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ioam / topographica

A general-purpose neural simulator focusing on topographic maps.
topographica.org
BSD 3-Clause "New" or "Revised" License
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some questions about gcal.ipnb #558

Closed kalok87 closed 10 years ago

kalok87 commented 10 years ago

Hallo, dear developers,

After using topo several times, I get some ideas but I do not how to implement it in the notebook gcal.ipnb, so I need your help, thank you.

1) Actually I see three different stimuli in code (one is Gaussian, one is natural photos, one is VGR). But I only see one stimulus throughout simulation which is Gaussian (I always save the activity). Is that possible to use other two stimuli? If it is, what should I do?

2) During the run, I want to save the plots of connection. Like topo.sim.V1.LGNOnAfferent.view(0,0) + topo.sim.V1.LateralInhibitory.view(0,0) + topo.sim.V1.LateralExcitatory.view(0,0), what is the command to access this task?

3) For getting a map with higher resolution, I need to do simulation in a larger map. So I decide to change retina_density and lgn_density to 48 and cortex_density to 98. But what else should I modify in order to avoid edge effect.

4) In the new update, a lot of fascinating features occur, like pinwheel estimator. But how to use those features in gcal.ipnb.

Thank you very much. Kalok

jlstevens commented 10 years ago

Sorry for the late reply!

1) From the commandline (if you aren't using the notebook) you can switch between stimuli as follows:

   ./topographica -p dataset='Nature' gcal.ty

The options are Gaussian', 'Nature' or 'VGR'

In the notebook environment you can switch by setting p.dataset='Nature' (for instance).

2) I've implemented the PlotSaver class to offer this functionality. For instance you can do:

   from dataviews.plots import PlotSaver
   PlotSaver(topo.sim.V1.LGNOnAfferent.view(0,0), filename='V1_CF.png')

Note: you will need to pull the latest topographica for this to work!

3) The simplest way to avoid edge effects is to increase the V1 area (e.g p.area=1.5) and then crop any maps you measure to the central unit area after you measure them.

4) We have added a new Tutorial which shows pinwheel and hypercolumn anaylsis (see the "GCAL Collector Tutorial")

Hope that helps! Again, sorry for the late reply...

I will close this issue now as I think I've answered all your questions. I will re-open this issue if you have any more comments about problems you have encountered.