Dear Jasper, dear Anno,

You are right, the figure does not correspond to the code snippet in the documentation. I actually don't think it is possible to create a regular grid with jitter with NEST 3, except for sending a positions vector as you are indicating. The following code should work, and create Figure 8 in the documentation, but we are of course trying to get away from lists of positions in NEST 3. I will create follow-up issues about this, both for the wrong code snippet and for the creation of grid with jitter.

import numpy as np import nest import matplotlib.pyplot as plt

xs = np.arange(-0.5,.501,0.1) poss = [[x,y] for y in xs for x in xs]

poss = [[p[0]+np.random.uniform(-0.03,0.03),p[1]+np.random.uniform(-0.03,0.03)] for p in poss] positions = nest.spatial.free(poss)

s_nodes = nest.Create('iaf_psc_alpha', positions=positions)

nest.PlotLayer(s_nodes) plt.show()

Best wishes, Stine ________________________________ Fra: Hans Ekkehard Plesser hans.ekkehard.plesser@nmbu.no Sendt: tirsdag 6. april 2021 16:28 Til: NEST User Mailing List users@nest-simulator.org Kopi: Kurth, Anno a.kurth@fz-juelich.de Emne: [NEST Users] Re: Spatial grid + jitter

Dear Jasper,

In NEST 3, this should be possible.

Stine or Håkon, could you provide some advice?

Best,

Hans Ekkehard

--

Prof. Dr. Hans Ekkehard Plesser

Head, Department of Data Science

Faculty of Science and Technology

Norwegian University of Life Sciences

PO Box 5003, 1432 Aas, Norway

Phone +47 6723 1560

Email hans.ekkehard.plesser@nmbu.nomailto:hans.ekkehard.plesser@nmbu.no

Home http://arken.nmbu.no/~plesser

On 06/04/2021, 12:05, "Albers, Jasper" <j.albers@fz-juelich.demailto:j.albers@fz-juelich.de> wrote:

Dear all,

a colleague of mine (in CC) and myself are implementing a spatially structured network in NEST (using current NEST master). We are wondering how to generate a population of neurons that are distributed on a regular grid plus a random jitter. This means that we want to end up with a spatial distribution as can be seen in Figure 8 in the tutorial for creating spatially structured networkshttps://nest-simulator.readthedocs.io/en/latest/tutorials/pynest_tutorial/part_4_spatially_structured_networks.html?highlight=jitter#defining-spatially-distributed-nodes. Below that figure one finds a code snippet; however, we believe that this does not correspond to the distribution of Figure 8.

In the documentation of NEST 2.20.1 we did find a code snippet that produces a jittered grid:

import numpy as np

# grid with jitter

jit = 0.03

xs = np.arange(-0.5,.501,0.1)

poss = [[x,y] for y in xs for x in xs]

poss = [[p[0]+np.random.uniform(-jit,jit),p[1]+np.random.uniform(-jit,jit)] for p in poss]

layer_dict_ex = {"positions": poss,

"extent" : [1.1,1.1],

"elements" : "iaf_psc_alpha"}

As is apparent, this code does not make use of NEST internal random number generation but rather produces a list of positions that is then passed to a layer.

Thus our question is: is it possible to create a jittered grid natively in NEST master?

Best regards,

Jasper and Anno

------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Frauke Melchior ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------