whitening_mat.npy problem

[blinklab]

In kilosort 2.0, the whitening_mat.npy file contains the real whitening matrix:
whiteningMatrix = rez.Wrot/rez.ops.scaleproc;
The inverse of this matrix is used to compute the template amplitude using this code
whiteningMatrixInv = whiteningMatrix^-1;

% here we compute the amplitude of every template...

% unwhiten all the templates
tempsUnW = zeros(size(templates));
for t = 1:size(templates,1)
    tempsUnW(t,:,:) = squeeze(templates(t,:,:))*whiteningMatrixInv;
end

% The amplitude on each channel is the positive peak minus the negative
tempChanAmps = squeeze(max(tempsUnW,[],2))-squeeze(min(tempsUnW,[],2));

By contrast, in kilosort 2.5 and kilosort 3.0, the whitening_mat.npy only contains a diagonal matrix that not correspond with the real whitening matrix used in the code:
whiteningMatrix = eye(size(rez.Wrot)) / rez.ops.scaleproc;

Which one is the reason to introduce this change in the code?.

[marius10p]

I don't think this is right, could you please send the line numbers?

[SEONGGAP]

@marius10p

I have a same issue.

After kilosort 2.5 and 3.0 (not 2.0), the whitening_mat.npy contains diagonal matrix.
For that reason, I cannot get template amplitude.

Are there any changes in calculating a template amplitude at kilosort 2.5 and 3.0?

[zhengyangwang]

I don't think this is right, could you please send the line numbers?

I think it was last updated here in rezToPhy and inherited by rezToPhy2, so "whitening_mat.npy" and "whitening_mat_inv.npy" do not contain the real matrices. Is there much significance to this change @marius10p ?

Kilosort/utils/rezToPhy.m

Lines 69 to 71 in ad462bd

	% whiteningMatrix = rez.Wrot/rez.ops.scaleproc;
	whiteningMatrix = eye(size(rez.Wrot)) / rez.ops.scaleproc;
	whiteningMatrixInv = whiteningMatrix^-1;

[JoeZiminski]

might this discussion be related to this issue?