, tile_length, extra_tags: Vec::new()
|
sample_format, tile_width, tile_length, extra_tags: Vec::new()
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
pub trait Bytes {
|
||||||
|
const BITS_PER_SAMPLE: u16;
|
||||||
|
const SAMPLE_FORMAT: u16;
|
||||||
|
|
||||||
|
fn bytes(&self) -> Vec<u8>;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
macro_rules! bytes_impl {
|
||||||
|
($T:ty, $bits_per_sample:expr, $sample_format:expr) => {
|
||||||
|
impl Bytes for $T {
|
||||||
|
const BITS_PER_SAMPLE: u16 = $bits_per_sample;
|
||||||
|
const SAMPLE_FORMAT: u16 = $sample_format;
|
||||||
|
|
||||||
|
#[inline]
|
||||||
|
fn bytes(&self) -> Vec<u8>
|
||||||
|
{
|
||||||
|
self.to_le_bytes().to_vec()
|
||||||
|
}
|
||||||
|
}
|
||||||
|
};
|
||||||
|
}
|
||||||
|
|
||||||
|
bytes_impl!(u8, 8, 1);
|
||||||
|
bytes_impl!(u16, 16, 1);
|
||||||
|
bytes_impl!(u32, 32, 1);
|
||||||
|
bytes_impl!(u64, 64, 1);
|
||||||
|
bytes_impl!(u128, 128, 1);
|
||||||
|
#[cfg(target_pointer_width = "64")]
|
||||||
|
bytes_impl!(usize, 64, 1);
|
||||||
|
#[cfg(target_pointer_width = "32")]
|
||||||
|
bytes_impl!(usize, 32, 1);
|
||||||
|
|
||||||
|
bytes_impl!(i8, 8, 2);
|
||||||
|
bytes_impl!(i16, 16, 2);
|
||||||
|
bytes_impl!(i32, 32, 2);
|
||||||
|
bytes_impl!(i64, 64, 2);
|
||||||
|
bytes_impl!(i128, 128, 2);
|
||||||
|
#[cfg(target_pointer_width = "64")]
|
||||||
|
bytes_impl!(isize, 64, 2);
|
||||||
|
#[cfg(target_pointer_width = "32")]
|
||||||
|
bytes_impl!(isize, 32, 2);
|
||||||
|
bytes_impl!(f32, 32, 3);
|
||||||
|
bytes_impl!(f64, 64, 3);
|
||||||
|
|
||||||
|
|
||||||
#[derive(Debug)]
|
#[derive(Debug)]
|
||||||
pub struct IJTiffFile {
|
pub struct IJTiffFile {
|
||||||
file: File,
|
file: File,
|
||||||
@@ -331,19 +381,6 @@ impl IJTiffFile {
|
|||||||
desc
|
desc
|
||||||
}
|
}
|
||||||
|
|
||||||
pub fn save(&mut self, frame: Array2<u16>, c: usize, z: usize, t: usize,
|
|
||||||
extra_tags: Option<Vec<Tag>>) -> Result<()> {
|
|
||||||
let mut compressed_frame = self.compress_frame(frame)?;
|
|
||||||
if let Some(tags) = extra_tags {
|
|
||||||
for tag in tags {
|
|
||||||
compressed_frame.extra_tags.push(tag);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
self.frames.insert(self.get_frame_number(c, z, t), compressed_frame);
|
|
||||||
Ok(())
|
|
||||||
}
|
|
||||||
|
|
||||||
fn get_frame_number(&self, c: usize, z: usize, t: usize) -> (usize, u8) {
|
fn get_frame_number(&self, c: usize, z: usize, t: usize) -> (usize, u8) {
|
||||||
if let (None, None) = (self.colormap.as_ref(), self.colors.as_ref()) {
|
if let (None, None) = (self.colormap.as_ref(), self.colors.as_ref()) {
|
||||||
(z + t * self.shape.1, c as u8)
|
(z + t * self.shape.1, c as u8)
|
||||||
@@ -352,7 +389,7 @@ impl IJTiffFile {
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
pub fn hash<T: Hash>(value: &T) -> u64 {
|
fn hash<T: Hash>(value: &T) -> u64 {
|
||||||
let mut hasher = DefaultHasher::new();
|
let mut hasher = DefaultHasher::new();
|
||||||
value.hash(&mut hasher);
|
value.hash(&mut hasher);
|
||||||
hasher.finish()
|
hasher.finish()
|
||||||
@@ -383,21 +420,32 @@ impl IJTiffFile {
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
fn compress_frame(&mut self, frame: Array2<u16>) -> Result<Frame> {
|
pub fn save<T: Bytes + Clone + Zero>(&mut self, frame: Array2<T>, c: usize, z: usize, t: usize,
|
||||||
|
extra_tags: Option<Vec<Tag>>) -> Result<()> {
|
||||||
|
self.compress_frame(frame, c, z, t, extra_tags);
|
||||||
|
Ok(())
|
||||||
|
}
|
||||||
|
|
||||||
|
fn compress_frame<T: Bytes + Clone + Zero>(&mut self, frame: Array2<T>, c: usize, z: usize, t: usize,
|
||||||
|
extra_tags: Option<Vec<Tag>>) {
|
||||||
let image_width = frame.shape()[0] as u32;
|
let image_width = frame.shape()[0] as u32;
|
||||||
let image_length = frame.shape()[1] as u32;
|
let image_length = frame.shape()[1] as u32;
|
||||||
let mut tilebyteoffsets = Vec::new();
|
let mut tilebyteoffsets = Vec::new();
|
||||||
let mut tilebytecounts = Vec::new();
|
let mut tilebytecounts = Vec::new();
|
||||||
let tiles = IJTiffFile::tile(frame.reversed_axes(), 64);
|
let tiles = IJTiffFile::tile(frame.reversed_axes(), 64);
|
||||||
for tile in tiles {
|
for tile in tiles {
|
||||||
let bytes: Vec<u8> = tile.into_flat().into_iter().map(
|
let bytes: Vec<u8> = tile.map(|x| x.bytes()).into_iter().flatten().collect();
|
||||||
|x| x.to_le_bytes()).into_iter().flatten().collect();
|
|
||||||
tilebytecounts.push(bytes.len() as u64);
|
tilebytecounts.push(bytes.len() as u64);
|
||||||
tilebyteoffsets.push(self.write(&bytes)?);
|
tilebyteoffsets.push(self.write(&bytes).unwrap());
|
||||||
}
|
}
|
||||||
|
let mut frame = Frame::new(tilebyteoffsets, tilebytecounts, image_width, image_length,
|
||||||
Ok(Frame::new(tilebyteoffsets, tilebytecounts, image_width, image_length,
|
T::BITS_PER_SAMPLE, T::SAMPLE_FORMAT, 64, 64);
|
||||||
16, 1, 64, 64))
|
if let Some(tags) = extra_tags {
|
||||||
|
for tag in tags {
|
||||||
|
frame.extra_tags.push(tag);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
self.frames.insert(self.get_frame_number(c, z, t), frame);
|
||||||
}
|
}
|
||||||
|
|
||||||
fn tile<T: Clone + Zero>(frame: Array2<T>, size: usize) -> Vec<Array2<T>> {
|
fn tile<T: Clone + Zero>(frame: Array2<T>, size: usize) -> Vec<Array2<T>> {
|
||||||
@@ -438,15 +486,13 @@ impl IJTiffFile {
|
|||||||
|
|
||||||
fn get_colormap(&self, colormap: &Vec<u16>) -> Result<Vec<u16>> {
|
fn get_colormap(&self, colormap: &Vec<u16>) -> Result<Vec<u16>> {
|
||||||
todo!();
|
todo!();
|
||||||
Ok(Vec::new())
|
|
||||||
}
|
}
|
||||||
|
|
||||||
fn get_color(&self, colors: (u8, u8, u8)) -> Result<Vec<u16>> {
|
fn get_color(&self, colors: (u8, u8, u8)) -> Result<Vec<u16>> {
|
||||||
todo!();
|
todo!();
|
||||||
Ok(Vec::new())
|
|
||||||
}
|
}
|
||||||
|
|
||||||
pub fn close(&mut self) -> Result<()> {
|
fn close(&mut self) -> Result<()> {
|
||||||
let mut where_to_write_next_ifd_offset = OFFSET - OFFSET_SIZE as u64;
|
let mut where_to_write_next_ifd_offset = OFFSET - OFFSET_SIZE as u64;
|
||||||
let mut warn = false;
|
let mut warn = false;
|
||||||
for frame_number in 0..self.n_frames {
|
for frame_number in 0..self.n_frames {
|
||||||
@@ -467,7 +513,7 @@ impl IJTiffFile {
|
|||||||
ifd.push_tag(Tag::long(256, vec![frame.image_width]));
|
ifd.push_tag(Tag::long(256, vec![frame.image_width]));
|
||||||
ifd.push_tag(Tag::long(257, vec![frame.image_length]));
|
ifd.push_tag(Tag::long(257, vec![frame.image_length]));
|
||||||
ifd.push_tag(Tag::short(258, vec![frame.bits_per_sample; frame_count]));
|
ifd.push_tag(Tag::short(258, vec![frame.bits_per_sample; frame_count]));
|
||||||
ifd.push_tag(Tag::short(259, vec![1]));
|
ifd.push_tag(Tag::short(259, vec![COMPRESSION]));
|
||||||
ifd.push_tag(Tag::ascii(270, &self.description()));
|
ifd.push_tag(Tag::ascii(270, &self.description()));
|
||||||
ifd.push_tag(Tag::short(277, vec![frame_count as u16]));
|
ifd.push_tag(Tag::short(277, vec![frame_count as u16]));
|
||||||
ifd.push_tag(Tag::ascii(305, "tiffwrite_rs"));
|
ifd.push_tag(Tag::ascii(305, "tiffwrite_rs"));
|
||||||
@@ -475,6 +521,7 @@ impl IJTiffFile {
|
|||||||
ifd.push_tag(Tag::short(323, vec![frame.tile_length]));
|
ifd.push_tag(Tag::short(323, vec![frame.tile_length]));
|
||||||
ifd.push_tag(Tag::long8(324, tilebyteoffsets));
|
ifd.push_tag(Tag::long8(324, tilebyteoffsets));
|
||||||
ifd.push_tag(Tag::long8(325, tilebytecounts));
|
ifd.push_tag(Tag::long8(325, tilebytecounts));
|
||||||
|
ifd.push_tag(Tag::short(339, vec![frame.sample_format]));
|
||||||
if frame_number == 0 {
|
if frame_number == 0 {
|
||||||
if let Some(colormap) = &self.colormap {
|
if let Some(colormap) = &self.colormap {
|
||||||
ifd.push_tag(Tag::short(320, self.get_colormap(colormap)?));
|
ifd.push_tag(Tag::short(320, self.get_colormap(colormap)?));
|
||||||
|
|||||||
29
src/main.rs
29
src/main.rs
@@ -1,28 +1,23 @@
|
|||||||
#[cfg(not(feature = "nopython"))]
|
|
||||||
mod py;
|
|
||||||
mod lib;
|
|
||||||
|
|
||||||
use anyhow::Result;
|
use anyhow::Result;
|
||||||
use ndarray::{s, Array2};
|
use ndarray::{s, Array2};
|
||||||
use rayon::prelude::*;
|
use tiffwrite::IJTiffFile;
|
||||||
use crate::lib::IJTiffFile;
|
|
||||||
|
|
||||||
|
|
||||||
fn main() -> Result<()> {
|
fn main() -> Result<()> {
|
||||||
println!("Hello World!");
|
println!("Hello World!");
|
||||||
let mut f = IJTiffFile::new("foo.tif", (1, 2, 1))?;
|
let mut f = IJTiffFile::new("foo.tif", (2, 1, 1))?;
|
||||||
let mut arr = Array2::<u16>::zeros((100, 100));
|
let mut arr = Array2::<u16>::zeros((100, 100));
|
||||||
// for i in 0..arr.shape()[0] {
|
for i in 0..arr.shape()[0] {
|
||||||
// for j in 0..arr.shape()[1] {
|
for j in 0..arr.shape()[1] {
|
||||||
// arr[[i, j]] = i as u16;
|
arr[[i, j]] = i as u16;
|
||||||
// }
|
}
|
||||||
// }
|
}
|
||||||
f.save(arr.to_owned(), 0, 0, 0, None)?;
|
f.save(arr.to_owned(), 0, 0, 0, None)?;
|
||||||
|
|
||||||
// let mut arr = Array2::<u16>::zeros((100, 100));
|
let mut arr = Array2::<u16>::zeros((100, 100));
|
||||||
// arr.slice_mut(s![64.., ..64]).fill(1);
|
arr.slice_mut(s![64.., ..64]).fill(1);
|
||||||
// arr.slice_mut(s![..64, 64..]).fill(2);
|
arr.slice_mut(s![..64, 64..]).fill(2);
|
||||||
// arr.slice_mut(s![64.., 64..]).fill(3);
|
arr.slice_mut(s![64.., 64..]).fill(3);
|
||||||
f.save(arr.to_owned(), 0, 1,0, None)?;
|
f.save(arr.to_owned(), 1, 0,0, None)?;
|
||||||
Ok(())
|
Ok(())
|
||||||
}
|
}
|
||||||
67
src/py.rs
67
src/py.rs
@@ -1,9 +1,8 @@
|
|||||||
use pyo3::prelude::*;
|
use pyo3::prelude::*;
|
||||||
use crate::lib::{IJTiffFile, Tag};
|
use crate::{IJTiffFile, Tag};
|
||||||
use std::time::Duration;
|
|
||||||
use pyo3::types::{PyInt, PyString};
|
|
||||||
use fraction::Fraction;
|
use fraction::Fraction;
|
||||||
use num::Complex;
|
use num::Complex;
|
||||||
|
use numpy::{PyReadonlyArray2, PyArrayMethods};
|
||||||
|
|
||||||
|
|
||||||
#[pyclass(subclass)]
|
#[pyclass(subclass)]
|
||||||
@@ -106,14 +105,14 @@ impl PyTag {
|
|||||||
#[pyo3(name = "IJTiffFile")]
|
#[pyo3(name = "IJTiffFile")]
|
||||||
#[derive(Debug)]
|
#[derive(Debug)]
|
||||||
struct PyIJTiffFile {
|
struct PyIJTiffFile {
|
||||||
ijtifffile: IJTiffFile
|
ijtifffile: Option<IJTiffFile>
|
||||||
}
|
}
|
||||||
|
|
||||||
#[pymethods]
|
#[pymethods]
|
||||||
impl PyIJTiffFile {
|
impl PyIJTiffFile {
|
||||||
#[new]
|
#[new]
|
||||||
fn new(path: &str, shape: (usize, usize, usize), dtype: &str) -> PyResult<Self> {
|
fn new(path: &str, shape: (usize, usize, usize)) -> PyResult<Self> {
|
||||||
Ok(PyIJTiffFile { ijtifffile: IJTiffFile::new(path, shape)? } )
|
Ok(PyIJTiffFile { ijtifffile: Some(IJTiffFile::new(path, shape)?) } )
|
||||||
}
|
}
|
||||||
|
|
||||||
fn with_colors(&mut self, colors: (u8, u8, u8)) -> Self {
|
fn with_colors(&mut self, colors: (u8, u8, u8)) -> Self {
|
||||||
@@ -140,19 +139,67 @@ impl PyIJTiffFile {
|
|||||||
todo!()
|
todo!()
|
||||||
}
|
}
|
||||||
|
|
||||||
fn append_extra_tag(&mut self, extra_tag: PyTag) {
|
fn append_extra_tag(&mut self, tag: PyTag) {
|
||||||
if let Some(extra_tags) = self.ijtifffile.extra_tags.as_mut() {
|
if let Some(ijtifffile) = self.ijtifffile.as_mut() {
|
||||||
extra_tags.push(extra_tag.tag);
|
if let Some(extra_tags) = ijtifffile.extra_tags.as_mut() {
|
||||||
|
extra_tags.push(tag.tag);
|
||||||
} else {
|
} else {
|
||||||
self.ijtifffile.extra_tags = Some(vec![extra_tag.tag]);
|
ijtifffile.extra_tags = Some(vec![tag.tag]);
|
||||||
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
fn extend_extra_tags(&mut self, tags: Vec<PyTag>) {
|
||||||
|
if let Some(ijtifffile) = self.ijtifffile.as_mut() {
|
||||||
|
if let Some(extra_tags) = ijtifffile.extra_tags.as_mut() {
|
||||||
|
extra_tags.extend(tags.into_iter().map(|x| x.tag));
|
||||||
|
} else {
|
||||||
|
ijtifffile.extra_tags = Some(tags.into_iter().map(|x| x.tag).collect());
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
fn close(&mut self) -> PyResult<()> {
|
||||||
|
self.ijtifffile.take();
|
||||||
|
Ok(())
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
macro_rules! impl_save {
|
||||||
|
($T:ty, $t:ident) => {
|
||||||
|
#[pymethods]
|
||||||
|
impl PyIJTiffFile {
|
||||||
|
fn $t(&mut self, frame: PyReadonlyArray2<$T>, c: usize, t: usize, z: usize,
|
||||||
|
extra_tags: Option<Vec<PyTag>>) -> PyResult<()> {
|
||||||
|
let extra_tags = if let Some(extra_tags) = extra_tags {
|
||||||
|
Some(extra_tags.into_iter().map(|x| x.tag).collect())
|
||||||
|
} else {
|
||||||
|
None
|
||||||
|
};
|
||||||
|
if let Some(ijtifffile) = self.ijtifffile.as_mut() {
|
||||||
|
ijtifffile.save(frame.to_owned_array(), c, t, z, extra_tags)?;
|
||||||
|
}
|
||||||
|
Ok(())
|
||||||
|
}
|
||||||
|
}
|
||||||
|
};
|
||||||
|
}
|
||||||
|
|
||||||
|
impl_save!(u8, save_u8);
|
||||||
|
impl_save!(u16, save_u16);
|
||||||
|
impl_save!(u32, save_u32);
|
||||||
|
impl_save!(u64, save_u64);
|
||||||
|
impl_save!(i8, save_i8);
|
||||||
|
impl_save!(i16, save_i16);
|
||||||
|
impl_save!(i32, save_i32);
|
||||||
|
impl_save!(i64, save_i64);
|
||||||
|
impl_save!(f32, save_f32);
|
||||||
|
impl_save!(f64, save_f64);
|
||||||
|
|
||||||
#[pymodule]
|
#[pymodule]
|
||||||
fn tiffwrite(m: &Bound<'_, PyModule>) -> PyResult<()> {
|
fn tiffwrite(m: &Bound<'_, PyModule>) -> PyResult<()> {
|
||||||
|
m.add_class::<PyTag>()?;
|
||||||
m.add_class::<PyIJTiffFile>()?;
|
m.add_class::<PyIJTiffFile>()?;
|
||||||
Ok(())
|
Ok(())
|
||||||
}
|
}
|
||||||
@@ -1,5 +1,92 @@
|
|||||||
|
from __future__ import annotations
|
||||||
|
|
||||||
|
import numpy as np
|
||||||
|
from typing import Any, Self, Sequence
|
||||||
|
from pathlib import Path
|
||||||
|
from numpy.typing import ArrayLike, DTypeLike
|
||||||
|
|
||||||
from . import tiffwrite as rs
|
from . import tiffwrite as rs
|
||||||
|
|
||||||
|
|
||||||
class IJTiffFile(rs.IJTiffFile):
|
__all__ = ['Tag', 'IJTiffFile', 'tiffwrite']
|
||||||
|
|
||||||
|
|
||||||
|
class IFD(dict):
|
||||||
pass
|
pass
|
||||||
|
|
||||||
|
|
||||||
|
class Tag(rs.Tag):
|
||||||
|
pass
|
||||||
|
|
||||||
|
|
||||||
|
class IJTiffFile(rs.IJTiffFile):
|
||||||
|
def __new__(cls, path: str | Path, shape: tuple[int, int, int], dtype: DTypeLike = 'uint16',
|
||||||
|
colors: Sequence[str] = None, colormap: str = None, pxsize: float = None,
|
||||||
|
deltaz: float = None, timeinterval: float = None, comment: str = None,
|
||||||
|
**extratags: Tag.Value | Tag) -> None:
|
||||||
|
new = super().__new__(cls, str(path), shape)
|
||||||
|
if colors is not None:
|
||||||
|
new = new.with_colors(colors)
|
||||||
|
if colormap is not None:
|
||||||
|
new = new.with_colormap(colormap)
|
||||||
|
if pxsize is not None:
|
||||||
|
new = new.with_pxsize(pxsize)
|
||||||
|
if deltaz is not None:
|
||||||
|
new = new.with_deltaz(deltaz)
|
||||||
|
if timeinterval is not None:
|
||||||
|
new = new.with_timeinterval(timeinterval)
|
||||||
|
if comment is not None:
|
||||||
|
new = new.with_comment(comment)
|
||||||
|
if extratags:
|
||||||
|
new = new.extend_extratags(extratags)
|
||||||
|
return new
|
||||||
|
|
||||||
|
def __init__(self, path: str | Path, shape: tuple[int, int, int], dtype: DTypeLike = 'uint16',
|
||||||
|
colors: Sequence[str] = None, colormap: str = None, pxsize: float = None,
|
||||||
|
deltaz: float = None, timeinterval: float = None, comment: str = None,
|
||||||
|
**extratags: Tag.Value | Tag) -> None:
|
||||||
|
self.path = Path(path)
|
||||||
|
self.dtype = np.dtype(dtype)
|
||||||
|
|
||||||
|
def __enter__(self) -> Self:
|
||||||
|
return self
|
||||||
|
|
||||||
|
def __exit__(self, exc_type, exc_val, exc_tb):
|
||||||
|
self.close()
|
||||||
|
|
||||||
|
def save(self, frame: ArrayLike, c: int, z: int, t: int) -> None:
|
||||||
|
frame = np.asarray(frame).astype(self.dtype)
|
||||||
|
match self.dtype:
|
||||||
|
case np.uint8:
|
||||||
|
self.save_u8(frame, c, z, t)
|
||||||
|
case np.uint16:
|
||||||
|
self.save_u16(frame, c, z, t)
|
||||||
|
case np.uint32:
|
||||||
|
self.save_u32(frame, c, z, t)
|
||||||
|
case np.uint64:
|
||||||
|
self.save_u64(frame, c, z, t)
|
||||||
|
case np.int8:
|
||||||
|
self.save_i8(frame, c, z, t)
|
||||||
|
case np.int16:
|
||||||
|
self.save_i16(frame, c, z, t)
|
||||||
|
case np.int32:
|
||||||
|
self.save_i32(frame, c, z, t)
|
||||||
|
case np.int64:
|
||||||
|
self.save_i64(frame, c, z, t)
|
||||||
|
case np.float32:
|
||||||
|
self.save_f32(frame, c, z, t)
|
||||||
|
case np.float64:
|
||||||
|
self.save_f64(frame, c, z, t)
|
||||||
|
case _:
|
||||||
|
raise TypeError(f'Cannot save type {self.dtype}')
|
||||||
|
|
||||||
|
|
||||||
|
def tiffwrite(file: str | Path, data: ArrayLike, axes: str = 'TZCXY', dtype: DTypeLike = None, bar: bool = False,
|
||||||
|
*args: Any, **kwargs: Any) -> None:
|
||||||
|
""" file: string; filename of the new tiff file
|
||||||
|
data: 2 to 5D numpy array
|
||||||
|
axes: string; order of dimensions in data, default: TZCXY for 5D, ZCXY for 4D, CXY for 3D, XY for 2D data
|
||||||
|
dtype: string; datatype to use when saving to tiff
|
||||||
|
bar: bool; whether to show a progress bar
|
||||||
|
other args: see IJTiffFile
|
||||||
|
"""
|
||||||
|
|||||||
Reference in New Issue
Block a user