rewrite in rust
This commit is contained in:
Wim Pomp
515
src/lib.rs
Normal file
515
src/lib.rs
Normal file
@@ -0,0 +1,515 @@
|
||||
use std::cmp::Ordering;
|
||||
use std::collections::HashMap;
|
||||
use std::fs::{File, OpenOptions};
|
||||
use std::io::{Read, Seek, SeekFrom, Write};
|
||||
use anyhow::Result;
|
||||
use fraction::Fraction;
|
||||
use num::{Complex, Zero};
|
||||
use num::complex::ComplexFloat;
|
||||
use ndarray::{s, Array2};
|
||||
use num::traits::ToBytes;
|
||||
use std::hash::{DefaultHasher, Hash, Hasher};
|
||||
use chrono::Utc;
|
||||
|
||||
|
||||
const TAG_SIZE: usize = 20;
|
||||
const OFFSET_SIZE: usize = 8;
|
||||
const OFFSET: u64 = 16;
|
||||
|
||||
|
||||
#[derive(Clone, Debug)]
|
||||
struct IFD {
|
||||
tags: Vec<Tag>
|
||||
}
|
||||
|
||||
impl IFD {
|
||||
pub fn new() -> Self {
|
||||
IFD { tags: Vec::new() }
|
||||
}
|
||||
|
||||
fn push_tag(&mut self, tag: Tag) {
|
||||
if !self.tags.contains(&tag) {
|
||||
self.tags.push(tag);
|
||||
}
|
||||
}
|
||||
|
||||
fn extend_tags(&mut self, tags: Vec<Tag>) {
|
||||
for tag in tags {
|
||||
self.push_tag(tag);
|
||||
}
|
||||
}
|
||||
|
||||
fn write(&mut self, ijtifffile: &mut IJTiffFile, where_to_write_offset: u64) -> Result<u64> {
|
||||
self.tags.sort();
|
||||
ijtifffile.file.seek(SeekFrom::End(0))?;
|
||||
if ijtifffile.file.stream_position()? % 2 == 1 {
|
||||
ijtifffile.file.write(&[0])?;
|
||||
}
|
||||
let offset = ijtifffile.file.stream_position()?;
|
||||
ijtifffile.file.write(&(self.tags.len() as u64).to_le_bytes())?;
|
||||
|
||||
for tag in self.tags.iter_mut() {
|
||||
tag.write_tag(ijtifffile)?;
|
||||
}
|
||||
let where_to_write_next_ifd_offset = ijtifffile.file.stream_position()?;
|
||||
ijtifffile.file.write(&vec![0u8; OFFSET_SIZE])?;
|
||||
for tag in self.tags.iter() {
|
||||
tag.write_data(ijtifffile)?;
|
||||
}
|
||||
ijtifffile.file.seek(SeekFrom::Start(where_to_write_offset))?;
|
||||
ijtifffile.file.write(&offset.to_le_bytes())?;
|
||||
Ok(where_to_write_next_ifd_offset)
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
#[derive(Clone, Debug, Eq)]
|
||||
pub struct Tag {
|
||||
code: u16,
|
||||
bytes: Vec<u8>,
|
||||
ttype: u16,
|
||||
offset: u64
|
||||
}
|
||||
|
||||
impl PartialOrd<Self> for Tag {
|
||||
fn partial_cmp(&self, other: &Self) -> Option<Ordering> {
|
||||
Some(self.cmp(other))
|
||||
}
|
||||
}
|
||||
|
||||
impl Ord for Tag {
|
||||
fn cmp(&self, other: &Self) -> Ordering {
|
||||
self.code.cmp(&other.code)
|
||||
}
|
||||
}
|
||||
|
||||
impl PartialEq for Tag {
|
||||
fn eq(&self, other: &Self) -> bool {
|
||||
self.code == other.code
|
||||
}
|
||||
}
|
||||
|
||||
impl Tag {
|
||||
pub fn new(code: u16, bytes: Vec<u8>, ttype: u16) -> Self {
|
||||
Tag { code, bytes, ttype, offset: 0 }
|
||||
}
|
||||
|
||||
pub fn byte(code: u16, byte: Vec<u8>) -> Self {
|
||||
Tag::new(code, byte, 1)
|
||||
}
|
||||
|
||||
pub fn ascii(code: u16, ascii: &str) -> Self {
|
||||
let mut bytes = ascii.as_bytes().to_vec();
|
||||
bytes.push(0);
|
||||
Tag::new(code, bytes, 2)
|
||||
}
|
||||
|
||||
pub fn short(code: u16, short: Vec<u16>) -> Self {
|
||||
Tag::new(code, short.into_iter().map(|x| x.to_le_bytes()).flatten().collect(), 3)
|
||||
}
|
||||
|
||||
pub fn long(code: u16, long: Vec<u32>) -> Self {
|
||||
Tag::new(code, long.into_iter().map(|x| x.to_le_bytes()).flatten().collect(), 4)
|
||||
}
|
||||
|
||||
pub fn rational(code: u16, rational: Vec<Fraction>) -> Self {
|
||||
Tag::new(code, rational.into_iter().map(|x|
|
||||
u32::try_from(*x.denom().unwrap()).unwrap().to_le_bytes().into_iter().chain(
|
||||
u32::try_from(*x.numer().unwrap()).unwrap().to_le_bytes()).collect::<Vec<_>>()
|
||||
).flatten().collect(), 5)
|
||||
}
|
||||
|
||||
pub fn sbyte(code: u16, sbyte: Vec<i8>) -> Self {
|
||||
Tag::new(code, sbyte.iter().map(|x| x.to_le_bytes()).flatten().collect(), 6)
|
||||
}
|
||||
|
||||
pub fn sshort(code: u16, sshort: Vec<i16>) -> Self {
|
||||
Tag::new(code, sshort.into_iter().map(|x| x.to_le_bytes()).flatten().collect(), 8)
|
||||
}
|
||||
|
||||
pub fn slong(code: u16, slong: Vec<i32>) -> Self {
|
||||
Tag::new(code, slong.into_iter().map(|x| x.to_le_bytes()).flatten().collect(), 9)
|
||||
}
|
||||
|
||||
pub fn srational(code: u16, srational: Vec<Fraction>) -> Self {
|
||||
Tag::new(code, srational.into_iter().map(|x|
|
||||
i32::try_from(*x.denom().unwrap()).unwrap().to_le_bytes().into_iter().chain(
|
||||
i32::try_from(*x.numer().unwrap()).unwrap().to_le_bytes()).collect::<Vec<_>>()
|
||||
).flatten().collect(), 10)
|
||||
}
|
||||
|
||||
pub fn float(code: u16, float: Vec<f32>) -> Self {
|
||||
Tag::new(code, float.into_iter().map(|x| x.to_le_bytes()).flatten().collect(), 11)
|
||||
}
|
||||
|
||||
pub fn double(code: u16, double: Vec<f64>) -> Self {
|
||||
Tag::new(code, double.into_iter().map(|x| x.to_le_bytes()).flatten().collect(), 12)
|
||||
}
|
||||
|
||||
pub fn ifd(code: u16, ifd: Vec<u32>) -> Self {
|
||||
Tag::new(code, ifd.into_iter().map(|x| x.to_le_bytes()).flatten().collect(), 13)
|
||||
}
|
||||
|
||||
pub fn unicode(code: u16, unicode: &str) -> Self {
|
||||
let mut bytes: Vec<u8> = unicode.encode_utf16().map(|x| x.to_le_bytes()).flatten().collect();
|
||||
bytes.push(0);
|
||||
Tag::new(code, bytes, 14)
|
||||
}
|
||||
|
||||
pub fn complex(code: u16, complex: Vec<Complex<f32>>) -> Self {
|
||||
Tag::new(code, complex.into_iter().map(|x|
|
||||
x.re().to_le_bytes().into_iter().chain(x.im().to_le_bytes()).collect::<Vec<_>>()
|
||||
).flatten().collect(), 15)
|
||||
}
|
||||
|
||||
pub fn long8(code: u16, long8: Vec<u64>) -> Self {
|
||||
Tag::new(code, long8.into_iter().map(|x| x.to_le_bytes()).flatten().collect(), 16)
|
||||
}
|
||||
|
||||
pub fn slong8(code: u16, slong8: Vec<i64>) -> Self {
|
||||
Tag::new(code, slong8.into_iter().map(|x| x.to_le_bytes()).flatten().collect(), 17)
|
||||
}
|
||||
|
||||
pub fn ifd8(code: u16, ifd8: Vec<u64>) -> Self {
|
||||
Tag::new(code, ifd8.into_iter().map(|x| x.to_le_bytes()).flatten().collect(), 18)
|
||||
}
|
||||
|
||||
pub fn count(&self) -> u64 {
|
||||
let c = match self.ttype {
|
||||
1 => self.bytes.len(), // BYTE
|
||||
2 => self.bytes.len(), // ASCII
|
||||
3 => self.bytes.len() / 2, // SHORT
|
||||
4 => self.bytes.len() / 4, // LONG
|
||||
5 => self.bytes.len() / 8, // RATIONAL
|
||||
6 => self.bytes.len(), // SBYTE
|
||||
7 => self.bytes.len(), // UNDEFINED
|
||||
8 => self.bytes.len() / 2, // SSHORT
|
||||
9 => self.bytes.len() / 4, // SLONG
|
||||
10 => self.bytes.len() / 8, // SRATIONAL
|
||||
11 => self.bytes.len() / 4, // FLOAT
|
||||
12 => self.bytes.len() / 8, // DOUBLE
|
||||
13 => self.bytes.len() / 4, // IFD
|
||||
14 => self.bytes.len() / 2, // UNICODE
|
||||
15 => self.bytes.len() / 8, // COMPLEX
|
||||
16 => self.bytes.len() / 8, // LONG8
|
||||
17 => self.bytes.len() / 8, // SLONG8
|
||||
18 => self.bytes.len() / 8, // IFD8
|
||||
_ => self.bytes.len(),
|
||||
};
|
||||
c as u64
|
||||
}
|
||||
|
||||
fn write_tag(&mut self, ijtifffile: &mut IJTiffFile) -> Result<()> {
|
||||
self.offset = ijtifffile.file.stream_position()?;
|
||||
ijtifffile.file.write(&self.code.to_le_bytes())?;
|
||||
ijtifffile.file.write(&self.ttype.to_le_bytes())?;
|
||||
ijtifffile.file.write(&self.count().to_le_bytes())?;
|
||||
if self.bytes.len() <= OFFSET_SIZE {
|
||||
ijtifffile.file.write(&self.bytes)?;
|
||||
for _ in self.bytes.len()..OFFSET_SIZE {
|
||||
ijtifffile.file.write(&[0])?;
|
||||
}
|
||||
} else {
|
||||
ijtifffile.file.write(&vec![0u8; OFFSET_SIZE])?;
|
||||
}
|
||||
Ok(())
|
||||
}
|
||||
|
||||
fn write_data(&self, ijtifffile: &mut IJTiffFile) -> Result<()> {
|
||||
if self.bytes.len() > OFFSET_SIZE {
|
||||
ijtifffile.file.seek(SeekFrom::End(0))?;
|
||||
let offset = ijtifffile.write(&self.bytes)?;
|
||||
ijtifffile.file.seek(SeekFrom::Start(
|
||||
self.offset + (TAG_SIZE - OFFSET_SIZE) as u64))?;
|
||||
ijtifffile.file.write(&offset.to_le_bytes())?;
|
||||
if ijtifffile.file.stream_position()? % 2 == 1 {
|
||||
ijtifffile.file.write(&[0u8])?;
|
||||
}
|
||||
}
|
||||
Ok(())
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
#[derive(Clone, Debug)]
|
||||
struct Frame {
|
||||
tilebyteoffsets: Vec<u64>,
|
||||
tilebytecounts: Vec<u64>,
|
||||
image_width: u32,
|
||||
image_length: u32,
|
||||
bits_per_sample: u16,
|
||||
compression: u16,
|
||||
tile_width: u16,
|
||||
tile_length: u16,
|
||||
extra_tags: Vec<Tag>
|
||||
}
|
||||
|
||||
impl Frame {
|
||||
fn new(
|
||||
tilebyteoffsets: Vec<u64>, tilebytecounts: Vec<u64>, image_width: u32,
|
||||
image_length: u32, bits_per_sample: u16, compression: u16, tile_width: u16, tile_length: u16
|
||||
) -> Self {
|
||||
Frame {
|
||||
tilebyteoffsets, tilebytecounts, image_width, image_length, bits_per_sample,
|
||||
compression, tile_width, tile_length, extra_tags: Vec::new()
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
#[derive(Debug)]
|
||||
pub struct IJTiffFile {
|
||||
file: File,
|
||||
frames: HashMap<(usize, u8), Frame>,
|
||||
hashes: HashMap<u64, u64>,
|
||||
pub shape: (usize, usize, usize),
|
||||
pub n_frames: usize,
|
||||
pub samples_per_pixel: u8,
|
||||
pub colormap: Option<Vec<u16>>,
|
||||
pub colors: Option<Vec<(u8, u8, u8)>>,
|
||||
pub comment: Option<String>,
|
||||
pub delta_z: Option<f64>,
|
||||
pub timeinterval: Option<f64>,
|
||||
pub extra_tags: Option<Vec<Tag>>
|
||||
}
|
||||
|
||||
impl Drop for IJTiffFile {
|
||||
fn drop(&mut self) {
|
||||
if let Err(e) = self.close() {
|
||||
println!("Error closing IJTiffFile: {:?}", e);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
impl IJTiffFile {
|
||||
pub fn new(path: &str, shape: (usize, usize, usize)) -> Result<Self> {
|
||||
let mut file = OpenOptions::new().create(true).truncate(true)
|
||||
.write(true).read(true).open(path)?;
|
||||
file.write(b"II")?;
|
||||
file.write(&43u16.to_le_bytes())?;
|
||||
file.write(&8u16.to_le_bytes())?;
|
||||
file.write(&0u16.to_le_bytes())?;
|
||||
file.write(&OFFSET.to_le_bytes())?;
|
||||
let colormap: Option<Vec<(u8, u8, u8)>> = None;
|
||||
let (spp, n_frames) = if let None = &colormap {
|
||||
(shape.0 as u8, shape.1 * shape.2)
|
||||
} else {
|
||||
(1, shape.0 * shape.1 * shape.2)
|
||||
};
|
||||
Ok(IJTiffFile { file, frames: HashMap::new(), hashes: HashMap::new(), shape, n_frames,
|
||||
samples_per_pixel: spp, colormap: None, colors: None, comment: None, delta_z: None,
|
||||
timeinterval: None, extra_tags: None } )
|
||||
}
|
||||
|
||||
pub fn description(&self) -> String {
|
||||
let mut desc: String = String::from("ImageJ=1.11a");
|
||||
if let (None, None) = (self.colormap.as_ref(), self.colors.as_ref()) {
|
||||
desc += &format!("\nimages={}", self.shape.0);
|
||||
desc += &format!("\nslices={}", self.shape.1);
|
||||
desc += &format!("\nframes={}", self.shape.2);
|
||||
} else {
|
||||
desc += &format!("\nimages={}", self.shape.0 * self.shape.1 * self.shape.2);
|
||||
desc += &format!("\nchannels={}", self.shape.0);
|
||||
desc += &format!("\nslices={}", self.shape.1);
|
||||
desc += &format!("\nframes={}", self.shape.2);
|
||||
};
|
||||
if self.shape.0 == 1 {
|
||||
desc += "\nmode=grayscale";
|
||||
} else {
|
||||
desc += "\nmode=composite";
|
||||
}
|
||||
desc += "\nhyperstack=true\nloop=false\nunit=micron";
|
||||
if let Some(delta_z) = self.delta_z {
|
||||
desc += &format!("\nspacing={}", delta_z);
|
||||
}
|
||||
if let Some(timeinterval) = self.timeinterval {
|
||||
desc += &format!("\ninterval={}", timeinterval);
|
||||
}
|
||||
if let Some(comment) = &self.comment {
|
||||
desc += &format!("\ncomment={}", comment);
|
||||
}
|
||||
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) {
|
||||
if let (None, None) = (self.colormap.as_ref(), self.colors.as_ref()) {
|
||||
(z + t * self.shape.1, c as u8)
|
||||
} else {
|
||||
(c + z * self.shape.0 + t * self.shape.0 * self.shape.1, 0)
|
||||
}
|
||||
}
|
||||
|
||||
pub fn hash<T: Hash>(value: &T) -> u64 {
|
||||
let mut hasher = DefaultHasher::new();
|
||||
value.hash(&mut hasher);
|
||||
hasher.finish()
|
||||
}
|
||||
|
||||
fn hash_check(&mut self, bytes: &Vec<u8>, offset: u64) -> Result<bool> {
|
||||
let current_offset = self.file.stream_position()?;
|
||||
self.file.seek(SeekFrom::Start(offset))?;
|
||||
let mut buffer = vec![0u8; bytes.len()];
|
||||
self.file.read_exact(&mut buffer)?;
|
||||
let same = bytes == &buffer;
|
||||
self.file.seek(SeekFrom::Start(current_offset))?;
|
||||
Ok(same)
|
||||
}
|
||||
|
||||
fn write(&mut self, bytes: &Vec<u8>) -> Result<u64> {
|
||||
let hash = IJTiffFile::hash(&bytes);
|
||||
if self.hashes.contains_key(&hash) && self.hash_check(&bytes, *self.hashes.get(&hash).unwrap())? {
|
||||
Ok(*self.hashes.get(&hash).unwrap())
|
||||
} else {
|
||||
if self.file.stream_position()? % 2 == 1 {
|
||||
self.file.write(&[0])?;
|
||||
}
|
||||
let offset = self.file.stream_position()?;
|
||||
self.hashes.insert(hash, offset);
|
||||
self.file.write(&bytes)?;
|
||||
Ok(offset)
|
||||
}
|
||||
}
|
||||
|
||||
fn compress_frame(&mut self, frame: Array2<u16>) -> Result<Frame> {
|
||||
let image_width = frame.shape()[0] as u32;
|
||||
let image_length = frame.shape()[1] as u32;
|
||||
let mut tilebyteoffsets = Vec::new();
|
||||
let mut tilebytecounts = Vec::new();
|
||||
let tiles = IJTiffFile::tile(frame.reversed_axes(), 64);
|
||||
for tile in tiles {
|
||||
let bytes: Vec<u8> = tile.into_flat().into_iter().map(
|
||||
|x| x.to_le_bytes()).into_iter().flatten().collect();
|
||||
tilebytecounts.push(bytes.len() as u64);
|
||||
tilebyteoffsets.push(self.write(&bytes)?);
|
||||
}
|
||||
|
||||
Ok(Frame::new(tilebyteoffsets, tilebytecounts, image_width, image_length,
|
||||
16, 1, 64, 64))
|
||||
}
|
||||
|
||||
fn tile<T: Clone + Zero>(frame: Array2<T>, size: usize) -> Vec<Array2<T>> {
|
||||
let shape = frame.shape();
|
||||
let mut tiles = Vec::new();
|
||||
let (n, m) = (shape[0] / size, shape[1] / size);
|
||||
for i in 0..n {
|
||||
for j in 0..m {
|
||||
tiles.push(frame.slice(
|
||||
s![i * size..(i + 1) * size, j * size..(j + 1) * size]).to_owned());
|
||||
}
|
||||
if shape[1] % size != 0 {
|
||||
let mut tile = Array2::<T>::zeros((size, size));
|
||||
tile.slice_mut(
|
||||
s![.., ..shape[1] - m * size]
|
||||
).assign(&frame.slice(s![i * size..(i + 1) * size, m * size..]));
|
||||
tiles.push(tile);
|
||||
}
|
||||
}
|
||||
if shape[0] % size != 0 {
|
||||
for j in 0..m {
|
||||
let mut tile = Array2::<T>::zeros((size, size));
|
||||
tile.slice_mut(
|
||||
s![..shape[0] - n * size, ..]
|
||||
).assign(&frame.slice(s![n * size.., j * size..(j + 1) * size]));
|
||||
tiles.push(tile);
|
||||
}
|
||||
if shape[1] % size != 0 {
|
||||
let mut tile = Array2::<T>::zeros((size, size));
|
||||
tile.slice_mut(
|
||||
s![..shape[0] - n * size, ..shape[1] - m * size]
|
||||
).assign(&frame.slice(s![n * size.., m * size..]));
|
||||
tiles.push(tile);
|
||||
}
|
||||
}
|
||||
tiles
|
||||
}
|
||||
|
||||
fn get_colormap(&self, colormap: &Vec<u16>) -> Result<Vec<u16>> {
|
||||
todo!();
|
||||
Ok(Vec::new())
|
||||
}
|
||||
|
||||
fn get_color(&self, colors: (u8, u8, u8)) -> Result<Vec<u16>> {
|
||||
todo!();
|
||||
Ok(Vec::new())
|
||||
}
|
||||
|
||||
pub fn close(&mut self) -> Result<()> {
|
||||
let mut where_to_write_next_ifd_offset = OFFSET - OFFSET_SIZE as u64;
|
||||
let mut warn = false;
|
||||
for frame_number in 0..self.n_frames {
|
||||
if let Some(frame) = self.frames.get(&(frame_number, 0)) {
|
||||
let mut tilebyteoffsets = Vec::new();
|
||||
let mut tilebytecounts = Vec::new();
|
||||
let mut frame_count = 0;
|
||||
for channel in 0..self.samples_per_pixel {
|
||||
if let Some(frame_n) = self.frames.get(&(frame_number, channel)) {
|
||||
tilebyteoffsets.extend(frame_n.tilebyteoffsets.iter());
|
||||
tilebytecounts.extend(frame_n.tilebytecounts.iter());
|
||||
frame_count += 1;
|
||||
} else {
|
||||
warn = true;
|
||||
}
|
||||
}
|
||||
let mut ifd = IFD::new();
|
||||
ifd.push_tag(Tag::long(256, vec![frame.image_width]));
|
||||
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(259, vec![1]));
|
||||
ifd.push_tag(Tag::ascii(270, &self.description()));
|
||||
ifd.push_tag(Tag::short(277, vec![frame_count as u16]));
|
||||
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, tilebyteoffsets));
|
||||
ifd.push_tag(Tag::long8(325, tilebytecounts));
|
||||
if frame_number == 0 {
|
||||
if let Some(colormap) = &self.colormap {
|
||||
ifd.push_tag(Tag::short(320, self.get_colormap(colormap)?));
|
||||
ifd.push_tag(Tag::short(262, vec![3])); // PhotometricInterpretation PHOTOMETRIC_PALETTE
|
||||
} else if let None = self.colors {
|
||||
ifd.push_tag(Tag::short(262, vec![1])); // PhotometricInterpretation PHOTOMETRIC_PALETTE
|
||||
}
|
||||
}
|
||||
if frame_number < self.samples_per_pixel as usize {
|
||||
if let Some(color) = &self.colors {
|
||||
ifd.push_tag(Tag::short(320, self.get_color(color[frame_number])?));
|
||||
ifd.push_tag(Tag::short(262, vec![3])); // PhotometricInterpretation PHOTOMETRIC_PALETTE
|
||||
}
|
||||
}
|
||||
if let (None, None) = (&self.colormap, &self.colors) {
|
||||
if self.shape.0 > 1 {
|
||||
ifd.push_tag(Tag::short(284, vec![2]))
|
||||
}
|
||||
}
|
||||
ifd.extend_tags(frame.extra_tags.to_owned());
|
||||
if let Some(extra_tags) = &self.extra_tags {
|
||||
ifd.extend_tags(extra_tags.to_owned());
|
||||
}
|
||||
ifd.push_tag(Tag::ascii(306, &format!("{}", Utc::now().format("%Y:%m:%d %H:%M:%S"))));
|
||||
where_to_write_next_ifd_offset = ifd.write(self, where_to_write_next_ifd_offset)?;
|
||||
} else {
|
||||
warn = true;
|
||||
}
|
||||
if warn {
|
||||
println!("Some frames were not added to the tif file, either you forgot them, \
|
||||
or an error occurred and the tif file was closed prematurely.")
|
||||
}
|
||||
}
|
||||
self.file.seek(SeekFrom::Start(where_to_write_next_ifd_offset))?;
|
||||
self.file.write(&0u64.to_le_bytes())?;
|
||||
Ok(())
|
||||
}
|
||||
}
|
||||
28
src/main.rs
Normal file
28
src/main.rs
Normal file
@@ -0,0 +1,28 @@
|
||||
#[cfg(not(feature = "nopython"))]
|
||||
mod py;
|
||||
mod lib;
|
||||
|
||||
use anyhow::Result;
|
||||
use ndarray::{s, Array2};
|
||||
use rayon::prelude::*;
|
||||
use crate::lib::IJTiffFile;
|
||||
|
||||
|
||||
fn main() -> Result<()> {
|
||||
println!("Hello World!");
|
||||
let mut f = IJTiffFile::new("foo.tif", (1, 2, 1))?;
|
||||
let mut arr = Array2::<u16>::zeros((100, 100));
|
||||
// for i in 0..arr.shape()[0] {
|
||||
// for j in 0..arr.shape()[1] {
|
||||
// arr[[i, j]] = i as u16;
|
||||
// }
|
||||
// }
|
||||
f.save(arr.to_owned(), 0, 0, 0, None)?;
|
||||
|
||||
// let mut arr = Array2::<u16>::zeros((100, 100));
|
||||
// arr.slice_mut(s![64.., ..64]).fill(1);
|
||||
// arr.slice_mut(s![..64, 64..]).fill(2);
|
||||
// arr.slice_mut(s![64.., 64..]).fill(3);
|
||||
f.save(arr.to_owned(), 0, 1,0, None)?;
|
||||
Ok(())
|
||||
}
|
||||
158
src/py.rs
Normal file
158
src/py.rs
Normal file
@@ -0,0 +1,158 @@
|
||||
use pyo3::prelude::*;
|
||||
use crate::lib::{IJTiffFile, Tag};
|
||||
use std::time::Duration;
|
||||
use pyo3::types::{PyInt, PyString};
|
||||
use fraction::Fraction;
|
||||
use num::Complex;
|
||||
|
||||
|
||||
#[pyclass(subclass)]
|
||||
#[pyo3(name = "Tag")]
|
||||
#[derive(Clone, Debug)]
|
||||
struct PyTag {
|
||||
tag: Tag
|
||||
}
|
||||
|
||||
#[pymethods]
|
||||
impl PyTag {
|
||||
#[staticmethod]
|
||||
fn byte(code: u16, byte: Vec<u8>) -> Self {
|
||||
PyTag { tag: Tag::byte(code, byte) }
|
||||
}
|
||||
|
||||
#[staticmethod]
|
||||
fn ascii(code: u16, ascii: &str) -> Self {
|
||||
PyTag { tag: Tag::ascii(code, ascii) }
|
||||
}
|
||||
|
||||
#[staticmethod]
|
||||
fn short(code: u16, short: Vec<u16>) -> Self {
|
||||
PyTag { tag: Tag::short(code, short) }
|
||||
}
|
||||
|
||||
#[staticmethod]
|
||||
fn long(code: u16, long: Vec<u32>) -> Self {
|
||||
PyTag { tag: Tag::long(code, long) }
|
||||
}
|
||||
|
||||
#[staticmethod]
|
||||
fn rational(code: u16, rational: Vec<f64>) -> Self {
|
||||
PyTag { tag: Tag::rational(code, rational.into_iter().map(|x| Fraction::from(x)).collect()) }
|
||||
}
|
||||
|
||||
#[staticmethod]
|
||||
fn sbyte(code: u16, sbyte: Vec<i8>) -> Self {
|
||||
PyTag { tag: Tag::sbyte(code, sbyte) }
|
||||
}
|
||||
|
||||
#[staticmethod]
|
||||
fn sshort(code: u16, sshort: Vec<i16>) -> Self {
|
||||
PyTag { tag: Tag::sshort(code, sshort) }
|
||||
}
|
||||
|
||||
#[staticmethod]
|
||||
fn slong(code: u16, slong: Vec<i32>) -> Self {
|
||||
PyTag { tag: Tag::slong(code, slong) }
|
||||
}
|
||||
|
||||
#[staticmethod]
|
||||
fn srational(code: u16, srational: Vec<f64>) -> Self {
|
||||
PyTag { tag: Tag::srational(code, srational.into_iter().map(|x| Fraction::from(x)).collect()) }
|
||||
}
|
||||
|
||||
#[staticmethod]
|
||||
fn float(code: u16, float: Vec<f32>) -> Self {
|
||||
PyTag { tag: Tag::float(code, float) }
|
||||
}
|
||||
|
||||
#[staticmethod]
|
||||
fn double(code: u16, double: Vec<f64>) -> Self {
|
||||
PyTag { tag: Tag::double(code, double) }
|
||||
}
|
||||
|
||||
#[staticmethod]
|
||||
fn ifd(code: u16, ifd: Vec<u32>) -> Self {
|
||||
PyTag { tag: Tag::ifd(code, ifd) }
|
||||
}
|
||||
|
||||
#[staticmethod]
|
||||
fn unicode(code: u16, unicode: &str) -> Self {
|
||||
PyTag { tag: Tag::unicode(code, unicode) }
|
||||
}
|
||||
|
||||
#[staticmethod]
|
||||
fn complex(code: u16, complex: Vec<(f32, f32)>) -> Self {
|
||||
PyTag { tag: Tag::complex(code, complex.into_iter().map(|(x, y)| Complex { re: x, im: y }).collect()) }
|
||||
}
|
||||
|
||||
#[staticmethod]
|
||||
fn long8(code: u16, long8: Vec<u64>) -> Self {
|
||||
PyTag { tag: Tag::long8(code, long8) }
|
||||
}
|
||||
|
||||
#[staticmethod]
|
||||
fn slong8(code: u16, slong8: Vec<i64>) -> Self {
|
||||
PyTag { tag: Tag::slong8(code, slong8) }
|
||||
}
|
||||
|
||||
#[staticmethod]
|
||||
fn ifd8(code: u16, ifd8: Vec<u64>) -> Self {
|
||||
PyTag { tag: Tag::ifd8(code, ifd8) }
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
#[pyclass(subclass)]
|
||||
#[pyo3(name = "IJTiffFile")]
|
||||
#[derive(Debug)]
|
||||
struct PyIJTiffFile {
|
||||
ijtifffile: IJTiffFile
|
||||
}
|
||||
|
||||
#[pymethods]
|
||||
impl PyIJTiffFile {
|
||||
#[new]
|
||||
fn new(path: &str, shape: (usize, usize, usize), dtype: &str) -> PyResult<Self> {
|
||||
Ok(PyIJTiffFile { ijtifffile: IJTiffFile::new(path, shape)? } )
|
||||
}
|
||||
|
||||
fn with_colors(&mut self, colors: (u8, u8, u8)) -> Self {
|
||||
todo!()
|
||||
}
|
||||
|
||||
fn with_colormap(&mut self, colormap: Vec<(u8, u8, u8)>) -> Self {
|
||||
todo!()
|
||||
}
|
||||
|
||||
fn with_px_size(&mut self, pxsize: f64) -> Self {
|
||||
todo!()
|
||||
}
|
||||
|
||||
fn with_delta_z(&mut self, delta_z: f64) -> Self {
|
||||
todo!()
|
||||
}
|
||||
|
||||
fn with_time_interval(&mut self, time_interval: f64) -> Self {
|
||||
todo!()
|
||||
}
|
||||
|
||||
fn with_comments(&mut self, comments: String) -> Self {
|
||||
todo!()
|
||||
}
|
||||
|
||||
fn append_extra_tag(&mut self, extra_tag: PyTag) {
|
||||
if let Some(extra_tags) = self.ijtifffile.extra_tags.as_mut() {
|
||||
extra_tags.push(extra_tag.tag);
|
||||
} else {
|
||||
self.ijtifffile.extra_tags = Some(vec![extra_tag.tag]);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
#[pymodule]
|
||||
fn tiffwrite(m: &Bound<'_, PyModule>) -> PyResult<()> {
|
||||
m.add_class::<PyIJTiffFile>()?;
|
||||
Ok(())
|
||||
}
|
||||
Reference in New Issue
Block a user