ipython notebook tutorial GCAL_Tutorial.ipynb issues

[mjabri]

While waiting on the GUI issue to be resolved, I thought i try the notebook tutorials. When trying to run the GCAL_Tutorial.ipynb tutorial it runs into import issues. Is this tutorial supposed to run out of the box? Note i am using a git clone of topographica.

I tried:

• without touching my PYTHONPATH running from the doc/Tutorials directory/
• putting the topographica path in my PYTHONPATH - Then it cannot find 'param'
• putting the externals paths in my PYTHONPATH - Still cannot find param...

It seems the modules definitions and paths are not defined and ipython cannot find them.

[philippjfr]

How are you running the notebooks? Topographica has a notebook command for the command line, which will set up the environment correctly. Try:

./topographica -n

[mjabri]

Great thanks. On Sep 29, 2015 9:46 AM, "Philipp Rudiger" notifications@github.com wrote:

How are you running the notebooks? Topographica has a notebook command for the command line, which will set up the environment correctly. Try:

./topographica -n

— Reply to this email directly or view it on GitHub https://github.com/ioam/topographica/issues/631#issuecomment-143920675.

[mjabri]

All seems to work in tutorial until the command

topo.sim.Retina.input_generator.anim(50)

which fails with output:

KeyError None

If i change the value 50 to anything other than 0, it produces same error. If use anim(0) i get a pattern displayed.

[mjabri]

After further investigation, it seems the actual call to anim(50) is not the problem. So if I do: myv = topo.sim.Retina.input_generator.anim(50) I can examine myv and display all the maps one by one by typing myv[n]. But it seems displaying the lot by simply typing 'myv' is triggering the "KeyError \n None". Am I supposed to see a tiled view of the input patterns (0 to 50)? BTW Other than that, all to seem to work ok in the tutorial.

[philippjfr]

I found the issue and will file an issue with HoloViews. For now though you can remove the call to:

holoviews.archive.auto()

This call tries to archive all the plotted figures in the notebook and seems to be failing in this particular case.

[mjabri]

Thanks Philipp. That seems to do the trick and now that tutorial can work and I can see the animation. Cool... I think the Notebook is a good approach, but it will require me to change my entire present work flow. Something I will invest in eventually, but first I need to work out ways to take advantage of GPUs in the settling sheets, so i am stuck with the inability to display projections in the GUI if I am to look at integrating the sparce/GPU work somehow.