111 lines
4.5 KiB
Markdown
111 lines
4.5 KiB
Markdown
[](https://github.com/wimpomp/tiffwrite/actions/workflows/pytest.yml)
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# Tiffwrite
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Write BioFormats/ImageJ compatible tiffs with zstd compression in parallel using Rust.
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## Features
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- Writes bigtiff files that open in ImageJ as hyperstack with correct dimensions.
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- Parallel compression.
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- Write individual frames in random order.
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- Compresses even more by referencing tag or image data which otherwise would have been saved several times.
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For example empty frames, or a long string tag on every frame. Editing tiffs becomes mostly impossible, but compression
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makes that very hard anyway.
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- Enables memory efficient scripts by saving frames whenever they're ready to be saved, not waiting for the whole stack.
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- Colormaps
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- Extra tags, globally or frame dependent.
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# Python
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## Installation
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```pip install tiffwrite```
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or
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- install [rust](https://rustup.rs/)
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- ``` pip install tiffwrite@git+https://github.com/wimpomp/tiffwrite ```
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## Usage
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### Write an image stack
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tiffwrite(file, data, axes='TZCXY', dtype=None, bar=False, *args, **kwargs)
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- file: string; filename of the new tiff file.
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- data: 2 to 5D numpy array in one of these datatypes: (u)int8, (u)int16, float32.
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- axes: string; order of dimensions in data, default: TZCXY for 5D, ZCXY for 4D, CXY for 3D, XY for 2D data.
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- dtype: string; cast data to dtype before saving, only (u)int8, (u)int16 and float32 are supported.
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- bar: bool; whether to show a progress bar.
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- args, kwargs: arguments to be passed to IJTiffFile, see below.
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### Write one frame at a time
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with IJTiffFile(file, dtype='uint16', colors=None, colormap=None, pxsize=None, deltaz=None,
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timeinterval=None, **extratags) as tif:
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some loop:
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tif.save(frame, c, z, t)
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- path: string; path to the new tiff file.
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- dtype: string; cast data to dtype before saving, only (u)int8, (u)int16 and float32 are supported by Fiji.
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- colors: iterable of strings; one color per channel, valid colors (also html) are defined in matplotlib.colors.
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Without colormap BioFormats will set the colors in this order: rgbwcmy.
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Note that the color green is dark, the usual green is named 'lime' here.
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- colormap: string; choose any colormap from the colorcet module. Colors and colormap cannot be used simultaneously.
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- pxsize: float; pixel size im um.
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- deltaz: float; z slice interval in um.
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- timeinterval: float; time between frames in seconds.
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- compression: int; zstd compression level: -7 to 22.
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- comment: str; comment to be saved in tif
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- extratags: Sequence\[Tag\]; other tags to be saved, example: Tag.ascii(315, 'John Doe') or Tag.ascii(33432, 'Made by me').
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- frame: 2D numpy array with data.
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- c, z, t: int; channel, z, time coordinates of the frame.
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## Examples
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### Write an image stack
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from tiffwrite import tiffwrite
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import numpy as np
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image = np.random.randint(0, 255, (5, 3, 64, 64), 'uint16')
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tiffwrite('file.tif', image, 'TCXY')
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### Write one frame at a time
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from tiffwrite import IJTiffFile
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import numpy as np
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with IJTiffFile('file.tif', pxsize=0.09707) as tif:
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for c in range(3):
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for z in range(5):
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for t in range(10):
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tif.save(np.random.randint(0, 10, (32, 32)), c, z, t)
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### Saving multiple tiffs simultaneously
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from tiffwrite import IJTiffFile
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import numpy as np
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with IJTiffFile('fileA.tif') as tif_a, IJTiffFile('fileB.tif') as tif_b:
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for c in range(3):
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for z in range(5):
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for t in range(10):
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tif_a.save(np.random.randint(0, 10, (32, 32)), c, z, t)
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tif_b.save(np.random.randint(0, 10, (32, 32)), c, z, t)
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# Rust
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use ndarray::Array2;
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use tiffwrite::IJTiffFile;
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{ // f will be closed when f goes out of scope
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let mut f = IJTiffFile::new("file.tif")?;
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for c in 0..3 {
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for z in 0..5 {
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for t in 0..10 {
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let arr = Array2::<u16>::zeros((100, 100));
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f.save(&arr, c, z, t)?;
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}
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}
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}
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}
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# Tricks & tips
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- The order of feeding frames to IJTiffFile is unimportant, IJTiffFile will order the ifd's such that the file will be opened as a correctly ordered hyperstack.
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- Using the colormap parameter you can make ImageJ open the file and apply the colormap. colormap='glasbey' is very useful.
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