User defined function to set play vectors

[Robert Claar]

I wanted to make this post to get some clarification about the behavior I am observing and also in case anyone else runs into a similar issue.

I am using the Vector.play method to set the values of a parameter inside one of my mod files. I started with a toy example that I found here in the forums viewtopic.php?p=19985&hilit=play+vectors#p19985. I made some minor modifications, mainly using single segment Sections.

For my use case it made sense to have my own function to set the play vectors, so I used the same code but took out the portion setting the play vectors and used it to create a function

Code: Select all

def set_play_vec(cell):
	
    data = h.Vector([0,5,17,2,4,38,22,43,1, 1])
    time = h.Vector([1,2,3,4,5,6,7,8,9,10])

    data.play(cell(0.5).playtest._ref_xx, time, True)
	
# Create NEURON Section
my_cell = h.Section("neurite")

# Set play vector
set_play_vec(my_cell)

t = h.Vector().record(h._ref_t)
xxp1 = h.Vector().record(my_cell(0.1).playtest._ref_xx)
xxp2 = h.Vector().record(my_cell(0.9).playtest._ref_xx)

h.finitialize(-65 * mV)
h.continuerun(10 * ms)

plt.plot(t, xxp1, label="xxp1")
plt.plot(t, xxp2, label="xxp2")
plt.legend()
plt.show()

However, when I did this I saw my recorded variables xxp1 and xxp2 were zero for all time points. After trying a bunch of different things I got it to work once I returned the data and time Vectors that I created inside my set_play_vecs function so they are available outside the scope of the function.

Code: Select all

def set_play_vec(cell):
	
    data = h.Vector([0,5,17,2,4,38,22,43,1, 1])
    time = h.Vector([1,2,3,4,5,6,7,8,9,10])

    data.play(cell(0.5).playtest.xx, time, True)
	
    return data, time
	
# Create NEURON Section	
my_cell = h.Section(name='neurite')

# Set play vector
data, time = set_play_vec(my_cell)

t = h.Vector().record(h._ref_t)
xxp1 = h.Vector().record(my_cell(0.1).playtest._ref_xx)
xxp2 = h.Vector().record(my_cell(0.9).playtest._ref_xx)

h.finitialize(-65 * mV)
h.continuerun(10 * ms)

plt.plot(t, xxp1, label="xxp1")
plt.plot(t, xxp2, label="xxp2")
plt.legend()
plt.show()

I also found that I could get it to work if I first made the time and data Vectors into global variables

Code: Select all

global data
global time
data = h.Vector([ 1,5,17,2,4,38,22,43,1, 1])
time = h.Vector([1,2,3,4,5,6,7,8,9,10])

Can anyone explain why these variables need to be available outside the scope of my function? I'm guessing the data Vector itself is still being referenced to during the simulation.

[ted]

Can anyone explain why these variables need to be available outside the scope of my function?

"Can anyone"? Sure--and in particular, you. Create some variable x inside a function and assign it a value. Exit the function without passing the value of x to an external variable. Then try using x after exiting from the function e.g. by printing its value or adding 1 to it and printing the result. What happens and why? Suppose "using that variable after exiting from the function" involves running a simulation--how's that going to work?

[Robert Claar]

Sorry, some of my code was incorrect which makes my question seem silly (maybe it still will be when I correct it).

The initial chunk of code in my original post above should have been

Code: Select all

def set_play_vec(cell):
	
    data = h.Vector([0,5,17,2,4,38,22,43,1, 1])
    time = h.Vector([1,2,3,4,5,6,7,8,9,10])

    data.play(cell(0.5).playtest._ref_xx, time, True)
    
    return cell
	
# Create NEURON Section
my_cell = h.Section("neurite")

# Set play vector
my_cell = set_play_vec(my_cell)

t = h.Vector().record(h._ref_t)
xxp1 = h.Vector().record(my_cell(0.1).playtest._ref_xx)
xxp2 = h.Vector().record(my_cell(0.9).playtest._ref_xx)

h.cvode_active(True)
h.finitialize(-65 * mV)
h.continuerun(10 * ms)

plt.plot(t, xxp1, label="xxp1")
plt.plot(t, xxp2, label="xxp2")
plt.legend()
plt.show()

My initial instinct was to return the Section containing the mechanism that I am playing values into, but when I did this, my recording vectors xxp1 and xxp2 contained all zeros. However, when I did not return my Section but returned the data and time Vectors that contain my values I want played in, things worked as I expected.

Code: Select all

def set_play_vecs(cell):

    # Create some toy data
    data = h.Vector([4, 1, 5, 17, 2, 4, 38, 22, 43, 1, 1])
    time = h.Vector([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10])

    # Play the data vector values into the variable xx inside the mode file
    data.play(cell(0.5).playtest._ref_xx, time, True)

    # These vectors need to be returned so they are available outside the scope of this function
    # else no error will be raised but the variable will only take the value stated in the mod file
    return data, time

# Create a section
my_cell = h.Section("neurite")
my_cell.insert("playtest")

# Set play vectors
data, time = set_play_vecs(my_cell)

t = h.Vector().record(h._ref_t)
xxp1 = h.Vector().record(my_cell(0.1).playtest._ref_xx)
xxp2 = h.Vector().record(my_cell(0.9).playtest._ref_xx)

h.cvode_active(True)
h.finitialize(-65 * mV)
h.continuerun(10 * ms)

plt.plot(t, xxp1, label="xxp1")
plt.plot(t, xxp2, label="xxp2")
plt.legend()
plt.show()

This seemed odd to me since I am just returning, to my knowledge, two Vectors and not the Section containing the mechanism I am playing values into. However, now after a week or so of not looking at this, I notice that play is a method of Vector so I'm guessing that the data Vector contains the instructions to play into the xx variable inside the playtest mechanism inside my_cell, so it makes sense that I would need to return the vector being played instead of my Section.