edc126d079
- Support colormaps per channels via the colors argument. - No writer process anymore, the pool writes to the file by using a filehandle with a lock. - Can save extra tiff tags in every frame and/or per frame individually. - Header and IFD classes with support for reading files. - Multiplexing is now done automatically when multiple IJTiffFiles are initialized: the process pool is shared by all IJTiffFiles.
96 lines
4.3 KiB
Markdown
96 lines
4.3 KiB
Markdown
# Tiffwrite
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Exploiting [tifffile](https://pypi.org/project/tifffile/) in parallel to write BioFormats/ImageJ compatible tiffs with
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good compression.
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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.
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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, extra tags globally or frame dependent.
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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', 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 or not 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, shape, 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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- file: string; filename of the new tiff file.
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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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- 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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- extratags: other tags to be saved, example: Artist='John Doe', Tag4567=[400, 500] or
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Copyright=Tag('ascii', 'Made by me'). See tiff_tag_registry.items().
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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 IJTiffFile
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import numpy as np
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shape = (3, 5, 10) # channels, z, time
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with IJTiffFile('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 IJTiffFile
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import numpy as np
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shape = (3, 5, 10) # channels, z, time
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with IJTiffFile('fileA.tif', shape) as tif_a, IJTiffFile('fileB.tif', shape) as tif_b:
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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_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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## Tricks & tips
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- The order of feeding frames to IJTiffFile is unimportant, IJTiffFile 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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- IJTiffFile does not allow more than one pool of parallel processes to be open at a time. Therefore, when writing
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multiple tiff's simultaneously you have to open all before you start saving any frame, in this way all files share the
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same pool.
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