tifffolder 0.0.4

Parse filenames & slice a folder of images like a numpy array

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[:]