asiaszmek
commented
6 years ago Re 1. It already has been renamed, I'll delete it. Re 2. Yes, these are duplicates. https://github.com/Neuroinflab/kCSD-python/tree/master/figures/sKCSD_paper/morphology contains neuron morphologies used in the sKCSD paper and they are used only by https://github.com/Neuroinflab/kCSD-python/tree/master/figures/sKCSD_paper/run_LFP.py. I would prefer to leave these morphologies in https://github.com/Neuroinflab/kCSD-python/tree/master/figures/sKCSD_paper/morphology. Re 3. I'll move it to https://github.com/Neuroinflab/kCSD-python/tree/master/figures/sKCSD_paper/morphology. It is the electrode scheme used in one of the sKCSD figures and it is used by https://github.com/Neuroinflab/kCSD-python/tree/master/figures/sKCSD_paper/run_LFP.py. Re 4. skCSDcell is a class used for handling neuron morphologies for sKCSD. It is used by sKCSD in estimation of current source density and it is also used by validation/plotting_functions.py to transform CSD/potential from loops or neuron segments to 3D dimensions. Re 5-8: I'll fix those.
ccluri
Start from master now (tagged as version 1.2), create a branch that fixes all these issues and PR back, please. please comment below if you find any of these suggested changes redundant for the sake of documentation.
1) Rename https://github.com/Neuroinflab/kCSD-python/blob/master/figures/sKCSD_paper/functions.py 2) Is this (https://github.com/Neuroinflab/kCSD-python/tree/master/figures/sKCSD_paper/morphology) a duplicate of https://github.com/Neuroinflab/kCSD-python/tree/master/data/morphology 3) https://github.com/Neuroinflab/kCSD-python/blob/master/figures/sKCSD_paper/ElcoordsDomi14.txt file belongs elsewhere? 4) https://github.com/Neuroinflab/kCSD-python/blob/7dd7cdf2d52f4fa2879ba4fcba494ceff173bc92/kcsd/__init__.py#L6 is sKCSDCell used somewhere other than within the class itself - what is the difference between the sKCSD and sKCSDCell classes? 5) obj = Data("Data/gang_7x7_200") would fail, please use kcsd.sample_data_path instead. 6) please change this function name https://github.com/Neuroinflab/kCSD-python/blob/7dd7cdf2d52f4fa2879ba4fcba494ceff173bc92/kcsd/validation/plotting_functions.py#L215 7) Need atleast 1 line of docstring in these functions https://github.com/Neuroinflab/kCSD-python/blob/master/kcsd/validation/plotting_functions.py and https://github.com/Neuroinflab/kCSD-python/blob/master/kcsd/utility_functions.py 8) https://github.com/Neuroinflab/kCSD-python/blob/7dd7cdf2d52f4fa2879ba4fcba494ceff173bc92/kcsd/utility_functions.py#L41 why do this?
Cheers!