SyncLines not working in Tutorial 7

[Ivan Shevchenko]

Hi all,

I'm having trouble with getting SyncLines to show up on the raster plot in tutorial 7. Downloading tut7.py from

http://www.netpyne.org/tutorial.html#tutorial-7-modifying-the-instantiated-network-interactively ,

the raster plot doesn't even show to begin with. It gives the following error:

Plotting raster...
  There was an exception in plotRaster():
    'NoneType' object has no attribute 'plot .

To fix this error, I needed to comment out line 55:

simConfig.analysis['plotRaster'] = {'syncLines': True, 'saveFig': True}      # Plot a raster ,

and instead put the following line somewhere after line 77:

sim.analysis.plotRaster(timeRange=[0,500],syncLines=True,saveFig=True) ,

which is an alternative way of plotting the raster plot. This fixes the error I was getting before, and I am now getting the raster plot to show up, but it doesn't have any SyncLines plotted. I have also tried plotting SyncLines on some of the other tutorial files, but I run into the same issues. Running the code

print(sim.allSimData['spkt'])

confirms that the spike times are working as intended, so this likely isn't the problem. Any help would be appreciated.

Best,

Ivan

[Valery Bragin]

Hi Ivan,

Thanks for helping to identify the issue! The fix is now available in development version, which you can access by cloning the repo locally and installing it using `pip install -e /path/where/it/was/cloned`.

Best regards,

Valery

[Reza]

Hi all,

I have a similar issue here and cannot have the raster plot, as you can see below. 

[

There was an exception in plotRaster()

Plotting recorded cell traces ... cell

Traceback (most recent call last):
  File "/usr/local/lib/python3.10/dist-packages/netpyne/analysis/utils.py", line 87, in wrapper 

     return function(*args, **kwargs) 

  File "/usr/local/lib/python3.10/dist-packages/netpyne/plotting/plotRaster.py", line 395, in plotRaster
     rasterPlotter.axis.vlines(spkTimes, 0, len(cellInds), 'red', linewidth=0.1)
NameError: name 'cellInds' is not defined

]



I have to use sim.analysis.plotRaster() to see the plot but it has no syncLines and other information above the raster plot.

Preparing spike data... Plotting raster...

[Valery Bragin]

Hi all,

I missed one step in installation instructions, sorry about that. The fix is currently available in `development` branch only, so once you cloned the repo to your machine, you have to `cd` there, and do `git checkout development` (and then `git pull` to make sure you're up to date). Hope this helps, sorry again!

Best regards,

Valery

[Reza]

Hi Valery
Thank you for your time.
I have done all the above but it seems I still have issues plotting the raster plot.

[!git clone https://github.com/Neurosim-lab/netpyne.git

%cd netpyne

!git checkout development

!git pull

!pip install -e .

# ---------------------------------------------

# cd /content/netpyne/netpyne/plotting/

!pip install -e /content/netpyne/]

(....
....
"Successfully installed netpyne-1.0.6")

Please see the shot below. 




I would be grateful if you could guide me with that.
Thank you.

Reza