www.neuron.yale.edu

Posted: **Tue Jul 04, 2017 1:47 pm**

I am trying to understand why I must store the output of a Python function (regardless of the name of the variable I use, and regardless of whether I subsequently use that variable) for current clamping. I wasn't sure if the NEURON staff was aware of this problem or not.

The line of interest is here:

Code: Select all

clamp_output = attach_current_clamp(cell)

If I just write

Code: Select all

attach_current_clamp(cell)

, without storing the output of the function into a variable, the code does not work (plot is empty), and yet I don't use clamp_output at all. Why must I use a variable to store the output even without using the output?

Code: Select all

import sys
import numpy
sys.path.append('/Applications/NEURON-7.4/nrn/lib/python')
from neuron import h, gui
from matplotlib import pyplot

#SET UP CELL
class SingleCell(object):
    def __init__(self):
        self.soma = h.Section(name='soma', cell=self)
        self.soma.L = self.soma.diam = 12.6517
        self.all = h.SectionList()
        self.all.wholetree(sec=self.soma)
        self.soma.insert('pas')
        self.soma.e_pas = -65

        for sec in self.all:
            sec.cm = 20
#CURRENT CLAMP
def attach_current_clamp(cell):
    stim = h.IClamp(cell.soma(1))
    stim.delay = 100
    stim.dur = 300
    stim.amp = 0.2
    return stim

cell = SingleCell()

#IF I CALL THIS FUNCTION WITHOUT STORING THE OUTPUT, THEN IT DOES NOT WORK
clamp_output = attach_current_clamp(cell)

#RECORD AND PLOT
soma_v_vec = h.Vector()
t_vec = h.Vector()
soma_v_vec.record(cell.soma(0.5)._ref_v)
t_vec.record(h._ref_t)
h.tstop = 800
h.run()
pyplot.figure(figsize=(8,4))
soma_plot = pyplot.plot(t_vec,soma_v_vec)
pyplot.show()

Posted: **Tue Jul 04, 2017 7:01 pm**

There's no problem at all. NEURON is working exactly as it should. In fact, it's working exactly the same way Python works. Read about reference counting and garbage collection
https://en.wikipedia.org/wiki/Reference_counting
Then do the following two-step experiment and see if the answer to your question becomes clear.

Step 1. Change

Code: Select all

clamp_output = attach_current_clamp(cell)

to

Code: Select all

clamp_output = attach_current_clamp(cell)
print 'IClamp reference count:'
h.allobjects('IClamp')

Now use NEURON to execute your program. How many h.IClamp instances exist?

Step 2. Change

Code: Select all

clamp_output = attach_current_clamp(cell)

to

Code: Select all

attach_current_clamp(cell)

and use NEURON to execute your program again. How many h.IClamp instances exist this time?

By the way, clamp_output seems a rather misleading name for the thing that attach_current_clamp returns. What does Python tell you it is? (hint: at the >>> prompt, enter the command
print clamp_output
or simply
clamp_output
)

Posted: **Thu Jul 06, 2017 10:03 am**

Interesting, thanks for addressing my question!

Posted: **Thu Jul 06, 2017 10:55 am**

Thanks for asking it. It raised a couple of important points that may benefit many others.

Posted: **Thu Jul 06, 2017 11:03 am**

I hope it will help others. We stumbled across this during the NIH BRAIN Course at U Missouri and we were quite puzzled. Thanks again.

Posted: **Thu Jul 06, 2017 11:35 am**

Ouch. Is there some way to get this answer to the course's organizers and the other participants in the course?

Posted: **Fri Jul 07, 2017 9:35 pm**

I have sent this to Dr. Nair, the course director.
Thanks!

www.neuron.yale.edu

Required to return current clamp object

Required to return current clamp object

Re: Required to return current clamp object

Re: Required to return current clamp object

Re: Required to return current clamp object

Re: Required to return current clamp object

Re: Required to return current clamp object

Re: Required to return current clamp object