[NEST Users] Re: Spatial grid + jitter

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 &lt;hans.ekkehard.plesser(a)nmbu.no&gt; Sendt: tirsdag 6. april 2021 16:28 Til: NEST User Mailing List &lt;users(a)nest-simulator.org&gt; Kopi: Kurth, Anno &lt;a.kurth(a)fz-juelich.de&gt; 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.no<mailto:hans.ekkehard.plesser@nmbu.no> Home http://arken.nmbu.no/~plesser On 06/04/2021, 12:05, "Albers, Jasper" <j.albers@fz-juelich.de<mailto: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 networks<https://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 ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------