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.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
# acces 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.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
# acces 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 neo object with maplotlib.
"""
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'
urllib.urlretrieve(distantfile, localfile)
reader = neo.io.NeuroExplorerIO(filename='File_neuroexplorer_2.nex')
bl = reader.read(cascade=True, lazy=False)[0]
for seg in bl.segments:
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()