Convert python array to neuron vector

[Prokopiou]

Hello,

I have been trying to convert a python array ( numpy.ndarray ) into a neuron vector.

I used the command:

Code: Select all

neuron_vector.from_python(python_array)

and it does work (dimension-wise) but doesn't get the correct values. The only value the neuron vector stores is 0 but I noticed when the sign changes in python so does in neuron vector. So I have a vector full of -0 and 0.

This makes me think that there must be an error in the bits the number is represented, each value in the python array is a 'numpy.float64'.

Is there an issue in transferring 64 bit numbers using the from_python() function?

Thanks

[Prokopiou]

Hello,

Please ignore my previous post, it does convert the 64bit array when I test it with a different array which confuses me even more now...

Code: Select all

stim_vec = h.Vector()
time_vec = h.Vector()

time_vec.from_python(t)

i = 0
for sec in h.allsec():
    for seg in sec:
       stim_vec.from_python(external_voltage[:,i])
       stim_vec.play(seg._ref_e_extracellular, time_vec)
       i += 1

this is the code that seems to not work...
t is an array in python which converts just fine to a neuron vector.

the external_voltage[:,i] gives back 1D array (same length as t) but the stim_vec remains at zero with alternating sign (negative-positive) when the external_voltage changes value. I cant really see why it should do this.

Thanks

[hines]

Since there is only one instance of stim_vec, I would have expected every segment to get the same last external_voltage 1d array.
Perhaps you need an array of stim_vec as in
stim_vec = []
...........
stim_vec.append(Vector(external_voltage[:,i])
stim_vec[-1].play(seg....)
However, I would not have expected that last external voltage to be alternating +-0 so perhaps there is a bug in the
transfer of the numpy 1-d array to a Vector. Your fragment does not exhibit the creation of the 2-d numpy array. A complete
fragment would help me see the problem and work on a diagnosis. The following test

Code: Select all

import numpy
a=numpy.matrix([[1,2],[3,4]])
from neuron import h
v = h.Vector(a[:,0])
v.printf()
for i in range(0,2):
  v.from_python(a[:,i])
  v.printf()

produces the correct output

Code: Select all

1	3	
1	3	
2	4	

[Prokopiou]

I seem to have resolved the problem...in a way that doesn't make sense to me so it is still a problem I guess..

Im using a play , record pair to stimulate the cell with an external voltage and this is the code I use:

Code: Select all

time_vec = h.Vector()
time_vec.from_python(t)

test_vec = []

i = 0
for sec in h.allsec():
    for seg in sec:
       stim_vec = h.Vector()
       stim_vec.from_python(external_voltage[:,i])
       test_vec.append(stim_vec)
       stim_vec.play(seg._ref_e_extracellular, time_vec)
       
       i += 1
            
results = []
for sec in h.allsec():

    for seg in sec:  
        rec_vec = h.Vector()
        rec_vec.record(seg._ref_v)
        results.append(rec_vec)        

 
neuron.init()
neuron.run(time)

results_list = []
for v in results:
    temp = v.to_python()
    temp.remove(temp[0])
    results_list.append(temp)
    
    
internal_voltage = np.array(results_list)

this seems to work just fine, what I don't quite understand is when I comment out the test_vec like this:

Code: Select all

time_vec = h.Vector()
time_vec.from_python(t)

#test_vec = []

i = 0
for sec in h.allsec():
    for seg in sec:
       stim_vec = h.Vector()
       stim_vec.from_python(external_voltage[:,i])
       #test_vec.append(stim_vec)
       stim_vec.play(seg._ref_e_extracellular, time_vec)
       
       i += 1
            
results = []
for sec in h.allsec():

    for seg in sec:  
        rec_vec = h.Vector()
        rec_vec.record(seg._ref_v)
        results.append(rec_vec)        

 
neuron.init()
neuron.run(time)

results_list = []
for v in results:
    temp = v.to_python()
    temp.remove(temp[0])
    results_list.append(temp)
    
    
internal_voltage = np.array(results_list)

The problem I was talking about before seems to pop up again. This confuses me and makes me wonder if im using the play record pair correctly in this python code.

Thanks,
Andreas.

[hines]

by not putting the stim_vec instance in the test_vec, then when
stim_vec = h.Vector()
is executed, the reference count of the Vector previously referenced by stim_vec goes to 0
and that deletes that Vector.