Error in Neuron Book Example?

The basics of how to develop, test, and use models.
witchcraft
Posts: 1
Joined: Wed Nov 11, 2009 7:53 am

Error in Neuron Book Example?

Dear Neuroner's,

It is very unlikely that there is an error in pg. 139 -141 of The Neuron Book example. I am following my "paranoia setting" of trying all the examples in the book - okay nearly all. But i find that when i try the code below (pages 139 -141):

Code: Select all

``````
/////////////////////////////////////
/////////////////////////////////////
/* Model Specs */
/////////////////////////////////////
/////////////////////////////////////

/////////// Topology ////////////////

create soma, apical, basilar, axon
connect apical(0), soma(1)
connect basilar(0), soma(0)
connect axon(0), soma(0)

/////////// Geometry ////////////////

soma		{

L = 30
diam = 30
nseg = 1

}

apical		{

L = 600
diam = 1
nseg = 23

}

basilar		{

L = 200
diam = 2
nseg = 5

}

axon		{

L = 1000
diam = 1
nseg = 37

}

/////////// Biophysics ////////////////

forall		{

Ra = 100
cm = 1

}

soma		{

insert hh

}

apical		{

insert pas
g_pas = 0.0002
e_pas = -65

}

basilar		{

insert pas
g_pas = 0.0002
e_pas = -65

}

axon		{

insert hh

}

/////////////////////////////////////
/////////////////////////////////////
/*Instrumentation*/
/////////////////////////////////////
/////////////////////////////////////

/////////// Synaptic Input /////////

objref syn
soma syn = new AlphaSynapse(0.5)
syn. onset = 0.5
syn. tau = 0.1
syn. gmax = 0.05
syn. e = 0

/////////// Graphical Disp ////////////////

objref g
g = new Graph()
g.size(0.5, -80, 40)
g.addvar("soma.v (0.5)", 1, 1, 0.6, 0.9, 2)

/////////////////////////////////////
/////////////////////////////////////
/*Simulation Control*/
/////////////////////////////////////
/////////////////////////////////////

dt = 0.025
tstop = 5
v_init = -65

proc initialize()	{

finitialize (v_init)
fcurrent()

}

proc integrate()	{

g.begin()
while (t<stop)	{
g.plot (t)

}

g.flush
}

proc go()	{

initialize ()
integrate ()

}

``````
I get this response:

Code: Select all

``````-e
NEURON -- Release 7.1 (359:7f113b76a94b) 2009-10-26
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2008
See http://www.neuron.yale.edu/credits.html

/Applications/Neuron-7.1/nrn/i686/bin/nrniv.app/Contents/MacOS/nrniv: size not enough arguments
in neuromus.hoc near line 114
g.size(0.5, -80, 40)
^
Graph[0].size(0.5, -80, 40)
oc>go()
/Applications/Neuron-7.1/nrn/i686/bin/nrniv.app/Contents/MacOS/nrniv: go undefined function
near line 1
go()
^
go()
oc>
``````
I have checked the code as much as i can and i am quite certain i am missing something. Any pointers are appreciated.

With Kind Regards,

Witchcraft.
ted
Posts: 5810
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
Contact:

Re: Error in Neuron Book Example?

Code: Select all

``````nrniv: size not enough arguments
in neuromus.hoc near line 114
g.size(0.5, -80, 40)
^
Graph[0].size(0.5, -80, 40)``````
means the interpreter found a parse error. Parse errors stop the parser immediately. Nothing past this point is examined, so proc go() doesn't yet exist as far as NEURON is concerned.

The good news about parse errors is that the interpreter tells you where the error is. This would be a good time to read 12.3.2 Error handling in the NEURON Book, review the documentation of the Graph class's size() method, take a fresh look at the source code in the book and compare it with the statement that gagged the interpreter.

And marvel at the brain's ability to perceive something that it "knows is there" even when that something really isn't-- one aspect of being human that is a common hindrance to debugging. If Alexander Pope had been a programmer, might he have written "to err is a feature, not a bug"?
Bill Connelly
Posts: 86
Joined: Thu May 22, 2008 11:54 pm
Location: Australian National University

Re: Error in Neuron Book Example?

Just in case you still can't find the problem (because I think we've all been there), compare what you have

Code: Select all

``````g.size(0.5, -80, 40)
``````
to what the book has, very closely.

Hint: . and , are different things.