Examples

Introduction

A set of examples in neo/examples/ illustrates the use of Neo classes.

# -*- coding: utf-8 -*-
"""
This is an example for reading files with neo.io
"""

import urllib

import neo


# Plexon files
distantfile = 'https://portal.g-node.org/neo/plexon/File_plexon_3.plx'
localfile = './File_plexon_3.plx'
urllib.request.urlretrieve(distantfile, localfile)

# create a reader
reader = neo.io.PlexonIO(filename='File_plexon_3.plx')
# read the blocks
blks = reader.read(cascade=True, lazy=False)
print (blks)
# access to segments
for blk in blks:
    for seg in blk.segments:
        print (seg)
        for asig in seg.analogsignals:
            print (asig)
        for st in seg.spiketrains:
            print (st)


# CED Spike2 files
distantfile = 'https://portal.g-node.org/neo/spike2/File_spike2_1.smr'
localfile = './File_spike2_1.smr'
urllib.request.urlretrieve(distantfile, localfile)

# create a reader
reader = neo.io.Spike2IO(filename='File_spike2_1.smr')
# read the block
bl = reader.read(cascade=True, lazy=False)[0]
print (bl)
# access to segments
for seg in bl.segments:
    print (seg)
    for asig in seg.analogsignals:
        print (asig)
    for st in seg.spiketrains:
        print (st)

# -*- coding: utf-8 -*-
"""
This is an example for plotting a Neo object with matplotlib.
"""

import urllib

import numpy as np
import quantities as pq
from matplotlib import pyplot

import neo

url = 'https://portal.g-node.org/neo/'
# distantfile = url + 'neuroexplorer/File_neuroexplorer_2.nex'
# localfile = 'File_neuroexplorer_2.nex'

distantfile = 'https://portal.g-node.org/neo/plexon/File_plexon_3.plx'
localfile = './File_plexon_3.plx'


urllib.request.urlretrieve(distantfile, localfile)


# reader = neo.io.NeuroExplorerIO(filename='File_neuroexplorer_2.nex')
reader = neo.io.PlexonIO(filename='File_plexon_3.plx')


bl = reader.read(cascade=True, lazy=False)[0]
for seg in bl.segments:
    print ("SEG: "+str(seg.file_origin))
    fig = pyplot.figure()
    ax1 = fig.add_subplot(2, 1, 1)
    ax2 = fig.add_subplot(2, 1, 2)
    ax1.set_title(seg.file_origin)
    mint = 0 * pq.s
    maxt = np.inf * pq.s
    for i, asig in enumerate(seg.analogsignals):
        times = asig.times.rescale('s').magnitude        
        asig = asig.rescale('mV').magnitude
        ax1.plot(times, asig)

    trains = [st.rescale('s').magnitude for st in seg.spiketrains]
    colors = pyplot.cm.jet(np.linspace(0, 1, len(seg.spiketrains)))
    ax2.eventplot(trains, colors=colors)

pyplot.show()