Parameter Space Exploration in Python

[Joelle Zimmermann]

Hello - has anybody done parameter space exploration in Python? I understand that it is basically just like running a simulation but iterating through the parameters. But, an example to look off of for this kind of iterative parameter exploration would be a great help :) I cant seem to find much on github..

Thanks,

Joelle

[Marmaduke Woodman]

Hi Joelle,

In the simplest scenario, I suggest writing a function that does your single simulation, given the varying parameters, then calling it in a for loop:

import numpy as np
import tvb.simulator.lab as tvb

def runsim(a_i):
    mod = tvb.models.Generic2dOscillator(a=a_i)
    sim = tvb.simulator.Simulator(model=mod)
    sim.configure()
    results = []
    for (t, data), in sim(simulation_length=10.0):
        results.append(data)
    return np.array(results)

a = np.array([1.0, 2.0])

for i, a_i in enumerate(a):
    results = runsim(a_i)
    np.save('results_%03d.npy', results)

Multidimensional parameter explorations are slightly more elaborate and can be done in several ways; I do the following

from itertools import product

a = np.r_[-1:2:0.1]
b = np.r_[-0.3:0:0.05]
c = np.r_[-10:20:2]

for i, (ai, bi, ci) in product(a, b, c):
    np.save('results_%06.npy', runsim(ai, bi, ci))

Let us know if you have further questions on this,

cheers,
Marmaduke

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[Joelle Zimmermann]

Thanks very much Marmaduke :) This is great.

[Jan Stasiński]

Hi, I am trying to run a similar multiparameter space exploration code in python but a few years later :) 
The sample code that was suggested is throwing "too many values to unpack" error so is tvb my adaptation of that solution.

As this was a few years ago and perhaps there are some improved sample codes for running 3,4 parameter space exploration in python?
I am not a proficient coder so any suggestions will be much appreciated.
Best
Jan

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[WOODMAN Michael]

hi

which line does the error occur?

Marmaduke Woodman, TVB Engineer, INS AMU; +33 7 67 77 84 72

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From: tvb-...@googlegroups.com <tvb-...@googlegroups.com> on behalf of Jan Stasiński <ja.sta...@gmail.com>
Sent: Friday, June 12, 2020 4:40:50 PM
To: TVB Users
Subject: [TVB] Re: Parameter Space Exploration in Python

 

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[Jan Stasiński]

Hi Marmaduke, 

My apologies for the late answer. The line occurred in the first line I believe. I have managed to run PSE using a list comprehension with for loops finally.
Thank you for your response.

Best regards
Jan

On Friday, June 12, 2020 at 10:27:07 PM UTC+2, marmaduke.woodman wrote:

hi

which line does the error occur?

Marmaduke Woodman, TVB Engineer, INS AMU; +33 7 67 77 84 72

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[Borjan Milinkovic]

Hi all,

I know this is a few years off again, but using the same code as above, I am getting the same issue regarding "not enough values to unpack" 

The error is happening in the line:

for (data, time) in sim(simulation_length=2000): 

as sim does not have the two values data and time to unpack. I'm not so sure why this is happening. 

Any help would be much appreciated.

Thanks,

Boki

[WOODMAN Michael]

hi, 

you are missing the comma:

for (data, time), in sim

The simulator is returning samples from the monitors, so if you have several, then you would have something like 

for (eeg, t), (meg, t) in sim

but in the case of one monitor you still need the comma because of Python syntax for tuples of one element.

cheers,

Marmaduke 

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[Borjan Milinkovic]

Hi Marmaduke,

Ah, thanks so much--of course!

Much appreciated. 

Best,

Boki