Phy GUI Error - No Features Displayed in the FeatureView Window

Bapun Giri

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Nov 4, 2016, 12:57:13 PM11/4/16

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Hi Phy Users,

I am experiencing a strange error where some of the clusters in the Phy-GUI do not show the features in the feautureview window. When clicking on that cluster the terminal prints out the following error:

11:47:12 [E] cli:39 An error has occurred (IndexError): index 111569 is out of bounds for axis 1 with size 111549

11:47:13 [E] cli:39 An error has occurred (IndexError): index 111918 is out of bounds for axis 1 with size 111549

and for some clusters

11:53:36 [E] cli:39 An error has occurred (AssertionError):

11:53:37 [E] cli:39 An error has occurred (AssertionError):

11:53:38 [E] cli:39 An error has occurred (AssertionError):

11:53:39 [E] cli:39 An error has occurred (AssertionError):

11:53:40 [E] cli:39 An error has occurred (AssertionError):

11:53:41 [E] cli:39 An error has occurred (AssertionError):

11:53:42 [E] cli:39 An error has occurred (AssertionError):

11:53:43 [E] cli:39 An error has occurred (AssertionError):

I have attached the kwik files for you guys to have a look.

Thanks

tedmaze1-sh03.kwik

tedmaze1-sh03.prm

Cyrille Rossant

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Nov 7, 2016, 4:59:47 AM11/7/16

to Bapun Giri, phy-users

Hi, could you send me the kwx file too?

Thanks

Cyrille

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Mostafa Safaie

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Nov 7, 2016, 11:01:16 AM11/7/16

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I have the same problem. My phy, phycontrib, and klusta are the latest version (I don't think I had this error before recent updates). When I run phy kwik-gui, most of the clusters raise the following error:

15:53:45 [D] gui_component:393 Select clusters: 13.

15:53:45 [E] cli:39 An error has occurred (IndexError): index 1516749 is out of bounds for axis 1 with size 1516330

15:53:45 [D] cli:42 Traceback (most recent call last):

File "/home/david/anaconda3/envs/phy/lib/python3.5/site-packages/phy/gui/widgets.py", line 196, in _emit_from_js

self.emit(text_type(name), json.loads(text_type(arg_json)))

File "/home/david/anaconda3/envs/phy/lib/python3.5/site-packages/phy/gui/widgets.py", line 115, in emit

return self._event.emit(*args, **kwargs)

File "/home/david/anaconda3/envs/phy/lib/python3.5/site-packages/phy/utils/event.py", line 121, in emit

res.append(callback(*args, **kwargs))

File "/home/david/anaconda3/envs/phy/lib/python3.5/site-packages/phy/cluster/manual/gui_component.py", line 334, in on_select

self._emit_select(cluster_ids)

File "/home/david/anaconda3/envs/phy/lib/python3.5/site-packages/phy/cluster/manual/gui_component.py", line 395, in _emit_select

self.gui.emit('select', cluster_ids)

File "/home/david/anaconda3/envs/phy/lib/python3.5/site-packages/phy/gui/gui.py", line 228, in emit

return self._event.emit(*args, **kwargs)

File "/home/david/anaconda3/envs/phy/lib/python3.5/site-packages/phy/utils/event.py", line 121, in emit

res.append(callback(*args, **kwargs))

File "/home/david/anaconda3/envs/phy/lib/python3.5/site-packages/phy/cluster/manual/views.py", line 1214, in on_select

x = self._get_feature(x_dim[i, j], spike_ids, f)

File "/home/david/anaconda3/envs/phy/lib/python3.5/site-packages/phy/cluster/manual/views.py", line 1055, in _get_feature

return -1. + (2. / self.duration) * self.spike_times[spike_ids]

IndexError: index 1516749 is out of bounds for axis 1 with size 1516330

If you found a solution, please let me know as well.

Thanks.

Mostafa

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Bapun Giri

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Nov 7, 2016, 12:38:52 PM11/7/16

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Hi Cyrille,

Please find the attached .kwx file.

https://drive.google.com/open?id=0B1KdUXVXyc24MERkU3NKampQOWs

Thanks,

Bapun

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Cyrille Rossant

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Nov 8, 2016, 6:27:52 AM11/8/16

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Hi Mostafa and Bapun

I cannot reproduce the error on both of your datasets. It works fine on my computer with the latest development versions of klusta, phy, and phycontrib. Can you update the packages, delete the .phy subfolders, and try again?

Best,

Cyrille

Mostafa Safaie

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Nov 8, 2016, 8:55:30 AM11/8/16

to Cyrille Rossant, phy-users

Hi Cyrrile,

I did the following:

source activate phy

git clone https://github.com/kwikteam/
(
p
hy
/phy-contrib/klusta)

cd (phy/phy-contrib/klusta)

python setup.py develop

for each one of the three packages. After that using phy kwik-gui abcd.kwik unfortunately I still get the same error for most of the clusters.

Mostafa

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Bapun Giri

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Nov 8, 2016, 2:45:23 PM11/8/16

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Hi Cyrille,

Deleting the .phy folder did solve the issue. However, the error resurfaces once I move from one kwik file to the other, but deleting the .phy subfolder again resolves the issue.

Thanks for the help,

Bapun

Bapun Giri

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Nov 8, 2016, 2:46:34 PM11/8/16

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Hi Mostafa,

Have you tried deleting the .phy subfolder ?

Best,

Bapun

On Tuesday, November 8, 2016 at 7:55:30 AM UTC-6, Mostafa Safaie wrote:

Hi Cyrrile,

I did the following:

source activate phy
git clone https://github.com/kwikteam/
(
p
hy
/phy-contrib/klusta)
cd (phy/phy-contrib/klusta)
python setup.py develop
for each one of the three packages. After that using phy kwik-gui abcd.kwik unfortunately I still get the same error for most of the clusters.

Mostafa

On Tue, Nov 8, 2016 at 11:27 AM, Cyrille Rossant <cyrille...@gmail.com> wrote:

Hi Mostafa and Bapun
I cannot reproduce the error on both of your datasets. It works fine on my computer with the latest development versions of klusta, phy, and phycontrib. Can you update the packages, delete the .phy subfolders, and try again?
Best,
Cyrille

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Mostafa Safaie

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Nov 8, 2016, 2:50:33 PM11/8/16

to Bapun Giri, phy-users

Hi Bapun,

Yes, I did and it worked.

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Cyrille Rossant

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Nov 10, 2016, 5:10:26 AM11/10/16

to Bapun Giri, phy-users

This problem is now fixed in the development version of phycontrib. You no longer have to delete the .phy subfolder when you sort different kwik files in the same directory.

Boleslaw Osinski

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Jun 15, 2017, 5:50:45 PM6/15/17

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Hi all,

I'm running what I think are the latest versions of phy (1.0.9), phy-contrib (1.0.15), and klusta (3.0.16), but I'm still getting this error. Deleting the .phy subfolder fixes it as it did before. The error only occurs after I change a parameter and rerun klusta in the same folder. Just letting you know in case other people are still having it.