3d cell set position

[alejoe91]

in Cell.set_pos() the problem arises when pt3d = True:

• if cell has 3d points only x3d, y3d, z3d are updated, but not xstart, ystart, zstart and xend, yend, zend (if - else)
• _set_pt3d_pos() moves the 3d points with respect to the soma position, rather than diffx, diffy, diffz (one should pass diffx, diffy, and diffz as args)

--> when moving setting a cell multiple times to the same position, the 3d points keep drifting by the actual soma position

From LFPy/examples/example1

#!/usr/bin/env python
'''
Example plot for LFPy: Single-synapse contribution to the LFP
'''
import LFPy
import numpy as np
import os
import sys
if sys.version < '3':
from urllib2 import urlopen
else:
from urllib.request import urlopen
import zipfile
import matplotlib.pyplot as plt
from matplotlib.collections import PolyCollection
from os.path import join
plt.interactive(1)
plt.close('all')

#Fetch Mainen&Sejnowski 1996 model files
if not os.path.isfile(join('cells', 'cells', 'j4a.hoc')):
#get the model files:
u = urlopen('http://senselab.med.yale.edu/ModelDB/eavBinDown.asp?o=2488&a=23&mime=application/zip')
localFile = open('patdemo.zip', 'w')
localFile.write(u.read())
localFile.close()
#unzip:
myzip = zipfile.ZipFile('patdemo.zip', 'r')
myzip.extractall('.')
myzip.close()

################################################################################

Main script, set parameters and create cell, synapse and electrode objects

################################################################################

Define cell parameters

cell_parameters = { # various cell parameters,
'morphology' : join('cells', 'cells', 'j4a.hoc'), # Mainen&Sejnowski, 1996
'rm' : 30000., # membrane resistance
'cm' : 1.0, # membrane capacitance
'Ra' : 150, # axial resistance
'v_init' : -65., # initial crossmembrane potential
'e_pas' : -65., # reversal potential passive mechs
'passive' : True, # switch on passive mechs
'nsegs_method' : 'lambda_f',
'lambda_f' : 100.,
'timeres_NEURON' : 2.-3, # [ms] dt's should be in powers of 2 for both,
'timeres_python' : 2.-3, # need binary representation
'tstartms' : 0., # start time of simulation, recorders start at t=0
'tstopms' : 100., # stop simulation at 200 ms. These can be overridden
# by setting these arguments i cell.simulation()
'pt3d' : True
}

Create cell

cell = LFPy.Cell(**cell_parameters)

Align cell

cell.set_rotation(x=4.99, y=-4.33, z=3.14)

Define synapse parameters

synapse_parameters = {
'idx' : cell.get_closest_idx(x=-200., y=0., z=800.),
'e' : 0., # reversal potential
'syntype' : 'ExpSyn', # synapse type
'tau' : 5., # synaptic time constant
'weight' : .001, # synaptic weight
'record_current' : True, # record synapse current
}

Create synapse and set time of synaptic input

synapse = LFPy.Synapse(cell, **synapse_parameters)
synapse.set_spike_times(np.array([20.]))

Create a grid of measurement locations, in (mum)

X, Z = np.mgrid[-700:701:50, -400:1201:50]
Y = np.zeros(X.shape)

Define electrode parameters

grid_electrode_parameters = {
'sigma' : 0.3, # extracellular conductivity
'x' : X.flatten(), # electrode requires 1d vector of positions
'y' : Y.flatten(),
'z' : Z.flatten()
}

Define electrode parameters

point_electrode_parameters = {
'sigma' : 0.3, # extracellular conductivity
'x' : np.array([-130., -220.]),
'y' : np.array([ 0., 0.]),
'z' : np.array([ 0., 700.]),
}

Run simulation, electrode object argument in cell.simulate

print("running simulation...")
cell.simulate(rec_imem=True,rec_isyn=True)

Create electrode objects

grid_electrode = LFPy.RecExtElectrode(cell,**grid_electrode_parameters)
point_electrode = LFPy.RecExtElectrode(cell,**point_electrode_parameters)

Calculate LFPs

grid_electrode.calc_lfp()
point_electrode.calc_lfp()

print("done")

Issue (only when cell has pt3d = True)

print cell.somapos
print 'set soma position at: ', [50, 0, 0]
cell.set_pos(50, 0, 0)
print cell.somapos
print 'so far so good..'
print 'set soma position at: ', [50, 0, 0]
cell.set_pos(50, 0, 0)
print cell.somapos, ' drifting'
print 'set soma position at: ', [50, 0, 0]
cell.set_pos(50, 0, 0)
print cell.somapos, ' drifting'

[espenhgn]

@alejoe91 Can you paste the code example as code?

[alejoe91]

Sure! Sorry about it :)

At the end of LFPy/examples/example1.py just add:

print cell.somapos
print 'set soma position at: ', [50, 0, 0]
cell.set_pos(50, 0, 0)
print cell.somapos, ' so far so good..'
cell.set_pos(50, 0, 0)
print cell.somapos, ' drifting..'
cell.set_pos(50, 0, 0)
print cell.somapos, ' drifting..'

I have a working branch, I will try to send a pull request to LFPy/LFPy

[espenhgn]

This appear now to be fixed in PR #4

[espenhgn]

This fix introduced positioning errors when pt3d=False, see pull request #16

[espenhgn]

Closing issue, fixed by PR #17