is bz_ReadProbeMapFiles the same as bz_ReadProbeGeometryFiles

[englishdaniel]

I am trying to run bz_PreprocessExtracellEphysAnimal

and get Undefined function or variable 'bz_ReadProbeMapFiles'.

Error in Run_171108_143958_AnimalMetadataText (line 194) [PerGroupSuperficialToDeep,SpatialXY,NumChansPerProbe,GroupsPerChannel] = bz_ReadProbeMapFiles(AnimalMetadata.ExtracellEphys.Probes.ProbeLayoutFilenames);

is this because it should be calling bz_ReadProbeGeometryFiles not bz_ReadProbeMapFiles? if not, where an I find bz_ReadProbeMapFiles

[brendonw1]

I assume yes. I think regardless you can use the bz_ReadProbeGeometryFiles call instead. Wanna submit that change to the repository on the dev branch?

On Thu, Sep 6, 2018 at 1:09 PM englishdaniel notifications@github.com wrote:

I am trying to run bz_PreprocessExtracellEphysAnimal

and get Undefined function or variable 'bz_ReadProbeMapFiles'.

Error in Run_171108_143958_AnimalMetadataText (line 194) [PerGroupSuperficialToDeep,SpatialXY,NumChansPerProbe,GroupsPerChannel] =

bz_ReadProbeMapFiles(AnimalMetadata.ExtracellEphys.Probes.ProbeLayoutFilenames);

is this because it should be calling bz_ReadProbeGeometryFiles not bz_ReadProbeMapFiles? if not, where an I find bz_ReadProbeMapFiles

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[dlevenstein]

Question for all, especially those collecting new data (@DavidTingley, @brendonw1, @AntonioFR8, @samamckenzie, @evilrobotxoxo, @petersenpeter, @valegarman, @raswanson etc): how many are using bz_PreprocessExtracellEphysAnimal?

It seems like everyone still has their own separate preprocessing steps. Do we want to re-open the issue of standardizing preprocessing or shall we accept that people are inevitably going to have different preprocessing preferences and as long as all roads lead to buzcode we'll be OK.

[brendonw1]

I'd have a standard script with choose-able menu options. Insert or don't insert various steps as needed using input options but have all the core funcitonality coded up for people if they want to use it

On Fri, Sep 7, 2018 at 12:13 PM Dan Levenstein notifications@github.com wrote:

Question for all, especially those collecting new data (@DavidTingley https://github.com/DavidTingley, @brendonw1 https://github.com/brendonw1, @AntonioFR8 https://github.com/AntonioFR8, @samamckenzie https://github.com/samamckenzie, @evilrobotxoxo https://github.com/evilrobotxoxo, @petersenpeter https://github.com/petersenpeter, @valegarman https://github.com/valegarman, @raswanson https://github.com/raswanson etc): how many are using bz_PreprocessExtracellEphysAnimal?

It seems like everyone still has their own separate preprocessing steps. Do we want to re-open the issue of standardizing preprocessing or shall we accept that people are inevitably going to have different preprocessing preferences and as long as all roads lead to buzcode we'll be OK.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/buzsakilab/buzcode/issues/239#issuecomment-419489624, or mute the thread https://github.com/notifications/unsubscribe-auth/ADXrTal07VMZIlqeukIJuY7WY1fHxxH7ks5uYps-gaJpZM4WdWoG .

[dlevenstein]

Personally, I think it would be great to have something standardized, but this is definitely something that should be arrived on by the data-collectors in the group and I understand that people have different preprocessing desires. So as long as everything leads to buzcode-compadible files (and people are willing/able to make the end result of their preprocessing buzcode friendly) that's good enough.

If bz_PreprocessExtracellEphysAnimal isn't being used by anyone, we should remove it from the repo.

Also, we should update the metadata sections of the wiki to reflect what people are actually doing.

[brendonw1]

Should I try to put together a list of stuff people might want to do as far as automated pre-processing and then people add to that list? Stuff you'd want done on every file for some experiment in night number 1 after recording, for instance.

Then people can add to it

Then I can make a function that lets people specify what to include or not?

We can call it bz_PreprocessExtracellEphysAnimal and keep the defaults of that function the same but add options (ie call kilosort, etc)

?

[englishdaniel]

That sounds great to me. Call kilosort, extract LFP, etc?

On Mon, Sep 10, 2018 at 11:57 AM Brendon Watson notifications@github.com wrote:

Should I try to put together a list of stuff people might want to do as far as automated pre-processing and then people add to that list? Stuff you'd want done on every file for some experiment in night number 1 after recording, for instance.

Then people can add to it

Then I can make a function that lets people specify what to include or not?

We can call it bz_PreprocessExtracellEphysAnimal and keep the defaults of that function the same but add options (ie call kilosort, etc)

?

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-- Daniel F. English, Ph.D. Assistant Professor Virginia Tech - School of Neuroscience Email: neurodan83@vt.edu Website: www.englishneurolab.com http://www.danenglishneuro.com

[englishdaniel]

Did you add this to github? If it's not ready for that yet, could you you send it to me? Thanks

Dan

On Fri, Sep 7, 2018, 12:15 PM Brendon Watson notifications@github.com wrote:

I'd have a standard script with choose-able menu options. Insert or don't insert various steps as needed using input options but have all the core funcitonality coded up for people if they want to use it

On Fri, Sep 7, 2018 at 12:13 PM Dan Levenstein notifications@github.com wrote:

Question for all, especially those collecting new data (@DavidTingley https://github.com/DavidTingley, @brendonw1 https://github.com/brendonw1, @AntonioFR8 https://github.com/AntonioFR8, @samamckenzie https://github.com/samamckenzie, @evilrobotxoxo https://github.com/evilrobotxoxo, @petersenpeter https://github.com/petersenpeter, @valegarman https://github.com/valegarman, @raswanson < https://github.com/raswanson> etc): how many are using bz_PreprocessExtracellEphysAnimal?

It seems like everyone still has their own separate preprocessing steps. Do we want to re-open the issue of standardizing preprocessing or shall we accept that people are inevitably going to have different preprocessing preferences and as long as all roads lead to buzcode we'll be OK.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <https://github.com/buzsakilab/buzcode/issues/239#issuecomment-419489624 , or mute the thread < https://github.com/notifications/unsubscribe-auth/ADXrTal07VMZIlqeukIJuY7WY1fHxxH7ks5uYps-gaJpZM4WdWoG

.

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[brendonw1]

@DavidTingley are you OK with this? bz_PreprocessExtracellEphysAnimal was your file initially so I don't want to ruin your vision of it. I'd write it so it's backwards compatible and would give the same output as it does not, if it's something people use

[DavidTingley]

Hmm, I've actually never used bz_PreprocessExtracellEphysAnimal. Go for it.

[brendonw1]

Will do