Parallelised LIF-to-TIFF file conversion #282
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…unction; changed logic for naming and generating directories for processed files
tieneupin
added
enhancement
| "cyan", | ||
| "green", | ||
| "magenta", | ||
| "red", |
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Does yellow need to be included here?
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Missed it, oops. Will add yellow in new commit
src/murfey/util/lif.py
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| import numpy as np | ||
| from readlif.reader import LifFile | ||
| from readlif.reader import LifFile # , LifImage |
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Can drop commented out import
src/murfey/util/lif.py
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| imwrite( | ||
| save_name, | ||
| arr, | ||
| imagej=True, # ImageJ comppatible |
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typo on compatible, trivial but may as well catch it
src/murfey/util/lif.py
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| # Extract image data to array | ||
| logger.info("Loading image stack") | ||
| arr: np.ndarray = [] # Array to store frames in |
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This isn't an np.ndarray yet, it's a list
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Type hinting needs to be specified here, as this variable is very quickly converted into an array and used as such for the remainder of the function. MyPy throws a hissy fit when I remove it.
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I'm surprised mypy doesn't complain about it because np.ndarray has no append method. You could make it a numpy array at initialisation and use np.append inside the for loop
Helps with resolving #280. Part of continued work on #288.