88 lines
3.7 KiB
Markdown
88 lines
3.7 KiB
Markdown
# Tiffwrite
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Exploiting [tifffile](https://pypi.org/project/tifffile/) in parallel to write ImageJ compatible tiffs with good
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compression.
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## Features
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- Writes bigtiff file that opens 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 save several times.
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For example empty frames, or a long string tag on every frame.
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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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## Installation
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pip install tiffwrite
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or
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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', bar=False, colormap=None, pxsize=None)
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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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- bar: bool; whether or not to show a progress bar.
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- colormap: string; choose any colormap from the colorcet module.
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- pxsize: float; set tiff tag so ImageJ can read the pixel size (in um).
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## Write one frame at a time
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with IJTiffWriter(file, shape, dtype='uint16', colormap=None, nP=None, extratags=None, pxsize=None) as tif:
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some loop:
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tif.save(frame, c, z, t)
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- file: string; filename of the new tiff file, or list of filenames.
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- shape: iterable; shape (C, Z, T) of data to be written in file.
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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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- colormap: string; choose any colormap from the colorcet module.
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- nP: int; number of compressor workers to use
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- extratags: dict {int tagnr: (int type, data)}, extra tags to save on every frame, will cause a crash if not used
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correctly!
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- pxsize: float; set tiff tag so ImageJ can read the pixel size (in um).
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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 itertools import product
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from tiffwrite import IJTiffWriter
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import numpy as np
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shape = (3, 5, 10) # channels, z, time
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with IJTiffWriter('file.tif', shape, pxsize=0.09707) as tif:
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for c in range(shape[0]):
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for z in range(shape[1]):
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for t in range(shape[2]):
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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 itertools import product
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from tiffwrite import IJTiffWriter
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import numpy as np
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shape = (3, 5, 10) # channels, z, time
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with IJTiffWriter(('fileA.tif', 'fileB.tif'), shape) as tif:
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for c in range(shape[0]):
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for z in range(shape[1]):
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for t in range(shape[2]):
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tif.save('fileA.tif', np.random.randint(0, 10, (32, 32)), c, z, t)
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tif.save('fileB.tif', np.random.randint(0, 10, (32, 32)), c, z, t)
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## Tricks & tips
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- ImageJ colors channels in the order rgbwcym, and IJTiffwriter automatically and efficiently writes 0's when a frame is
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skipped. You can use this when specific colors are important, for example: you want to use only red and blue.
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- The order of feeding frames to IJTiffWriter is unimportant, IJTiffWriter will order de ifd's such that the file will
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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
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useful.
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