Kilosort 3 error in griddedInterpolant

[ntotah]

Hi,
I am getting an error during sorting. Same dat file works for Kilosort 2.0. Just thought you would like to know. It would be nice to see how 3.0 performs but so far haven't been able to get it to run. I hope the report is helpful for you. Thanks!

Error using griddedInterpolant
The grid vectors must contain unique points.

Error in interp1 (line 151)
F = griddedInterpolant(X,V,method);

Error in shift_batch_on_disk2 (line 14)
shifts = interp1(ysamp, shifts, rez.yc, 'makima', 'extrap');

Error in datashift2 (line 149)
dprev = shift_batch_on_disk2(rez, ibatch, dshift(ibatch, :), yblk, sig,
dprev);

Error in main_kilosort3 (line 38)
rez = datashift2(rez, 1);

[prophesyPPI]

Hi,
I encountered a similar problem. Thanks！

kilosort
Time 0s. Computing whitening matrix..
Getting channel whitening matrix...
Channel-whitening matrix computed.
Time 1s. Loading raw data and applying filters...
Time 24s. Finished preprocessing 275 batches.
vertical pitch size is 1
horizontal pitch size is 5
1.0000 3.3333 5.6667 8.0000

 3

0.24 sec, 1 batches, 300 spikes
10.17 sec, 101 batches, 42687 spikes
19.83 sec, 201 batches, 85587 spikes
26.81 sec, 275 batches, 115081 spikes
Error using griddedInterpolant
The coordinates of the input points must be finite values; Inf and NaN are not permitted.

Error in interp1 (line 151)
F = griddedInterpolant(X,V,method);

Error in shift_batch_on_disk2 (line 14)
shifts = interp1(ysamp, shifts, rez.yc, 'makima', 'extrap');

Error in datashift2 (line 149)
dprev = shift_batch_on_disk2(rez, ibatch, dshift(ibatch, :), yblk, sig, dprev);

Error in ksGUI/runPreproc (line 732)
obj.rez = datashift2(obj.rez, 1);

Error in ksGUI>@(,)obj.runPreproc() (line 333)
'Callback', @(,)obj.runPreproc());

Error while evaluating UIControl Callback.

[VegaLoki]

Getting this same error. Were either of you able to make progress with this?

[ntotah]

No update on this, So we went back to kilosort 2 for now.

…

On Mon, Jul 5, 2021, 22:21 VegaLoki ***@***.***> wrote: Getting this same error. Were either of you able to make progress with this? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#392 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALTNX7NNMFJLGIX66Q56HP3TWIA4PANCNFSM44AHOIIA> .

[farazmoradi]

No update on this, So we went back to kilosort 2 for now.
…
On Mon, Jul 5, 2021, 22:21 VegaLoki @.***> wrote: Getting this same error. Were either of you able to make progress with this? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#392 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALTNX7NNMFJLGIX66Q56HP3TWIA4PANCNFSM44AHOIIA .

Hi same Error. How did you get back to Kilosort 2?

[ntotah]

<!-- /* Font Definitions */ @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4;} @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0cm; font-size:11.0pt; font-family:"Calibri",sans-serif;} a:link, span.MsoHyperlink {mso-style-priority:99; color:blue; text-decoration:underline;} span.EmailStyle21 {mso-style-type:personal-reply; font-family:"Calibri",sans-serif; color:windowtext;} .MsoChpDefault {mso-style-type:export-only; font-size:10.0pt;} @page WordSection1 {size:612.0pt 792.0pt; margin:72.0pt 72.0pt 72.0pt 72.0pt;} div.WordSection1 {page:WordSection1;} -->We KS2 and KS3 are different paths, so you would just need to use the KS2 folders for your work instead of the KS3  From: farazmoradi ***@***.***>Date: Sunday, 25. July 2021 at 15.48To: MouseLand/Kilosort ***@***.***>Cc: ntotah ***@***.***>, Author ***@***.***>Subject: Re: [MouseLand/Kilosort] Kilosort 3 error in griddedInterpolant (#392)No update on this, So we went back to kilosort 2 for now.…On Mon, Jul 5, 2021, 22:21 VegaLoki @.***> wrote: Getting this same error. Were either of you able to make progress with this? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#392 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALTNX7NNMFJLGIX66Q56HP3TWIA4PANCNFSM44AHOIIA .Hi same Error. How did you get back to Kilosort 2?—You are receiving this because you authored the thread.Reply to this email directly, view it on GitHub, or unsubscribe.

[farazmoradi]

We KS2 and KS3 are different paths, so you would just need to use the KS2 folders for your work instead of the KS3  From: farazmoradi ***@***.***>Date: Sunday, 25. July 2021 at 15.48To: MouseLand/Kilosort ***@***.***>Cc: ntotah ***@***.***>, Author ***@***.***>Subject: Re: [MouseLand/Kilosort] Kilosort 3 error in griddedInterpolant (#392)No update on this, So we went back to kilosort 2 for now.…On Mon, Jul 5, 2021, 22:21 VegaLoki @.***> wrote: Getting this same error. Were either of you able to make progress with this? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#392 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALTNX7NNMFJLGIX66Q56HP3TWIA4PANCNFSM44AHOIIA .Hi same Error. How did you get back to Kilosort 2?—You are receiving this because you authored the thread.Reply to this email directly, view it on GitHub, or unsubscribe.

Do you know how can I see my Kilosort version?

[ntotah]

<!-- /* Font Definitions */ @font-face {font-family:"Cambria Math"; panose-1:2 4 5 3 5 4 6 3 2 4;} @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {margin:0cm; font-size:11.0pt; font-family:"Calibri",sans-serif;} a:link, span.MsoHyperlink {mso-style-priority:99; color:blue; text-decoration:underline;} span.EmailStyle19 {mso-style-type:personal-reply; font-family:"Calibri",sans-serif; color:windowtext;} .MsoChpDefault {mso-style-type:export-only; font-size:10.0pt;} @page WordSection1 {size:612.0pt 792.0pt; margin:72.0pt 72.0pt 72.0pt 72.0pt;} div.WordSection1 {page:WordSection1;} -->This I don’t know. The code is different for the two versions, so they should be different folders. If you’re not sure which folder has KS2, then you could just download KS2 again and use that path going forward. From: farazmoradi ***@***.***>Date: Sunday, 25. July 2021 at 16.32To: MouseLand/Kilosort ***@***.***>Cc: ntotah ***@***.***>, Author ***@***.***>Subject: Re: [MouseLand/Kilosort] Kilosort 3 error in griddedInterpolant (#392)We KS2 and KS3 are different paths, so you would just need to use the KS2 folders for your work instead of the KS3  From: farazmoradi ***@***.***>Date: Sunday, 25. July 2021 at 15.48To: MouseLand/Kilosort ***@***.***>Cc: ntotah ***@***.***>, Author ***@***.***>Subject: Re: [MouseLand/Kilosort] Kilosort 3 error in griddedInterpolant (#392)No update on this, So we went back to kilosort 2 for now.…On Mon, Jul 5, 2021, 22:21 VegaLoki @.***> wrote: Getting this same error. Were either of you able to make progress with this? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#392 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALTNX7NNMFJLGIX66Q56HP3TWIA4PANCNFSM44AHOIIA .Hi same Error. How did you get back to Kilosort 2?—You are receiving this because you authored the thread.Reply to this email directly, view it on GitHub, or unsubscribe. Do you know how can I see my Kilosort version?—You are receiving this because you authored the thread.Reply to this email directly, view it on GitHub, or unsubscribe.