Using vectors as arguments for pt3dadd

When Python is the interpreter, what is a good
design for the interface to the basic NEURON
concepts.

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neuromau
Posts: 97
Joined: Mon Apr 20, 2009 7:02 pm

Using vectors as arguments for pt3dadd

Post by neuromau » Mon Mar 02, 2020 3:46 pm

Looking through the documentation for pt3dadd, I see:
h.pt3dadd(xvec, yvec, zvec, dvec, sec=section)
...
Add the 3d location and diameter point (or points in the second form) at the end of the current pt3d list
...
Note: A more object-oriented approach is to use sec.pt3dclear() instead.
I am struggling with implementing this when I have a list of values for, say, 4 points that I want to add:

Code: Select all

from neuron import h, gui
import numpy as np
dend=h.Section(name='dend')
dend.pt3dclear()
xvec=h.Vector(np.array([-0.72,-0.72,-0.72,-0.72]))
yvec=h.Vector(np.array([-16.42,-18.16,-22.14,-24.13]))
zvec=h.Vector(np.array([0.0,0.0,0.0,0.0]))
dvec=h.Vector(np.array([2.4,2.2,2.0,1.96]))
dend.pt3dadd(xvec, yvec, zvec, dvec)
Gives the error
TypeError: must be real number, not hoc.HocObject
I get the same error with:

Code: Select all

xvec=h.Vector([-0.72,-0.72,-0.72,-0.72])
While I get other errors when trying the following:

Code: Select all

xvec=[-0.72,-0.72,-0.72,-0.72] # gives the error: must be real number, not list
 
xvec=np.array([-0.72,-0.72,-0.72,-0.72]) # gives the error: TypeError: only size-1 arrays can be converted to Python scalars
I'm using Neuron 7.7.2:

Code: Select all

print(neuron.version)
7.7.2
What am I doing incorrectly when trying to supply vectors instead of scalars as arguments to pt3dadd?

ramcdougal
Posts: 207
Joined: Fri Nov 28, 2008 3:38 pm
Location: Yale School of Public Health

Re: Using vectors as arguments for pt3dadd

Post by ramcdougal » Tue Mar 03, 2020 8:34 am

There are two ways to define 3D points.

The more object-oriented way is to use sections, e.g.

Code: Select all

soma.pt3dadd(x, y, z, d)
Unfortunately, that way requires numbers for the arguments.

The older (and, apparently, more flexible in that it supports Vectors) way uses h and requires a sec= argument; in particular, it is not a method of the section:

Code: Select all

from neuron import h

soma = h.Section(name='soma')

x = h.Vector([0, 5, 10])
y = h.Vector([0, 0, 0])
z = h.Vector([4, 3, 8])
d = h.Vector([1, 2, 1])

h.pt3dadd(x, y, z, d, sec=soma)

for i in range(soma.n3d()):
    print(soma.x3d(i), soma.y3d(i), soma.z3d(i), soma.diam3d(i))

neuromau
Posts: 97
Joined: Mon Apr 20, 2009 7:02 pm

Re: Using vectors as arguments for pt3dadd

Post by neuromau » Tue Mar 03, 2020 9:06 pm

Thank you, I will try using that syntax instead!

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