Python code for analyzing hippocampus data
To install, launch Anaconda Navigator. On the left sidebar, select Environments. Select “base (root)” or another environment that you are using. Click on the triangle icon, and select “Open Terminal”. In the Terminal window, change to the PyHipp directory and do:
cd ~/Documents/Python/PyHipp
pip install -r requirements.txt
pip install -e .
Clone pyedfread for reading Eyelink files from GitHub to your computer by selecting Clone->Open in Desktop:
https://github.com/nwilming/pyedfread
While still in the Terminal window, change directory to where the pyedfread code is saved, and do:
cd ~/Documents/Python/pyedfread pip install .
You should also clone the following two repositories:
https://github.com/grero/DataProcessingTools
https://github.com/grero/PanGUI
Change to the directory where the code is saved, and install them using:
pip install -e .
Close the Terminal window, select Home in the sidebar of the Anaconda Navigator window, and launch Spyder. Type the following from the python prompt:
import PyHipp as pyh
You should be able to use the functions by doing:
pyh.pyhcheck('hello')
cd ~/Documents/Python/PyHipp
# count number of items in the directory
df1 = pyh.DirFiles()
cd PyHipp
# count number of items in the directory
df2 = pyh.DirFiles()
# add both objects together
df1.append(df2)
# plot the number of items in the first directory
df1.plot(i=0)
# plot the number of items in the second directory
df1.plot(i=1)
Test to make sure you are able to read EDF files: Change to a directory that contains EDF files, e.g.:
cd /Volumes/Hippocampus/Data/picasso-misc/20181105
Enter the following command:
samples, events, messages = edf.pread('181105.edf', filter='all')
You can create objects by doing:
rl = pyh.RPLParallel()
uy = pyh.Unity()
el = pyh.Eyelink()
You can create plots by doing:
rp = PanGUI.create_window(rl)
up = PanGUI.create_window(uy)
ep = PanGUI.create_window(el)