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  • Committer: Package Import Robot
  • Author(s): Yaroslav Halchenko
  • Date: 2014-07-30 11:29:44 UTC
  • mfrom: (6.1.2 experimental)
  • Revision ID: package-import@ubuntu.com-20140730112944-ln0ogbq0kpyyuz47
Tags: 1.4.1-2
* Forgotten upload to unstable
* debian/control
  - policy boost to 3.9.5
  - updated Vcs- fields given migration to anonscm.d.o and provided -b
    debian

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examples/electrophysiology/compensation_ex2_spikes.py
 
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#!/usr/bin/env python
 
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"""
 
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Example of spike detection method. Requires binary files 
 
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"current.npy" and "rawtrace.npy".
 
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    Rossant et al., "A calibration-free electrode compensation method"
 
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    J. Neurophysiol 2012
 
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"""
 
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import os
 
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from brian import *
 
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import numpy as np
 
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from brian.library.electrophysiology import *
 
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working_dir = os.path.dirname(__file__)
 
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# load data
 
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dt = 0.1*ms
 
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current = np.load(os.path.join(working_dir, "current.npy"))  # 10000-long vector, 1s duration
 
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rawtrace = np.load(os.path.join(working_dir, "trace.npy"))  # 10000-long vector, 1s duration
 
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t = linspace(0., 1., len(current))
 
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# find spikes and compute score
 
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spikes, scores = find_spikes(rawtrace, dt=dt, check_quality=True)
 
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# plot trace and spikes
 
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plot(t, rawtrace, 'k')
 
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plot(t[spikes], rawtrace[spikes], 'or')
 
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show()
 
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