- start some color(map) support in python

- compress_frame function in python for backwards compatibility
- save all extra tags in a single hashmap
- construct tags from references
- store frames by c, z, t
- save px_size in tiff
- some getters and setters in py.rs

py/tiffwrite/__init__.py

@@ -4,7 +4,9 @@ from itertools import product
 from pathlib import Path
 from typing import Any, Sequence
 
+import colorcet
 import numpy as np
+from matplotlib import colors as mpl_colors
 from numpy.typing import ArrayLike, DTypeLike
 from tqdm.auto import tqdm
 
@@ -27,29 +29,29 @@ class Tag(rs.Tag):
 
 Strip = tuple[list[int], list[int]]
 CZT = tuple[int, int, int]
-FrameInfo = tuple[IFD, Strip, CZT]
+FrameInfo = tuple[np.ndarray, None, CZT]
 
 
 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) -> IJTiffFile:
+                **extratags: Tag) -> IJTiffFile:
         new = super().__new__(cls, str(path), shape)
         if colors is not None:
-            new = new.with_colors(colors)
+            new.colors = np.array([get_color(color) for color in colors])
         if colormap is not None:
-            new = new.with_colormap(colormap)
+            new.colormap = get_colormap(colormap)
         if pxsize is not None:
-            new = new.with_pxsize(pxsize)
+            new.px_size = float(pxsize)
         if deltaz is not None:
-            new = new.with_deltaz(deltaz)
+            new.delta_z = float(deltaz)
         if timeinterval is not None:
-            new = new.with_timeinterval(timeinterval)
+            new.time_interval = float(timeinterval)
         if comment is not None:
-            new = new.with_comment(comment)
+            new.comment = comment
-        if extratags:
+        for extra_tag in extratags:
-            new = new.extend_extratags(extratags)
+            new.append_extra_tag(extra_tag, None)
         return new
 
     def __init__(self, path: str | Path, shape: tuple[int, int, int], dtype: DTypeLike = 'uint16',  # noqa
@@ -66,30 +68,43 @@ class IJTiffFile(rs.IJTiffFile):
         self.close()
 
     def save(self, frame: ArrayLike, c: int, z: int, t: int) -> None:
-        frame = np.asarray(frame).astype(self.dtype)
+        for frame, _, (cn, zn, tn) in self.compress_frame(frame):
-        match self.dtype:
+            frame = np.asarray(frame).astype(self.dtype)
-            case np.uint8:
+            match self.dtype:
-                self.save_u8(frame, c, z, t)
+                case np.uint8:
-            case np.uint16:
+                    self.save_u8(frame, c + cn, z + zn, t + tn)
-                self.save_u16(frame, c, z, t)
+                case np.uint16:
-            case np.uint32:
+                    self.save_u16(frame, c + cn, z + zn, t + tn)
-                self.save_u32(frame, c, z, t)
+                case np.uint32:
-            case np.uint64:
+                    self.save_u32(frame, c + cn, z + zn, t + tn)
-                self.save_u64(frame, c, z, t)
+                case np.uint64:
-            case np.int8:
+                    self.save_u64(frame, c + cn, z + zn, t + tn)
-                self.save_i8(frame, c, z, t)
+                case np.int8:
-            case np.int16:
+                    self.save_i8(frame, c + cn, z + zn, t + tn)
-                self.save_i16(frame, c, z, t)
+                case np.int16:
-            case np.int32:
+                    self.save_i16(frame, c + cn, z + zn, t + tn)
-                self.save_i32(frame, c, z, t)
+                case np.int32:
-            case np.int64:
+                    self.save_i32(frame, c + cn, z + zn, t + tn)
-                self.save_i64(frame, c, z, t)
+                case np.int64:
-            case np.float32:
+                    self.save_i64(frame, c + cn, z + zn, t + tn)
-                self.save_f32(frame, c, z, t)
+                case np.float32:
-            case np.float64:
+                    self.save_f32(frame, c + cn, z + zn, t + tn)
-                self.save_f64(frame, c, z, t)
+                case np.float64:
-            case _:
+                    self.save_f64(frame, c + cn, z + zn, t + tn)
-                raise TypeError(f'Cannot save type {self.dtype}')
+                case _:
+                    raise TypeError(f'Cannot save type {self.dtype}')
+
+    def compress_frame(self, frame: ArrayLike) -> tuple[FrameInfo]:  # noqa
+        return (frame, None, (0, 0, 0)),
+
+def get_colormap(colormap: str) -> np.ndarray:
+    colormap = getattr(colorcet, colormap)
+    colormap[0] = '#ffffff'
+    colormap[-1] = '#000000'
+    return np.array([[int(''.join(i), 16) for i in zip(*[iter(s[1:])] * 2)] for s in colormap]).astype('uint8')
+
+def get_color(color: str) -> np.ndarray:
+    return np.array([int(''.join(i), 16) for i in zip(*[iter(mpl_colors.to_hex(color)[1:])] * 2)]).astype('uint8')
 
 
 def tiffwrite(file: str | Path, data: np.ndarray, axes: str = 'TZCXY', dtype: DTypeLike = None, bar: bool = False,

pyproject.toml

@@ -12,7 +12,7 @@ classifiers = [
     "Programming Language :: Python :: Implementation :: CPython",
     "Programming Language :: Python :: Implementation :: PyPy",
 ]
-dependencies = ["numpy", "tqdm"]
+dependencies = ["colorcet", "matplotlib", "numpy", "tqdm"]
 
 [project.optional-dependencies]
 test = ["pytest"]

src/lib.rs

@@ -1,31 +1,29 @@
 // #[cfg(not(feature = "nopython"))]
 mod py;
 
+use anyhow::Result;
+use chrono::Utc;
+use ndarray::{s, Array2};
+use num::traits::ToBytes;
+use num::{Complex, FromPrimitive, Rational32, Zero};
+use rayon::prelude::*;
 use std::cmp::Ordering;
 use std::collections::HashMap;
 use std::fs::{File, OpenOptions};
-use std::io::{Read, Seek, SeekFrom, Write};
-use anyhow::Result;
-use num::{Complex, Rational32, Zero};
-use ndarray::{s, Array2};
-use num::traits::ToBytes;
 use std::hash::{DefaultHasher, Hash, Hasher};
+use std::io::{Read, Seek, SeekFrom, Write};
 use std::thread;
 use std::thread::JoinHandle;
-use chrono::Utc;
 use zstd::stream::encode_all;
-use rayon::prelude::*;
-
 
 const TAG_SIZE: usize = 20;
 const OFFSET_SIZE: usize = 8;
 const OFFSET: u64 = 16;
 const COMPRESSION: u16 = 50000;
 
-
 #[derive(Clone, Debug)]
 struct IFD {
-    tags: Vec<Tag>
+    tags: Vec<Tag>,
 }
 
 impl IFD {
@@ -39,12 +37,6 @@ impl IFD {
         }
     }
 
-    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))?;
@@ -52,7 +44,9 @@ impl IFD {
             ijtifffile.file.write(&[0])?;
         }
         let offset = ijtifffile.file.stream_position()?;
-        ijtifffile.file.write(&(self.tags.len() as u64).to_le_bytes())?;
+        ijtifffile
+            .file
+            .write(&(self.tags.len() as u64).to_le_bytes())?;
 
         for tag in self.tags.iter_mut() {
             tag.write_tag(ijtifffile)?;
@@ -62,19 +56,20 @@ impl IFD {
         for tag in self.tags.iter() {
             tag.write_data(ijtifffile)?;
         }
-        ijtifffile.file.seek(SeekFrom::Start(where_to_write_offset))?;
+        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
+    offset: u64,
 }
 
 impl PartialOrd<Self> for Tag {
@@ -97,11 +92,16 @@ impl PartialEq for Tag {
 
 impl Tag {
     pub fn new(code: u16, bytes: Vec<u8>, ttype: u16) -> Self {
-        Tag { code, bytes, ttype, offset: 0 }
+        Tag {
+            code,
+            bytes,
+            ttype,
+            offset: 0,
+        }
     }
 
-    pub fn byte(code: u16, byte: Vec<u8>) -> Self {
+    pub fn byte(code: u16, byte: &Vec<u8>) -> Self {
-        Tag::new(code, byte, 1)
+        Tag::new(code, byte.to_owned(), 1)
     }
 
     pub fn ascii(code: u16, ascii: &str) -> Self {
@@ -110,96 +110,213 @@ impl Tag {
         Tag::new(code, bytes, 2)
     }
 
-    pub fn short(code: u16, short: Vec<u16>) -> Self {
+    pub fn short(code: u16, short: &Vec<u16>) -> Self {
-        Tag::new(code, short.into_iter().map(|x| x.to_le_bytes()).flatten().collect(), 3)
+        Tag::new(
+            code,
+            short
+                .into_iter()
+                .map(|x| x.to_le_bytes())
+                .flatten()
+                .collect(),
+            3,
+        )
     }
 
-    pub fn long(code: u16, long: Vec<u32>) -> Self {
+    pub fn long(code: u16, long: &Vec<u32>) -> Self {
-        Tag::new(code, long.into_iter().map(|x| x.to_le_bytes()).flatten().collect(), 4)
+        Tag::new(
+            code,
+            long.into_iter()
+                .map(|x| x.to_le_bytes())
+                .flatten()
+                .collect(),
+            4,
+        )
     }
 
-    pub fn rational(code: u16, rational: Vec<Rational32>) -> Self {
+    pub fn rational(code: u16, rational: &Vec<Rational32>) -> Self {
-        Tag::new(code, rational.into_iter().map(|x|
+        Tag::new(
-            u32::try_from(*x.denom()).unwrap().to_le_bytes().into_iter().chain(
+            code,
-                u32::try_from(*x.numer()).unwrap().to_le_bytes()).collect::<Vec<_>>()
+            rational
-        ).flatten().collect(), 5)
+                .into_iter()
+                .map(|x| {
+                    u32::try_from(*x.denom())
+                        .unwrap()
+                        .to_le_bytes()
+                        .into_iter()
+                        .chain(u32::try_from(*x.numer()).unwrap().to_le_bytes())
+                        .collect::<Vec<_>>()
+                })
+                .flatten()
+                .collect(),
+            5,
+        )
     }
 
-    pub fn sbyte(code: u16, sbyte: Vec<i8>) -> Self {
+    pub fn sbyte(code: u16, sbyte: &Vec<i8>) -> Self {
-        Tag::new(code, sbyte.iter().map(|x| x.to_le_bytes()).flatten().collect(), 6)
+        Tag::new(
+            code,
+            sbyte.iter().map(|x| x.to_le_bytes()).flatten().collect(),
+            6,
+        )
     }
 
-    pub fn sshort(code: u16, sshort: Vec<i16>) -> Self {
+    pub fn sshort(code: u16, sshort: &Vec<i16>) -> Self {
-        Tag::new(code, sshort.into_iter().map(|x| x.to_le_bytes()).flatten().collect(), 8)
+        Tag::new(
+            code,
+            sshort
+                .into_iter()
+                .map(|x| x.to_le_bytes())
+                .flatten()
+                .collect(),
+            8,
+        )
     }
 
-    pub fn slong(code: u16, slong: Vec<i32>) -> Self {
+    pub fn slong(code: u16, slong: &Vec<i32>) -> Self {
-        Tag::new(code, slong.into_iter().map(|x| x.to_le_bytes()).flatten().collect(), 9)
+        Tag::new(
+            code,
+            slong
+                .into_iter()
+                .map(|x| x.to_le_bytes())
+                .flatten()
+                .collect(),
+            9,
+        )
     }
 
-    pub fn srational(code: u16, srational: Vec<Rational32>) -> Self {
+    pub fn srational(code: u16, srational: &Vec<Rational32>) -> Self {
-        Tag::new(code, srational.into_iter().map(|x|
+        Tag::new(
-            i32::try_from(*x.denom()).unwrap().to_le_bytes().into_iter().chain(
+            code,
-                i32::try_from(*x.numer()).unwrap().to_le_bytes()).collect::<Vec<_>>()
+            srational
-        ).flatten().collect(), 10)
+                .into_iter()
+                .map(|x| {
+                    i32::try_from(*x.denom())
+                        .unwrap()
+                        .to_le_bytes()
+                        .into_iter()
+                        .chain(i32::try_from(*x.numer()).unwrap().to_le_bytes())
+                        .collect::<Vec<_>>()
+                })
+                .flatten()
+                .collect(),
+            10,
+        )
     }
 
-    pub fn float(code: u16, float: Vec<f32>) -> Self {
+    pub fn float(code: u16, float: &Vec<f32>) -> Self {
-        Tag::new(code, float.into_iter().map(|x| x.to_le_bytes()).flatten().collect(), 11)
+        Tag::new(
+            code,
+            float
+                .into_iter()
+                .map(|x| x.to_le_bytes())
+                .flatten()
+                .collect(),
+            11,
+        )
     }
 
-    pub fn double(code: u16, double: Vec<f64>) -> Self {
+    pub fn double(code: u16, double: &Vec<f64>) -> Self {
-        Tag::new(code, double.into_iter().map(|x| x.to_le_bytes()).flatten().collect(), 12)
+        Tag::new(
+            code,
+            double
+                .into_iter()
+                .map(|x| x.to_le_bytes())
+                .flatten()
+                .collect(),
+            12,
+        )
     }
 
-    pub fn ifd(code: u16, ifd: Vec<u32>) -> Self {
+    pub fn ifd(code: u16, ifd: &Vec<u32>) -> Self {
-        Tag::new(code, ifd.into_iter().map(|x| x.to_le_bytes()).flatten().collect(), 13)
+        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();
+        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 {
+    pub fn complex(code: u16, complex: &Vec<Complex<f32>>) -> Self {
-        Tag::new(code, complex.into_iter().map(|x|
+        Tag::new(
-            x.re.to_le_bytes().into_iter().chain(x.im.to_le_bytes()).collect::<Vec<_>>()
+            code,
-        ).flatten().collect(), 15)
+            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 {
+    pub fn long8(code: u16, long8: &Vec<u64>) -> Self {
-        Tag::new(code, long8.into_iter().map(|x| x.to_le_bytes()).flatten().collect(), 16)
+        Tag::new(
+            code,
+            long8
+                .into_iter()
+                .map(|x| x.to_le_bytes())
+                .flatten()
+                .collect(),
+            16,
+        )
     }
 
-    pub fn slong8(code: u16, slong8: Vec<i64>) -> Self {
+    pub fn slong8(code: u16, slong8: &Vec<i64>) -> Self {
-        Tag::new(code, slong8.into_iter().map(|x| x.to_le_bytes()).flatten().collect(), 17)
+        Tag::new(
+            code,
+            slong8
+                .into_iter()
+                .map(|x| x.to_le_bytes())
+                .flatten()
+                .collect(),
+            17,
+        )
     }
 
-    pub fn ifd8(code: u16, ifd8: Vec<u64>) -> Self {
+    pub fn ifd8(code: u16, ifd8: &Vec<u64>) -> Self {
-        Tag::new(code, ifd8.into_iter().map(|x| x.to_le_bytes()).flatten().collect(), 18)
+        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
+            1 => self.bytes.len(),      // BYTE
-            2 => self.bytes.len(),  // ASCII
+            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
+            6 => self.bytes.len(),      // SBYTE
-            7 => self.bytes.len(),  // UNDEFINED
+            7 => self.bytes.len(),      // UNDEFINED
             8 => self.bytes.len() / 2,  // SSHORT
             9 => self.bytes.len() / 4,  // SLONG
-            10 => self.bytes.len() / 8,  // SRATIONAL
+            10 => self.bytes.len() / 8, // SRATIONAL
-            11 => self.bytes.len() / 4,  // FLOAT
+            11 => self.bytes.len() / 4, // FLOAT
-            12 => self.bytes.len() / 8,  // DOUBLE
+            12 => self.bytes.len() / 8, // DOUBLE
-            13 => self.bytes.len() / 4,  // IFD
+            13 => self.bytes.len() / 4, // IFD
-            14 => self.bytes.len() / 2,  // UNICODE
+            14 => self.bytes.len() / 2, // UNICODE
-            15 => self.bytes.len() / 8,  // COMPLEX
+            15 => self.bytes.len() / 8, // COMPLEX
-            16 => self.bytes.len() / 8,  // LONG8
+            16 => self.bytes.len() / 8, // LONG8
-            17 => self.bytes.len() / 8,  // SLONG8
+            17 => self.bytes.len() / 8, // SLONG8
-            18 => self.bytes.len() / 8,  // IFD8
+            18 => self.bytes.len() / 8, // IFD8
             _ => self.bytes.len(),
         };
         c as u64
@@ -226,7 +343,8 @@ impl Tag {
             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))?;
+                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])?;
@@ -236,17 +354,16 @@ impl Tag {
     }
 }
 
-
+#[derive(Debug)]
 struct CompressedFrame {
     bytes: Vec<Vec<u8>>,
     image_width: u32,
     image_length: u32,
     tile_size: usize,
     bits_per_sample: u16,
-    sample_format: u16
+    sample_format: u16,
 }
 
-
 #[derive(Clone, Debug)]
 struct Frame {
     tileoffsets: Vec<u64>,
@@ -261,17 +378,28 @@ struct Frame {
 
 impl Frame {
     fn new(
-        tileoffsets: Vec<u64>, tilebytecounts: Vec<u64>, image_width: u32, image_length: u32,
+        tileoffsets: Vec<u64>,
-        bits_per_sample: u16, sample_format: u16, tile_width: u16, tile_length: u16
+        tilebytecounts: Vec<u64>,
+        image_width: u32,
+        image_length: u32,
+        bits_per_sample: u16,
+        sample_format: u16,
+        tile_width: u16,
+        tile_length: u16,
     ) -> Self {
         Frame {
-            tileoffsets, tilebytecounts, image_width, image_length, bits_per_sample,
+            tileoffsets,
-            sample_format, tile_width, tile_length
+            tilebytecounts,
+            image_width,
+            image_length,
+            bits_per_sample,
+            sample_format,
+            tile_width,
+            tile_length,
         }
     }
 }
 
-
 pub trait Bytes {
     const BITS_PER_SAMPLE: u16;
     const SAMPLE_FORMAT: u16;
@@ -279,7 +407,6 @@ pub trait Bytes {
     fn bytes(&self) -> Vec<u8>;
 }
 
-
 macro_rules! bytes_impl {
     ($T:ty, $bits_per_sample:expr, $sample_format:expr) => {
         impl Bytes for $T {
@@ -315,23 +442,26 @@ bytes_impl!(isize, 32, 2);
 bytes_impl!(f32, 32, 3);
 bytes_impl!(f64, 64, 3);
 
+#[derive(Clone, Debug)]
+pub enum Colors {
+    None,
+    Colors(Vec<Vec<u8>>),
+    Colormap(Vec<Vec<u8>>),
+}
 
 #[derive(Debug)]
 pub struct IJTiffFile {
     file: File,
-    frames: HashMap<(usize, u8), Frame>,
+    frames: HashMap<(usize, usize, usize), Frame>,
     hashes: HashMap<u64, u64>,
-    threads: HashMap<(usize, u8), JoinHandle<CompressedFrame>>,
+    threads: HashMap<(usize, usize, usize), JoinHandle<CompressedFrame>>,
     pub shape: (usize, usize, usize),
-    pub n_frames: usize,
+    pub colors: Colors,
-    pub samples_per_pixel: u8,
-    pub colormap: Option<Vec<u16>>,
-    pub colors: Option<Vec<(u8, u8, u8)>>,
     pub comment: Option<String>,
+    pub px_size: Option<f64>,
     pub delta_z: Option<f64>,
-    pub timeinterval: Option<f64>,
+    pub time_interval: Option<f64>,
-    pub extra_tags: Vec<Tag>,
+    pub extra_tags: HashMap<Option<(usize, usize, usize)>, Vec<Tag>>,
-    pub extra_tags_frame: HashMap<usize, Vec<Tag>>
 }
 
 impl Drop for IJTiffFile {
@@ -344,28 +474,35 @@ impl Drop for IJTiffFile {
 
 impl IJTiffFile {
     pub fn new(path: &str, shape: (usize, usize, usize)) -> Result<Self> {
-        let mut file = OpenOptions::new().create(true).truncate(true)
+        let mut file = OpenOptions::new()
-            .write(true).read(true).open(path)?;
+            .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;
+        Ok(IJTiffFile {
-        let (spp, n_frames) = if let None = &colormap {
+            file,
-            (shape.0 as u8, shape.1 * shape.2)
+            frames: HashMap::new(),
-        } else {
+            hashes: HashMap::new(),
-            (1, shape.0 * shape.1 * shape.2)
+            threads: HashMap::new(),
-        };
+            shape,
-        Ok(IJTiffFile { file, frames: HashMap::new(), hashes: HashMap::new(),
+            colors: Colors::None,
-            threads: HashMap::new(), shape, n_frames,
+            comment: None,
-            samples_per_pixel: spp, colormap: None, colors: None, comment: None, delta_z: None,
+            px_size: None,
-            timeinterval: None, extra_tags: Vec::new(), extra_tags_frame: HashMap::new() } )
+            delta_z: None,
+            time_interval: None,
+            extra_tags: HashMap::new(),
+        })
     }
 
     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()) {
+        if let Colors::None = self.colors {
             desc += &format!("\nimages={}", self.shape.0);
             desc += &format!("\nslices={}", self.shape.1);
             desc += &format!("\nframes={}", self.shape.2);
@@ -384,7 +521,7 @@ impl IJTiffFile {
         if let Some(delta_z) = self.delta_z {
             desc += &format!("\nspacing={}", delta_z);
         }
-        if let Some(timeinterval) = self.timeinterval {
+        if let Some(timeinterval) = self.time_interval {
             desc += &format!("\ninterval={}", timeinterval);
         }
         if let Some(comment) = &self.comment {
@@ -393,11 +530,27 @@ impl IJTiffFile {
         desc
     }
 
-    fn get_frame_number(&self, c: usize, z: usize, t: usize) -> (usize, u8) {
+    fn get_czt(&self, frame_number: usize, channel: u8) -> (usize, usize, usize) {
-        if let (None, None) = (self.colormap.as_ref(), self.colors.as_ref()) {
+        if let Colors::None = self.colors {
-            (z + t * self.shape.1, c as u8)
+            (
+                channel as usize,
+                frame_number % self.shape.1,
+                frame_number / self.shape.1,
+            )
         } else {
-            (c + z * self.shape.0 + t * self.shape.0 * self.shape.1, 0)
+            (
+                frame_number % self.shape.0,
+                frame_number / self.shape.0 % self.shape.1,
+                frame_number / self.shape.0 / self.shape.1,
+            )
+        }
+    }
+
+    fn spp_and_n_frames(&self) -> (u8, usize) {
+        if let Colors::None = &self.colors {
+            (self.shape.0 as u8, self.shape.1 * self.shape.2)
+        } else {
+            (1, self.shape.0 * self.shape.1 * self.shape.2)
         }
     }
 
@@ -419,7 +572,9 @@ impl IJTiffFile {
 
     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())? {
+        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 {
@@ -432,64 +587,88 @@ impl IJTiffFile {
         }
     }
 
-    pub fn save<T>(&mut self, frame: Array2<T>, c: usize, z: usize, t: usize,
+    pub fn save<T>(&mut self, frame: Array2<T>, c: usize, z: usize, t: usize) -> Result<()>
-                   extra_tags: Option<Vec<Tag>>) -> Result<()>
+    where
-    where T: Bytes + Clone + Send + Sync + Zero + 'static {
+        T: Bytes + Clone + Send + Sync + Zero + 'static,
-        let key = self.get_frame_number(c, z, t);
+    {
-        if let Some(extra_tags) = extra_tags {
+        self.compress_frame(frame.reversed_axes(), c, z, t)?;
-            if let Some(extra_tags_frame) = self.extra_tags_frame.get_mut(&key.0) {
-                extra_tags_frame.extend(extra_tags);
-            } else {
-                self.extra_tags_frame.insert(key.0, extra_tags);
-            }
-        }
-        self.compress_frame(frame.reversed_axes(), key)?;
         Ok(())
     }
 
-    fn compress_frame<T>(&mut self, frame: Array2<T>, key: (usize, u8)) -> Result<()>
+    fn compress_frame<T>(&mut self, frame: Array2<T>, c: usize, z: usize, t: usize) -> Result<()>
-    where T: Bytes + Clone + Zero + Send + 'static {
+    where
+        T: Bytes + Clone + Zero + Send + 'static,
+    {
         fn compress<T>(frame: Array2<T>) -> CompressedFrame
-        where T: Bytes + Clone + Zero {
+        where
+            T: Bytes + Clone + Zero,
+        {
             let image_width = frame.shape()[0] as u32;
             let image_length = frame.shape()[1] as u32;
-            let tile_size = 2usize.pow(((image_width as f64 * image_length as f64 / 64f64
+            let tile_size = 2usize
-                ).log2() / 2f64).round() as u32).max(16).min(1024);
+                .pow(
+                    ((image_width as f64 * image_length as f64 / 64f64).log2() / 2f64).round()
+                        as u32,
+                )
+                .max(16)
+                .min(1024);
             let tiles = IJTiffFile::tile(frame.reversed_axes(), tile_size);
-            let byte_tiles: Vec<Vec<u8>> = tiles.into_iter().map(
+            let byte_tiles: Vec<Vec<u8>> = tiles
-                |tile| tile.map(|x| x.bytes()).into_iter().flatten().collect()
+                .into_iter()
-            ).collect();
+                .map(|tile| tile.map(|x| x.bytes()).into_iter().flatten().collect())
-            let bytes = byte_tiles.into_par_iter().map(|x| encode_all(&*x, 3).unwrap()).collect::<Vec<_>>();
+                .collect();
-            CompressedFrame { bytes, image_width, image_length, tile_size,
+            let bytes = byte_tiles
-                bits_per_sample: T::BITS_PER_SAMPLE, sample_format: T::SAMPLE_FORMAT }
+                .into_par_iter()
-        }
+                .map(|x| encode_all(&*x, 3).unwrap())
-        self.threads.insert(key, thread::spawn(move || compress(frame)));
+                .collect::<Vec<_>>();
-        for key in self.threads.keys().cloned().collect::<Vec<(usize, u8)>>() {
+            CompressedFrame {
-            if self.threads[&key].is_finished() {
+                bytes,
-
+                image_width,
+                image_length,
+                tile_size,
+                bits_per_sample: T::BITS_PER_SAMPLE,
+                sample_format: T::SAMPLE_FORMAT,
             }
         }
+        self.threads
+            .insert((c, z, t), thread::spawn(move || compress(frame)));
+        for key in self
+            .threads
+            .keys()
+            .cloned()
+            .collect::<Vec<(usize, usize, usize)>>()
+        {
+            if self.threads[&key].is_finished() {}
+        }
 
-        for key in self.threads.keys().cloned().collect::<Vec<(usize, u8)>>() {
+        for (c, z, t) in self.threads.keys().cloned().collect::<Vec<_>>() {
-            if self.threads[&key].is_finished() {
+            if self.threads[&(c, z, t)].is_finished() {
-                if let Some(thread) = self.threads.remove(&key) {
+                if let Some(thread) = self.threads.remove(&(c, z, t)) {
-                    self.write_frame(thread.join().unwrap(), key)?;
+                    self.write_frame(thread.join().unwrap(), c, z, t)?;
                 }
             }
         }
-    Ok(())
+        Ok(())
     }
 
-    fn write_frame(&mut self, frame: CompressedFrame, key: (usize, u8)) -> Result<()> {
+    fn write_frame(&mut self, frame: CompressedFrame, c: usize, z: usize, t: usize) -> Result<()> {
         let mut tileoffsets = Vec::new();
         let mut tilebytecounts = Vec::new();
         for tile in frame.bytes {
             tilebytecounts.push(tile.len() as u64);
             tileoffsets.push(self.write(&tile)?);
         }
-        let frame = Frame::new(tileoffsets, tilebytecounts, frame.image_width, frame.image_length,
+        let frame = Frame::new(
-                               frame.bits_per_sample, frame.sample_format, frame.tile_size as u16, frame.tile_size as u16);
+            tileoffsets,
-        self.frames.insert(key, frame);
+            tilebytecounts,
+            frame.image_width,
+            frame.image_length,
+            frame.bits_per_sample,
+            frame.sample_format,
+            frame.tile_size as u16,
+            frame.tile_size as u16,
+        );
+        self.frames.insert((c, z, t), frame);
         Ok(())
     }
 
@@ -499,59 +678,74 @@ impl IJTiffFile {
         let (n, m) = (shape[0] / size, shape[1] / size);
         for i in 0..n {
             for j in 0..m {
-                tiles.push(frame.slice(
+                tiles.push(
-                    s![i * size..(i + 1) * size, j * size..(j + 1) * size]).to_owned());
+                    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(
+                tile.slice_mut(s![.., ..shape[1] - m * size])
-                    s![.., ..shape[1] - m * size]
+                    .assign(&frame.slice(s![i * size..(i + 1) * size, 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(
+                tile.slice_mut(s![..shape[0] - n * size, ..])
-                    s![..shape[0] - n * size, ..]
+                    .assign(&frame.slice(s![n * size.., j * size..(j + 1) * 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(
+                tile.slice_mut(s![..shape[0] - n * size, ..shape[1] - m * size])
-                    s![..shape[0] - n * size, ..shape[1] - m * size]
+                    .assign(&frame.slice(s![n * size.., m * size..]));
-                ).assign(&frame.slice(s![n * size.., m * size..]));
                 tiles.push(tile);
             }
         }
         tiles
     }
 
-    fn get_colormap(&self, _colormap: &Vec<u16>) -> Result<Vec<u16>> {
+    fn get_colormap(&self, colormap: &Vec<Vec<u8>>, bits_per_sample: u16) -> Vec<u16> {
-        todo!();
+        if bits_per_sample == 8 {
+            colormap
+                .iter()
+                .flatten()
+                .map(|x| (*x as u16) * 256)
+                .collect()
+        } else {
+            colormap
+                .iter()
+                .map(|x| vec![x; 256])
+                .flatten()
+                .flatten()
+                .map(|x| (*x as u16) * 256)
+                .collect()
+        }
     }
 
-    fn get_color(&self, _colors: (u8, u8, u8)) -> Result<Vec<u16>> {
+    fn get_color(&self, _colors: &Vec<u8>, _bits_per_sample: u16) -> Result<Vec<u16>> {
         todo!();
     }
 
     fn close(&mut self) -> Result<()> {
-        for key in self.threads.keys().cloned().collect::<Vec<(usize, u8)>>() {
+        for (c, z, t) in self.threads.keys().cloned().collect::<Vec<_>>() {
-            if let Some(thread) = self.threads.remove(&key) {
+            if let Some(thread) = self.threads.remove(&(c, z, t)) {
-                self.write_frame(thread.join().unwrap(), key)?;
+                self.write_frame(thread.join().unwrap(), c, z, t)?;
             }
         }
         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 {
+        let (samples_per_pixel, n_frames) = self.spp_and_n_frames();
-            if let Some(frame) = self.frames.get(&(frame_number, 0)) {
+        for frame_number in 0..n_frames {
+            if let Some(frame) = self.frames.get(&self.get_czt(frame_number, 0)) {
                 let mut tileoffsets = Vec::new();
                 let mut tilebytecounts = Vec::new();
                 let mut frame_count = 0;
-                for channel in 0..self.samples_per_pixel {
+                for channel in 0..samples_per_pixel {
-                    if let Some(frame_n) = self.frames.get(&(frame_number, channel)) {
+                    if let Some(frame_n) = self.frames.get(&self.get_czt(frame_number, channel)) {
                         tileoffsets.extend(frame_n.tileoffsets.iter());
                         tilebytecounts.extend(frame_n.tilebytecounts.iter());
                         frame_count += 1;
@@ -560,52 +754,80 @@ impl IJTiffFile {
                     }
                 }
                 let mut ifd = IFD::new();
-                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![COMPRESSION]));
+                ifd.push_tag(Tag::short(259, &vec![COMPRESSION]));
                 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::short(322, vec![frame.tile_width]));
+                ifd.push_tag(Tag::short(322, &vec![frame.tile_width]));
-                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, tileoffsets));
+                ifd.push_tag(Tag::long8(324, &tileoffsets));
-                ifd.push_tag(Tag::long8(325, tilebytecounts));
+                ifd.push_tag(Tag::long8(325, &tilebytecounts));
-                ifd.push_tag(Tag::short(339, vec![frame.sample_format]));
+                ifd.push_tag(Tag::short(339, &vec![frame.sample_format]));
+                if let Some(px_size) = self.px_size {
+                    let r = vec![Rational32::from_f64(px_size).unwrap()];
+                    ifd.push_tag(Tag::rational(282, &r));
+                    ifd.push_tag(Tag::rational(283, &r));
+                    ifd.push_tag(Tag::short(296, &vec![1]));
+                }
+
                 if frame_number == 0 {
-                    if let Some(colormap) = &self.colormap {
+                    if let Colors::Colormap(colormap) = &self.colors {
-                        ifd.push_tag(Tag::short(320, self.get_colormap(colormap)?));
+                        ifd.push_tag(Tag::short(
-                        ifd.push_tag(Tag::short(262, vec![3]));  // PhotometricInterpretation PHOTOMETRIC_PALETTE
+                            320,
-                    } else if let None = self.colors {
+                            &self.get_colormap(colormap, frame.bits_per_sample),
-                        ifd.push_tag(Tag::short(262, vec![1]));  // PhotometricInterpretation PHOTOMETRIC_PALETTE
+                        ));
+                        ifd.push_tag(Tag::short(262, &vec![3]));
+                    } else if let Colors::None = self.colors {
+                        ifd.push_tag(Tag::short(262, &vec![1]));
                     }
                 }
-                if frame_number < self.samples_per_pixel as usize {
+                if frame_number < samples_per_pixel as usize {
-                    if let Some(color) = &self.colors {
+                    if let Colors::Colors(colors) = &self.colors {
-                        ifd.push_tag(Tag::short(320, self.get_color(color[frame_number])?));
+                        ifd.push_tag(Tag::short(
-                        ifd.push_tag(Tag::short(262, vec![3]));  // PhotometricInterpretation PHOTOMETRIC_PALETTE
+                            320,
+                            &self.get_color(&colors[frame_number], frame.bits_per_sample)?,
+                        ));
+                        ifd.push_tag(Tag::short(262, &vec![3]));
                     }
                 }
-                if let (None, None) = (&self.colormap, &self.colors) {
+                if let Colors::None = &self.colors {
                     if self.shape.0 > 1 {
-                        ifd.push_tag(Tag::short(284, vec![2]))
+                        ifd.push_tag(Tag::short(284, &vec![2]))
                     }
                 }
-                if self.extra_tags_frame.contains_key(&frame_number) {
+                for channel in 0..samples_per_pixel {
-                    ifd.extend_tags(self.extra_tags_frame[&frame_number].to_owned());
+                    let czt = self.get_czt(frame_number, channel);
+                    if let Some(extra_tags) = self.extra_tags.get(&Some(czt)) {
+                        for tag in extra_tags {
+                            ifd.push_tag(tag.to_owned())
+                        }
+                    }
                 }
-                ifd.extend_tags(self.extra_tags.to_owned());
+                if let Some(extra_tags) = self.extra_tags.get(&None) {
-                ifd.push_tag(Tag::ascii(306, &format!("{}", Utc::now().format("%Y:%m:%d %H:%M:%S"))));
+                    for tag in extra_tags {
+                        ifd.push_tag(tag.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, \
+                println!(
-                    or an error occurred and the tif file was closed prematurely.")
+                    "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
+            .seek(SeekFrom::Start(where_to_write_next_ifd_offset))?;
         self.file.write(&0u64.to_le_bytes())?;
         Ok(())
     }

src/main.rs

@@ -2,7 +2,6 @@ use anyhow::Result;
 use ndarray::{s, Array2};
 use tiffwrite::IJTiffFile;
 
-
 fn main() -> Result<()> {
     println!("Hello World!");
     let mut f = IJTiffFile::new("foo.tif", (2, 1, 1))?;
@@ -12,12 +11,12 @@ fn main() -> Result<()> {
             arr[[i, j]] = i as u16;
         }
     }
-    f.save(arr.to_owned(), 0, 0, 0, None)?;
+    f.save(arr.to_owned(), 0, 0, 0)?;
 
     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(), 1, 0,0, None)?;
+    f.save(arr.to_owned(), 1, 0, 0)?;
     Ok(())
 }

src/py.rs

@@ -1,101 +1,153 @@
+use crate::{Colors, IJTiffFile, Tag};
+use ndarray::s;
+use num::{Complex, FromPrimitive, Rational32};
+use numpy::{PyArrayMethods, PyReadonlyArray2};
 use pyo3::prelude::*;
-use crate::{IJTiffFile, Tag};
-use num::{Complex, Rational32, FromPrimitive};
-use numpy::{PyReadonlyArray2, PyArrayMethods};
-
 
 #[pyclass(subclass)]
 #[pyo3(name = "Tag")]
 #[derive(Clone, Debug)]
 struct PyTag {
-    tag: Tag
+    tag: Tag,
 }
 
 #[pymethods]
 impl PyTag {
     #[staticmethod]
     fn byte(code: u16, byte: Vec<u8>) -> Self {
-        PyTag { tag: Tag::byte(code, byte) }
+        PyTag {
+            tag: Tag::byte(code, &byte),
+        }
     }
 
     #[staticmethod]
     fn ascii(code: u16, ascii: &str) -> Self {
-        PyTag { tag: Tag::ascii(code, ascii) }
+        PyTag {
+            tag: Tag::ascii(code, ascii),
+        }
     }
 
     #[staticmethod]
     fn short(code: u16, short: Vec<u16>) -> Self {
-        PyTag { tag: Tag::short(code, short) }
+        PyTag {
+            tag: Tag::short(code, &short),
+        }
     }
 
     #[staticmethod]
     fn long(code: u16, long: Vec<u32>) -> Self {
-        PyTag { tag: Tag::long(code, long) }
+        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| Rational32::from_f64(x).unwrap()).collect()) }
+        PyTag {
+            tag: Tag::rational(
+                code,
+                &rational
+                    .into_iter()
+                    .map(|x| Rational32::from_f64(x).unwrap())
+                    .collect(),
+            ),
+        }
     }
 
     #[staticmethod]
     fn sbyte(code: u16, sbyte: Vec<i8>) -> Self {
-        PyTag { tag: Tag::sbyte(code, sbyte) }
+        PyTag {
+            tag: Tag::sbyte(code, &sbyte),
+        }
     }
 
     #[staticmethod]
     fn sshort(code: u16, sshort: Vec<i16>) -> Self {
-        PyTag { tag: Tag::sshort(code, sshort) }
+        PyTag {
+            tag: Tag::sshort(code, &sshort),
+        }
     }
 
     #[staticmethod]
     fn slong(code: u16, slong: Vec<i32>) -> Self {
-        PyTag { tag: Tag::slong(code, slong) }
+        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| Rational32::from_f64(x).unwrap()).collect()) }
+        PyTag {
+            tag: Tag::srational(
+                code,
+                &srational
+                    .into_iter()
+                    .map(|x| Rational32::from_f64(x).unwrap())
+                    .collect(),
+            ),
+        }
     }
 
     #[staticmethod]
     fn float(code: u16, float: Vec<f32>) -> Self {
-        PyTag { tag: Tag::float(code, float) }
+        PyTag {
+            tag: Tag::float(code, &float),
+        }
     }
 
     #[staticmethod]
     fn double(code: u16, double: Vec<f64>) -> Self {
-        PyTag { tag: Tag::double(code, double) }
+        PyTag {
+            tag: Tag::double(code, &double),
+        }
     }
 
     #[staticmethod]
     fn ifd(code: u16, ifd: Vec<u32>) -> Self {
-        PyTag { tag: Tag::ifd(code, ifd) }
+        PyTag {
+            tag: Tag::ifd(code, &ifd),
+        }
     }
 
     #[staticmethod]
     fn unicode(code: u16, unicode: &str) -> Self {
-        PyTag { tag: Tag::unicode(code, unicode) }
+        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()) }
+        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) }
+        PyTag {
+            tag: Tag::long8(code, &long8),
+        }
     }
 
     #[staticmethod]
     fn slong8(code: u16, slong8: Vec<i64>) -> Self {
-        PyTag { tag: Tag::slong8(code, slong8) }
+        PyTag {
+            tag: Tag::slong8(code, &slong8),
+        }
     }
 
     #[staticmethod]
     fn ifd8(code: u16, ifd8: Vec<u64>) -> Self {
-        PyTag { tag: Tag::ifd8(code, ifd8) }
+        PyTag {
+            tag: Tag::ifd8(code, &ifd8),
+        }
     }
 
     fn count(&self) -> u64 {
@@ -103,55 +155,157 @@ impl PyTag {
     }
 }
 
-
 #[pyclass(subclass)]
 #[pyo3(name = "IJTiffFile")]
 #[derive(Debug)]
 struct PyIJTiffFile {
-    ijtifffile: Option<IJTiffFile>
+    ijtifffile: Option<IJTiffFile>,
 }
 
 #[pymethods]
 impl PyIJTiffFile {
     #[new]
     fn new(path: &str, shape: (usize, usize, usize)) -> PyResult<Self> {
-        Ok(PyIJTiffFile { ijtifffile: Some(IJTiffFile::new(path, shape)?) } )
+        Ok(PyIJTiffFile {
+            ijtifffile: Some(IJTiffFile::new(path, shape)?),
+        })
     }
 
-    fn with_colors(&mut self, colors: (u8, u8, u8)) -> Self {
+    #[getter]
-        todo!()
+    fn get_colors(&self) -> PyResult<Option<Vec<Vec<u8>>>> {
+        if let Some(ijtifffile) = &self.ijtifffile {
+            if let Colors::Colors(colors) = &ijtifffile.colors {
+                return Ok(Some(colors.to_owned()));
+            }
+        }
+        Ok(None)
     }
 
-    fn with_colormap(&mut self, colormap: Vec<(u8, u8, u8)>) -> Self {
+    #[setter]
-        todo!()
+    fn set_colors(&mut self, colors: PyReadonlyArray2<u8>) -> PyResult<()> {
+        if let Some(ijtifffile) = &mut self.ijtifffile {
+            let a = colors.to_owned_array();
+            ijtifffile.colors = Colors::Colors(
+                (0..a.shape()[0])
+                    .map(|i| Vec::from(a.slice(s![i, ..]).as_slice().unwrap()))
+                    .collect(),
+            );
+        }
+        Ok(())
     }
 
-    fn with_px_size(&mut self, pxsize: f64) -> Self {
+    #[getter]
-        todo!()
+    fn get_colormap(&mut self) -> PyResult<Option<Vec<Vec<u8>>>> {
+        if let Some(ijtifffile) = &self.ijtifffile {
+            if let Colors::Colormap(colormap) = &ijtifffile.colors {
+                return Ok(Some(colormap.to_owned()));
+            }
+        }
+        Ok(None)
     }
 
-    fn with_delta_z(&mut self, delta_z: f64) -> Self {
+    #[setter]
-        todo!()
+    fn set_colormap(&mut self, colormap: PyReadonlyArray2<u8>) -> PyResult<()> {
+        if let Some(ijtifffile) = &mut self.ijtifffile {
+            let a = colormap.to_owned_array();
+            ijtifffile.colors = Colors::Colormap(
+                (0..a.shape()[0])
+                    .map(|i| Vec::from(a.slice(s![i, ..]).as_slice().unwrap()))
+                    .collect(),
+            );
+        }
+        Ok(())
     }
 
-    fn with_time_interval(&mut self, time_interval: f64) -> Self {
+    #[getter]
-        todo!()
+    fn get_px_size(&self) -> PyResult<Option<f64>> {
-    }
+        if let Some(ijtifffile) = &self.ijtifffile {
-
+            Ok(ijtifffile.px_size)
-    fn with_comments(&mut self, comments: String) -> Self {
+        } else {
-        todo!()
+            Ok(None)
-    }
-
-    fn append_extra_tag(&mut self, tag: PyTag) {
-        if let Some(ijtifffile) = self.ijtifffile.as_mut() {
-            ijtifffile.extra_tags.push(tag.tag);
         }
     }
 
-    fn extend_extra_tags(&mut self, tags: Vec<PyTag>) {
+    #[setter]
-        if let Some(ijtifffile) = self.ijtifffile.as_mut() {
+    fn set_px_size(&mut self, px_size: f64) -> PyResult<()> {
-            ijtifffile.extra_tags.extend(tags.into_iter().map(|x| x.tag));
+        if let Some(ijtifffile) = &mut self.ijtifffile {
+            ijtifffile.px_size = Some(px_size);
         }
+        Ok(())
+    }
+
+    #[getter]
+    fn get_delta_z(&self) -> PyResult<Option<f64>> {
+        if let Some(ijtifffile) = &self.ijtifffile {
+            Ok(ijtifffile.delta_z)
+        } else {
+            Ok(None)
+        }
+    }
+
+    #[setter]
+    fn set_delta_z(&mut self, delta_z: f64) -> PyResult<()> {
+        if let Some(ijtifffile) = &mut self.ijtifffile {
+            ijtifffile.delta_z = Some(delta_z);
+        }
+        Ok(())
+    }
+
+    #[getter]
+    fn get_time_interval(&self) -> PyResult<Option<f64>> {
+        if let Some(ijtifffile) = &self.ijtifffile {
+            Ok(ijtifffile.time_interval)
+        } else {
+            Ok(None)
+        }
+    }
+
+    #[setter]
+    fn set_time_interval(&mut self, time_interval: f64) -> PyResult<()> {
+        if let Some(ijtifffile) = &mut self.ijtifffile {
+            ijtifffile.time_interval = Some(time_interval);
+        }
+        Ok(())
+    }
+
+    #[getter]
+    fn get_comment(&self) -> PyResult<Option<String>> {
+        if let Some(ijtifffile) = &self.ijtifffile {
+            Ok(ijtifffile.comment.clone())
+        } else {
+            Ok(None)
+        }
+    }
+
+    #[setter]
+    fn set_comment(&mut self, comment: &str) -> PyResult<()> {
+        if let Some(ijtifffile) = &mut self.ijtifffile {
+            ijtifffile.comment = Some(String::from(comment));
+        }
+        Ok(())
+    }
+
+    fn append_extra_tag(&mut self, tag: PyTag, czt: Option<(usize, usize, usize)>) {
+        if let Some(ijtifffile) = self.ijtifffile.as_mut() {
+            if let Some(extra_tags) = ijtifffile.extra_tags.get_mut(&czt) {
+                extra_tags.push(tag.tag)
+            }
+        }
+    }
+
+    fn get_tags(&self, czt: Option<(usize, usize, usize)>) -> PyResult<Vec<PyTag>> {
+        if let Some(ijtifffile) = &self.ijtifffile {
+            if let Some(extra_tags) = ijtifffile.extra_tags.get(&czt) {
+                let v = extra_tags
+                    .iter()
+                    .map(|tag| PyTag {
+                        tag: tag.to_owned(),
+                    })
+                    .collect();
+                return Ok(v);
+            }
+        }
+        Ok(Vec::new())
     }
 
     fn close(&mut self) -> PyResult<()> {
@@ -160,20 +314,19 @@ impl PyIJTiffFile {
     }
 }
 
-
 macro_rules! impl_save {
     ($T:ty, $t:ident) => {
         #[pymethods]
         impl PyIJTiffFile {
-            fn $t(&mut self, frame: PyReadonlyArray2<$T>, c: usize, t: usize, z: usize,
+            fn $t(
-                extra_tags: Option<Vec<PyTag>>) -> PyResult<()> {
+                &mut self,
-                let extra_tags = if let Some(extra_tags) = extra_tags {
+                frame: PyReadonlyArray2<$T>,
-                    Some(extra_tags.into_iter().map(|x| x.tag).collect())
+                c: usize,
-                } else {
+                t: usize,
-                    None
+                z: usize,
-                };
+            ) -> PyResult<()> {
                 if let Some(ijtifffile) = self.ijtifffile.as_mut() {
-                    ijtifffile.save(frame.to_owned_array(), c, t, z, extra_tags)?;
+                    ijtifffile.save(frame.to_owned_array(), c, t, z)?;
                 }
                 Ok(())
             }
@@ -192,7 +345,6 @@ impl_save!(i64, save_i64);
 impl_save!(f32, save_f32);
 impl_save!(f64, save_f64);
 
-
 #[pymodule]
 #[pyo3(name = "tiffwrite_rs")]
 fn tiffwrite_rs(m: &Bound<'_, PyModule>) -> PyResult<()> {