bz_RankOrder #369
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bz_RankOrder #369
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up to date version
Now it does the conversion without need of moving files from folders.
update on bz_PhaseModulation to work properly when wavelet method is selected
Adding the same process to power threshold in wavelet as in hilbert
updating bz_PhaseModulation and old function to convert phy/kilo to neurosuite Merging the PR - will make another issue for bz_WaveSpec/bz_Filter update
This reverts commit 32db167.
new place field function vol1
This reverts commit 8b0e855.
new detect swr
Update bz_firingMapAvg.m
Addition of speed threshold
work in progress
Merging bz_getSpikes and bz_LoadPhy. Updated bz_firingMapAvg
find place fields - work in progress
Tune some parameters to search place fields, and do it buzcode compatible
Update bz_findPlaceFields1D.m
updating my fork/branch
Made alternate version of read_Intan... be subfunction of bz_DatFileMetadata.m
bz_LFPfromDat.m: Gave option to specify no GPU use
…sonLabWorkingBranch
Gave option to not use gpu on bz_LFPFromDat.m
update monosyn code
add function to extract accelerometer data
updates on the CFC functions
Uploading new folder buzcode/analysis/RankOrder/ Also, test committing.
Inside analysis/RankOrder folder, main changes: - Rename file from bz_getEventRank to bz_RankOrder - Rename file from bz_getEventSpikes to bz_getSpikesRank - Now there is the option to test rank order from one group of events against another group (e.g. spontaneous vs induced ripples), through the 'eventIDs' input.
The last TODO of this function. Now the following fields from rankStats structure: - corrMean - corrStd - corrEvents - corrpvalEvents have an extradimension for each condition in X.placeFieldTemplate.mat, if the 'templateType' is either 'Peak' or 'CenterofMass'
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Hey Andrea - let's hold off on pulling all these changes into master until we've had time to use them. It looks like they're already in dev. |
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( Sorry, that last comment was from me - I forgot to log out of the Buzsaki lab account) |
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Hi Dan!
Antonio told me to do a pull request to notify him this was ready, so he
could test the code with his analysis.
Sorry for the inconvenience!
Andrea
El lun., 18 nov. 2019 a las 19:10, Dan Levenstein (<[email protected]>)
escribió:
… ( Sorry, that last comment was from me - I forgot to log out of the
Buzsaki lab account)
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The code is already in dev so he can try it out there. |
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Sure!
El lun., 18 nov. 2019 a las 19:14, Dan Levenstein (<[email protected]>)
escribió:
… The code is already in dev so he can try it out there.
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I bet he meant to pull request from your fork into buzsakilab/dev. Pulling from dev into master would bring in all the changes over the last few weeks, before we've all had time to test them and find any bugs/incompatibilities. In general I think it's good practice to do updates on your own fork (instead of the buzsakilab/dev branch) and then pull from your fork into dev. The git desktop app does have a silly thing where it starts with a branch called "dev" on your fork, that actually makes the updates on the group repository (buzsakilab), so I recommend making a personal dev branch on your fork (e.g. mine is called "DLdev"). We should definitely update the wiki to spell this out more clearly (as part of issue #349) |
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Oh I see!
Again, sorry! I'm so used to use git on my own, and I haven't really been
in any group dynamics.
I can remove my contributions to dev, go to our branch, add them there, and
then make a pull request from that branch to dev. Does that make sense?
Thank you for clarifying this for me!
El lun., 18 nov. 2019 a las 19:24, Dan Levenstein (<[email protected]>)
escribió:
… I bet he meant to pull request from your fork into buzsakilab/dev. Pulling
from dev into master would bring in all the changes over the last few
weeks, before we've all had time to test them and find any
bugs/incompatibilities. In general I think it's good practice to do updates
on your own fork (instead of the buzsakilab/dev branch) and then pull from
your fork into dev.
The git desktop app does have a silly thing where it starts with a branch
called "dev" on your fork, that actually makes the updates on the group
repository (buzsakilab), so I recommend making a personal dev branch on
your fork (e.g. mine is called "DLdev"). We should definitely update the
wiki to spell this out more clearly (as part of issue #349
<#349>)
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No worries at all (: this is fine - everything is in dev where it belongs :p |
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Git... :)
…On Mon, Nov 18, 2019 at 1:36 PM Dan Levenstein ***@***.***> wrote:
No worries at all (: this is fine - everything is in dev where it belongs
:p
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I tried looking at this. I don't understand what this code is for,
although I bet it's cool. Can you add comments at the top about what it is
trying to accomplish?
Same with
bz_getSpikesRank.m
On Mon, Nov 18, 2019 at 1:39 PM Brendon Watson <[email protected]>
wrote:
… Git... :)
On Mon, Nov 18, 2019 at 1:36 PM Dan Levenstein ***@***.***>
wrote:
> No worries at all (: this is fine - everything is in dev where it belongs
> :p
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub
> <#369?email_source=notifications&email_token=AA26WTNKXXIDUFKRJEPWW2DQULODJA5CNFSM4JOX62QKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEELOV5I#issuecomment-555150069>,
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Yeah, sure! I will comment them more extensively. Basically they are a tandem of functions to perform a rank order analysis (from Stark et al 2015 PNAS) to find significant sequences in your data (ripples, theta, etc..). There are more details that I will try to clarify also in the documentation. Thanks for your suggestion! -------- Mensaje original --------De: Brendon Watson <[email protected]>Fecha: lun., 18 nov. 2019 20:32Para: buzsakilab/buzcode <[email protected]>Cc: Andrea Navas-Olive <[email protected]>, Author <[email protected]>Asunto: Re: [buzsakilab/buzcode] bz_RankOrder (#369)I tried looking at this. I don't understand what this code is for,
although I bet it's cool. Can you add comments at the top about what it is
trying to accomplish?
Same with
bz_getSpikesRank.m
On Mon, Nov 18, 2019 at 1:39 PM Brendon Watson <[email protected]>
wrote:
Git... :)
On Mon, Nov 18, 2019 at 1:36 PM Dan Levenstein ***@***.***>
wrote:
> No worries at all (: this is fine - everything is in dev where it belongs
> :p
>
> —
> You are receiving this because you are subscribed to this thread.
> Reply to this email directly, view it on GitHub
> <#369?email_source=notifications&email_token=AA26WTNKXXIDUFKRJEPWW2DQULODJA5CNFSM4JOX62QKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEELOV5I#issuecomment-555150069>,
> or unsubscribe
> <https://github.com/notifications/unsubscribe-auth/AA26WTIFCIFXFHVKBMDGKVLQULODJANCNFSM4JOX62QA>
> .
>
—You are receiving this because you authored the thread.Reply to this email directly, view it on GitHub, or unsubscribe.
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bz_RankOrder (and its complementary script bz_getSpikesRank) are now finished and ready to be tested. They are stored inside ./analysis/RankOrder/.