Parse filenames & slice a folder of images like a numpy array
Project description
tifffolder
Read a subset of data from a folder of images like a numpy array
Example:
>>> from tifffolder import TiffFolder
>>> tf = TiffFolder('/folder/of/files', tpattern='_stack{:04d}_', cpattern='_ch{}_')
# extract data with numpy slicing with axes [t,c,z,y,x]
# for instance get timepoints 1-100, stepping by 10,
# in the first channel, last 10 z planes, cropping somewhere in the middle of y
>>> data = tf[0:100:10, 0, -10:, 200:400, :]
>>> data.shape
(10, 1, 10, 200, 512) # (nt, nc, nz, ny, nx)
Can also be used as an iterator/generator for lazily reading data
>>> for timepoint in tf:
>>> do_something(timepoint)
# or just load the whole thing
>>> alldata = tf[:]
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