spykeutils: loading units from DB

[Orkan Oz]

Hello all,

I am using neo 0.3.3 and OpenElectrophy 0.3.4 and spykeutils 0.4.1.

I have elicited spike trains and I want to analyse them with spykeutils. I load units in my script as below:


u1 = Unit.load (id=160)

u2 = Unit.load (id=172)

import spykeutils.rate_estimation

st_dict = {}

units = [1,2]

st_dict[units[0]] = u1.spiketrains

st_dict[units[1]] = u2.spiketrains

kernel_sizes = sp.logspace(2, 3.3, 100) * pq.ms

spykeutils.rate_estimation.spike_density_estimation(st_dict, optimize_steps=kernel_sizes)[0]

but I get the following error:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\WinPython32\python-2.7.6\lib\site-packages\spyderlib\widgets\externalshell\sitecustomize.py", line 540, in runfile
    execfile(filename, namespace)
  File "C:/WinPython32/python-2.7.6/Scripts/isi_140903.py", line 164, in <module>
    spykeutils.rate_estimation.spike_density_estimation(st_dict, optimize_steps=kernel_sizes)[0]
  File "C:\WinPython32\python-2.7.6\lib\site-packages\spykeutils\rate_estimation.py", line 181, in spike_density_estimation
    c = collapsed_spike_trains(t)
  File "C:\WinPython32\python-2.7.6\lib\site-packages\spykeutils\rate_estimation.py", line 215, in collapsed_spike_trains
    return neo.SpikeTrain([], 0 * pq.s)
  File "C:\WinPython32\python-2.7.6\lib\site-packages\neo\core\spiketrain.py", line 195, in __new__
    raise ValueError('you must specify units')
ValueError: you must specify units

Can you please help me with this problem?

Regards

Orkan
--

Orcun Orkan OZCAN

PhD student (NeuroTime)

Tel : +33 (0)3 88 45 66 32
Institute of Cellular and Integrative Neuroscience (INCI)
CNRS UPR 3212, University of Strasbourg
5, rue Blaise Pascal
67084 Strasbourg

[Robert Pröpper]

Hi Orkan,

it looks like you found a bug in spykeutils. It should be fixed in my most recent commit, so you can get a version without the bug from GitHub: https://github.com/rproepp/spykeutils/commit/1d070170425e1517972cf4760af528b75a645501

The bug only occurs for empty lists of spike trains, so it seems that at least one of your units doesn't have spikes. Also, I think it would be more convenient for you to just use the units as index for st_dict (i.e. in your example: st_dict[u1] = u1.spiketrains).

Best,
Robert

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[Orkan Oz]

Hi Robert,

Thank you very much for the answer and the fix. I have another problem now, unfortunately.

I am running the script

import numpy

from neuronpy.graphics import spikeplot

from OpenElectrophy import *

import matplotlib

import matplotlib.colors as colors

import matplotlib.pyplot as plt

import spykeutils.plot

import neuronpy

import scipy as sp

import sys,os

from numpy import*# unique, ones, mean, std, arange, where, random, unique1d

open_db( url = url, myglobals= globals(), use_global_session = True)

" spike density estimation "

u1 = Unit.load (id=303)

u2 = Unit.load (id=321)

import spykeutils.rate_estimation

st_dict = {}

units=[]

units.append(u1)

units.append(u1)

units[0].spiketrains = u1.spiketrains

units[1].spiketrains = u2.spiketrains

st_dict[units[0]] = units[0].spiketrains

st_dict[units[1]] = units[1].spiketrains

kernel_sizes = sp.logspace(2, 3.3, 100) * pq.ms

spykeutils.rate_estimation.spike_density_estimation(st_dict, optimize_steps=kernel_sizes)[0]

spykeutils.plot.sde(st_dict, maximum_kernel=3000*pq.ms, optimize_steps=100)

and I get the following error:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\WinPython32\python-2.7.6\lib\site-packages\spyderlib\widgets\externalshell\sitecustomize.py", line 540, in runfile
    execfile(filename, namespace)

  File "C:/WinPython32/python-2.7.6/Scripts/rate_est_O.py", line 151, in <module>
    spykeutils.rate_estimation.spike_density_estimation(st_dict, optimize_steps=kernel_sizes)[0]
  File "C:\WinPython32\python-2.7.6\lib\site-packages\spykeutils\rate_estimation.py", line 184, in spike_density_estimation
    c = collapsed_spike_trains(t)
  File "C:\WinPython32\python-2.7.6\lib\site-packages\spykeutils\rate_estimation.py", line 225, in collapsed_spike_trains
    collapsed.extend(sp.asarray(t.rescale(stop.units)))
AttributeError: 'SpikeTrain' object has no attribute 'rescale'


Can you please check this?

Best,
Orkan

[Robert Pröpper]

I suspect that the spike train lists you get from OpenElectrophy (e.g. u1.spiketrains) do not actually contain Neo SpikeTrain objects, but something similar that is linked to the database. That explains why they don't have a rescale method.

I don't use OpenElectrophy myself, but there should be an easy way to convert these objects into real Neo SpikeTrains. You would need to do that for the contents of your lists before passing them to spykeutils.

Best,
Robert

[Orkan Oz]

Thanks again Robert.

I will check the contents of OE outputs.

Best
Orkan