rezToPhy clusterIDs are not assigned

[babaq]

Hi,

when I do [spikeTimes, clusterIDs, amplitudes, templates, templateFeatures, ... templateFeatureInds, pcFeatures, pcFeatureInds]=rezToPhy(rez, rootdir); matlab error said it's not assigned, and indeed in rezToPhy function.

it seems the spike_clusters.npy is saved but not reflected in the clusterIDs variable in line 107.

If my guess is correct, the clusterIDs is meant to have the same meaning of spike_cluster.npy, then it could be easily fixed.

[marius10p]

Not sure what that function is supposed to return, but if you want to use the clustering results in Matlab, you are better served by the rez structure. I think I forgot to document these outputs, I'll do that soon.

[marius10p]

Actually, nvm, it's in the wiki: https://github.com/MouseLand/Kilosort2/wiki/7.-Output-variables

[nsteinme]

Sorry yes those return arguments were a deprecated old idea. As Marius says, just use rez directly, or if you discarded rez then you can load data with this function which has similar output to that list of return arguments: https://github.com/cortex-lab/spikes/blob/master/preprocessing/phyHelpers/loadKSdir.m

Fixed via: Removed the return arguments from the function e7740f6

[babaq]

thanks for point out the functions to read Phy exported data, but i am wandering if someone just need the spikeStruct that the loadKSdir returns without Phy workaround, it's the best place within the rezToPhy to return this spikeStruct.

[nsteinme]

That information is in the "rez" struct already, see the documentation that Marius linked to above. Or, you can write your own function based on rezToPhy.

[babaq]

yeah, I guess it's better letting rezToPhy to do just converting job, and write another function to extract similar data from rez.
But the similar data have already been extracted in rezToPhy, so I thought why not return it out. it's fairly Straightforward, I could make a pull request if you permit.

[nsteinme]

Well that was the original logic of having those return arguments, but I think at this point it is better to leave rezToPhy alone since it is a core component of the pipeline. Logically speaking, it has a separate function. Thanks -

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On Tue, Mar 26, 2019 at 10:35 AM Li Alex Zhang ***@***.***> wrote: yeah, I guess it's better letting rezToPhy to do just converting job, and write another function to extract similar data from rez. But the similar data have already been extracted in rezToPhy, so I thought why not return it out. it's fairly Straightforward, I could make a pull request if you permit. — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub <#36 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHPUP-MUWmQpxSur3T9gLSauNN_sTTJVks5valp5gaJpZM4cEJML> .

[babaq]

ok, I got it, thanks