Reading inputs from pkl or h5 format

[albertoarturovergani]

The aim is to get as input the pkl files or h5 file and making processing and visualization.

[albertoarturovergani]

• Created the notebook https://github.com/SpikeAI/2020-11_brainhack_Project7/blob/main/dev/3_C_loading_inputs.ipynb
• Still there are issues in reading file
• installing hdfcompass to open the gui to explore h5 file from https://github.com/HDFGroup/hdf-compass there are issues too on my Ubuntu 16.04

[JuliaSprenger]

@albertoarturovergani Is this for reading a nix-hdf5 file or a generic hdf5 file?

[albertoarturovergani]

@JuliaSprenger they are generated by NixIO in https://github.com/SpikeAI/2020-11_brainhack_Project7/blob/main/dev/3_boilerplate.ipynb, so nix-hdf5

[JuliaSprenger]

Then why don't you just use Neo and it's NixIO to load them again if you are anyway using Python?

[JuliaSprenger]

Just in case:
:)

import neo
with neo.Nixio('filename') as io:
    block = io.read_block()

[albertoarturovergani]

---

AttributeError Traceback (most recent call last)
in
1 import neo
----> 2 with neo.Nixio(pathName) as io:
3 block = io.read_block()

AttributeError: module 'neo' has no attribute 'Nixio'

[JuliaSprenger]

sorry. my typo.
It's of course the same IO you used for saving, so

neo.NixIO(pathName)

Python is case sensitive ;)

[albertoarturovergani]

Ok, now it's imported the nix-hdf5, but still to do the plotting.
I made working the pkl reading and plotted the results https://github.com/SpikeAI/2020-11_brainhack_Project7/blob/main/dev/3_C_loading_inputs.ipynb