Suite2P
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cortex-lab
bug in GetRandFrames() due to reshape()
Hi guys!
In lines 65 and 109 you reshape the data from a 3-dimensional array into a 4-dimensional array with dimensions: [Ly, Lx, nPlanes, nFrames]. Hence, the code crashes if the length of the 3rd dimension is not divisible by nplanes. For example, say you have a tiff file with 2000 frames and you want to sample from 7 planes.
Do you have target frame non-empty? I can see how that block could error (line 65 if min(ops.NimgFirstRegistration, numFrnplanesnchannels) is the ops.NimgFirstRegistration).
However, in the else statement (line 102), tiffs that don't have enough frames should be skipped. And if it has enough frames then nchannels*nplanes*nfmax should be divisible by nplanes correct? What are the ichanset values that you're getting? are those divisible by nplanes?
Yes, target frame is non-empty. I get the error in line 65.
Sent from my Samsung Galaxy smartphone.
-------- Original message -------- From: carsen-stringer [email protected] Date: 18/03/2019 20:12 (GMT+00:00) To: cortex-lab/Suite2P [email protected] Cc: "Diamanti, Efthymia" [email protected], Author [email protected] Subject: Re: [cortex-lab/Suite2P] bug in GetRandFrames() due to reshape() (#166)
Do you have target frame non-empty? I can see how that block could error (line 65 if min(ops.NimgFirstRegistration, numFrnplanesnchannels) is the ops.NimgFirstRegistration).
However, in the else statement (line 102), tiffs that don't have enough frames should be skipped. And if it has enough frames then nchannelsnplanesnfmax should be divisible by nplanes correct? What are the ichanset values that you're getting? are those divisible by nplanes?
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ah okay, is numFr an integer? The line to check and change is 54. numFrnchannelsnplanes should be an integer and also less than the number of frames in your tiff.
sorry github changed formatting
numFr*nchannels*nplanes
should be an integer
Thanks Carsen!
Yes now I understand!
-------- Original message -------- From: carsen-stringer [email protected] Date: 18/03/2019 20:57 (GMT+00:00) To: cortex-lab/Suite2P [email protected] Cc: "Diamanti, Efthymia" [email protected], Author [email protected] Subject: Re: [cortex-lab/Suite2P] bug in GetRandFrames() due to reshape() (#166)
ah okay, is numFr an integer? The line to check and change is 54. numFrnchannelsnplanes should be an integer and also less than the number of frames in your tiff.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/cortex-lab/Suite2P/issues/166#issuecomment-474098042, or mute the threadhttps://github.com/notifications/unsubscribe-auth/APMNo9kOZDdut11dChfYQnhrcHr-PRmsks5vX_3BgaJpZM4b6oua.
also if you figure out a fix can you please test it and then make a pull request with the fix :)
Sure! I'll get back to it tomorrow.
Sent from my Samsung Galaxy smartphone.
-------- Original message -------- From: carsen-stringer [email protected] Date: 18/03/2019 21:00 (GMT+00:00) To: cortex-lab/Suite2P [email protected] Cc: "Diamanti, Efthymia" [email protected], Author [email protected] Subject: Re: [cortex-lab/Suite2P] bug in GetRandFrames() due to reshape() (#166)
also if you figure out a fix can you please test it and then make a pull request with the fix :)
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