metadata format and entry #86
Comments
DavidTingley
assigned brendonw1, DavidTingley, dlevenstein, juneshuoyang, AntonioFR8, samamckenzie and raswanson
|
-I think we need something that is GUI based |
|
I have been talking with June about this. I think we should make one *.mat
file that has everything we want and then build a GUI to populate it. This
should be in addition to and somewhat redundant with the XML for now and
perhaps one day we drop the XML, or the *.mat, but for now I think we need
both
…On Thu, Aug 17, 2017 at 6:50 PM, Dan Levenstein ***@***.***> wrote:
-I think we need something that is GUI based
-An update to the .xml would be ideal - the xml already works with
neuroscope and has a gui editor. All we need to do is add the fields we
need, update the GUI, and improve LoadParameters to reflect the new fields.
(and get rid of depreciated fields)
-with the GUI we can enforce required/suggested/optional
-we already have a list fields that we'd like to add that brendon worked
on pretty extensively, can be refined as we go
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As it is now, the .SessionMetadata includes the animal metadata so they are
unified.
Furthermore I made it so .xml is not redundant but is BASED on the .mats,
so no risk of mistakes. Making the animal metadata lets you create the
.xml from it... which I wrote code for. So you can record that way on day
1 before you have a session to make metadata for. So you make animal
metadata once and make the .xml from that so it's NOT redundant, but
the.mat is more primary... which is how it should be
Then when making session metadata you can just incorporate that animal
metadata
Finally, I think GUIs are fine but actually very inefficient as far as
time... ie every single day you have to open the GUI. So if you do that
then make it so there's another way to do it for people who find text more
efficient than GUI... in my case I just have a .m file that's a script for
creating the SessionMetadata.mat
On Thu, Aug 17, 2017 at 6:52 PM samamckenzie <[email protected]>
wrote:
… I have been talking with June about this. I think we should make one *.mat
file that has everything we want and then build a GUI to populate it. This
should be in addition to and somewhat redundant with the XML for now and
perhaps one day we drop the XML, or the *.mat, but for now I think we need
both
On Thu, Aug 17, 2017 at 6:50 PM, Dan Levenstein ***@***.***>
wrote:
> -I think we need something that is GUI based
> -An update to the .xml would be ideal - the xml already works with
> neuroscope and has a gui editor. All we need to do is add the fields we
> need, update the GUI, and improve LoadParameters to reflect the new
fields.
> (and get rid of depreciated fields)
> -with the GUI we can enforce required/suggested/optional
> -we already have a list fields that we'd like to add that brendon worked
> on pretty extensively, can be refined as we go
>
> —
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how do you update the metadata for the unique properties of a session? here
a prepopulated GUI would be nice
On Thu, Aug 17, 2017 at 7:15 PM, Brendon Watson <[email protected]>
wrote:
… As it is now, the .SessionMetadata includes the animal metadata so they are
unified.
Furthermore I made it so .xml is not redundant but is BASED on the .mats,
so no risk of mistakes. Making the animal metadata lets you create the
.xml from it... which I wrote code for. So you can record that way on day
1 before you have a session to make metadata for. So you make animal
metadata once and make the .xml from that so it's NOT redundant, but
the.mat is more primary... which is how it should be
Then when making session metadata you can just incorporate that animal
metadata
Finally, I think GUIs are fine but actually very inefficient as far as
time... ie every single day you have to open the GUI. So if you do that
then make it so there's another way to do it for people who find text more
efficient than GUI... in my case I just have a .m file that's a script for
creating the SessionMetadata.mat
On Thu, Aug 17, 2017 at 6:52 PM samamckenzie ***@***.***>
wrote:
> I have been talking with June about this. I think we should make one
*.mat
> file that has everything we want and then build a GUI to populate it.
This
> should be in addition to and somewhat redundant with the XML for now and
> perhaps one day we drop the XML, or the *.mat, but for now I think we
need
> both
>
> On Thu, Aug 17, 2017 at 6:50 PM, Dan Levenstein <
***@***.***>
> wrote:
>
> > -I think we need something that is GUI based
> > -An update to the .xml would be ideal - the xml already works with
> > neuroscope and has a gui editor. All we need to do is add the fields we
> > need, update the GUI, and improve LoadParameters to reflect the new
> fields.
> > (and get rid of depreciated fields)
> > -with the GUI we can enforce required/suggested/optional
> > -we already have a list fields that we'd like to add that brendon
worked
> > on pretty extensively, can be refined as we go
> >
> > —
> > You are receiving this because you were assigned.
> > Reply to this email directly, view it on GitHub
> > <#86#
issuecomment-323215077
> >,
> > or mute the thread
> > <https://github.com/notifications/unsubscribe-auth/ANnfgOEUI0bC6Mhswv-
> DfOCsRSqhaMewks5sZMOpgaJpZM4O62X5>
> > .
> >
>
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You can do that or I just copy the .m file that made the one from the
previous day (sitting in the previous folder, or actually in the folder
above as a template) and copy that. But yeah you can do it with a gui.
On Thu, Aug 17, 2017 at 4:26 PM, samamckenzie <[email protected]>
wrote:
… how do you update the metadata for the unique properties of a session? here
a prepopulated GUI would be nice
On Thu, Aug 17, 2017 at 7:15 PM, Brendon Watson ***@***.***>
wrote:
> As it is now, the .SessionMetadata includes the animal metadata so they
are
> unified.
>
> Furthermore I made it so .xml is not redundant but is BASED on the .mats,
> so no risk of mistakes. Making the animal metadata lets you create the
> .xml from it... which I wrote code for. So you can record that way on day
> 1 before you have a session to make metadata for. So you make animal
> metadata once and make the .xml from that so it's NOT redundant, but
> the.mat is more primary... which is how it should be
>
> Then when making session metadata you can just incorporate that animal
> metadata
>
> Finally, I think GUIs are fine but actually very inefficient as far as
> time... ie every single day you have to open the GUI. So if you do that
> then make it so there's another way to do it for people who find text
more
> efficient than GUI... in my case I just have a .m file that's a script
for
> creating the SessionMetadata.mat
>
>
>
>
>
> On Thu, Aug 17, 2017 at 6:52 PM samamckenzie ***@***.***>
> wrote:
>
> > I have been talking with June about this. I think we should make one
> *.mat
> > file that has everything we want and then build a GUI to populate it.
> This
> > should be in addition to and somewhat redundant with the XML for now
and
> > perhaps one day we drop the XML, or the *.mat, but for now I think we
> need
> > both
> >
> > On Thu, Aug 17, 2017 at 6:50 PM, Dan Levenstein <
> ***@***.***>
> > wrote:
> >
> > > -I think we need something that is GUI based
> > > -An update to the .xml would be ideal - the xml already works with
> > > neuroscope and has a gui editor. All we need to do is add the fields
we
> > > need, update the GUI, and improve LoadParameters to reflect the new
> > fields.
> > > (and get rid of depreciated fields)
> > > -with the GUI we can enforce required/suggested/optional
> > > -we already have a list fields that we'd like to add that brendon
> worked
> > > on pretty extensively, can be refined as we go
> > >
> > > —
> > > You are receiving this because you were assigned.
> > > Reply to this email directly, view it on GitHub
> > > <#86#
> issuecomment-323215077
> > >,
> > > or mute the thread
> > > <https://github.com/notifications/unsubscribe-
auth/ANnfgOEUI0bC6Mhswv-
> > DfOCsRSqhaMewks5sZMOpgaJpZM4O62X5>
> > > .
> > >
> >
> > —
> > You are receiving this because you were assigned.
> >
> >
> > Reply to this email directly, view it on GitHub
> > <#86#
issuecomment-323215392
> >,
> > or mute the thread
> > <https://github.com/notifications/unsubscribe-auth/ADXrTT2-AmJ6-
> zRG3fbo6s0IuhjduUd6ks5sZMQagaJpZM4O62X5>
> > .
> >
>
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> <#86 (comment)
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This can be done by building an import function on the GUI. Each time, a
user can import an existing file, modify it, and save it to a new location
via the GUI.
On Thu, Aug 17, 2017 at 7:29 PM, Brendon Watson <[email protected]>
wrote:
… You can do that or I just copy the .m file that made the one from the
previous day (sitting in the previous folder, or actually in the folder
above as a template) and copy that. But yeah you can do it with a gui.
On Thu, Aug 17, 2017 at 4:26 PM, samamckenzie ***@***.***>
wrote:
> how do you update the metadata for the unique properties of a session?
here
> a prepopulated GUI would be nice
>
> On Thu, Aug 17, 2017 at 7:15 PM, Brendon Watson <
***@***.***>
> wrote:
>
>
> > As it is now, the .SessionMetadata includes the animal metadata so they
> are
> > unified.
> >
> > Furthermore I made it so .xml is not redundant but is BASED on the
.mats,
> > so no risk of mistakes. Making the animal metadata lets you create the
> > .xml from it... which I wrote code for. So you can record that way on
day
> > 1 before you have a session to make metadata for. So you make animal
> > metadata once and make the .xml from that so it's NOT redundant, but
> > the.mat is more primary... which is how it should be
> >
> > Then when making session metadata you can just incorporate that animal
> > metadata
> >
> > Finally, I think GUIs are fine but actually very inefficient as far as
> > time... ie every single day you have to open the GUI. So if you do that
> > then make it so there's another way to do it for people who find text
> more
> > efficient than GUI... in my case I just have a .m file that's a script
> for
> > creating the SessionMetadata.mat
> >
> >
> >
> >
> >
> > On Thu, Aug 17, 2017 at 6:52 PM samamckenzie ***@***.***
>
> > wrote:
> >
> > > I have been talking with June about this. I think we should make one
> > *.mat
> > > file that has everything we want and then build a GUI to populate it.
> > This
> > > should be in addition to and somewhat redundant with the XML for now
> and
> > > perhaps one day we drop the XML, or the *.mat, but for now I think we
> > need
> > > both
> > >
> > > On Thu, Aug 17, 2017 at 6:50 PM, Dan Levenstein <
> > ***@***.***>
> > > wrote:
> > >
> > > > -I think we need something that is GUI based
> > > > -An update to the .xml would be ideal - the xml already works with
> > > > neuroscope and has a gui editor. All we need to do is add the
fields
> we
> > > > need, update the GUI, and improve LoadParameters to reflect the new
> > > fields.
> > > > (and get rid of depreciated fields)
> > > > -with the GUI we can enforce required/suggested/optional
> > > > -we already have a list fields that we'd like to add that brendon
> > worked
> > > > on pretty extensively, can be refined as we go
> > > >
> > > > —
> > > > You are receiving this because you were assigned.
> > > > Reply to this email directly, view it on GitHub
> > > > <#86#
> > issuecomment-323215077
> > > >,
> > > > or mute the thread
> > > > <https://github.com/notifications/unsubscribe-
> auth/ANnfgOEUI0bC6Mhswv-
> > > DfOCsRSqhaMewks5sZMOpgaJpZM4O62X5>
> > > > .
> > > >
> > >
> > > —
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> > >
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> > > <#86#
> issuecomment-323215392
> > >,
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> >
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Yes.
What I set up was a system that does the following when you tell it to, ie
after a new recording:
1) Copies .dats from the recording computer (via a mapped drive on wherever
you're running MATLAB)
2) Concatenates .dats, makes .lfp
(Stores lengths of each dat, timestamps etc etc)
3) Then searches for a template .SessionMetadata in the animal folder and
copies it down into the new session folder
- you can open the gui or texteditor to edit the session metadata by
opening one or the other at that point
On Thu, Aug 17, 2017 at 4:35 PM, juneshuoyang <[email protected]>
wrote:
… This can be done by building an import function on the GUI. Each time, a
user can import an existing file, modify it, and save it to a new location
via the GUI.
On Thu, Aug 17, 2017 at 7:29 PM, Brendon Watson ***@***.***>
wrote:
> You can do that or I just copy the .m file that made the one from the
> previous day (sitting in the previous folder, or actually in the folder
> above as a template) and copy that. But yeah you can do it with a gui.
>
> On Thu, Aug 17, 2017 at 4:26 PM, samamckenzie ***@***.***>
> wrote:
>
>
> > how do you update the metadata for the unique properties of a session?
> here
> > a prepopulated GUI would be nice
> >
> > On Thu, Aug 17, 2017 at 7:15 PM, Brendon Watson <
> ***@***.***>
> > wrote:
> >
> >
> > > As it is now, the .SessionMetadata includes the animal metadata so
they
> > are
> > > unified.
> > >
> > > Furthermore I made it so .xml is not redundant but is BASED on the
> .mats,
> > > so no risk of mistakes. Making the animal metadata lets you create
the
> > > .xml from it... which I wrote code for. So you can record that way on
> day
> > > 1 before you have a session to make metadata for. So you make animal
> > > metadata once and make the .xml from that so it's NOT redundant, but
> > > the.mat is more primary... which is how it should be
> > >
> > > Then when making session metadata you can just incorporate that
animal
> > > metadata
> > >
> > > Finally, I think GUIs are fine but actually very inefficient as far
as
> > > time... ie every single day you have to open the GUI. So if you do
that
> > > then make it so there's another way to do it for people who find text
> > more
> > > efficient than GUI... in my case I just have a .m file that's a
script
> > for
> > > creating the SessionMetadata.mat
> > >
> > >
> > >
> > >
> > >
> > > On Thu, Aug 17, 2017 at 6:52 PM samamckenzie <
***@***.***
> >
> > > wrote:
> > >
> > > > I have been talking with June about this. I think we should make
one
> > > *.mat
> > > > file that has everything we want and then build a GUI to populate
it.
> > > This
> > > > should be in addition to and somewhat redundant with the XML for
now
> > and
> > > > perhaps one day we drop the XML, or the *.mat, but for now I think
we
> > > need
> > > > both
> > > >
> > > > On Thu, Aug 17, 2017 at 6:50 PM, Dan Levenstein <
> > > ***@***.***>
> > > > wrote:
> > > >
> > > > > -I think we need something that is GUI based
> > > > > -An update to the .xml would be ideal - the xml already works
with
> > > > > neuroscope and has a gui editor. All we need to do is add the
> fields
> > we
> > > > > need, update the GUI, and improve LoadParameters to reflect the
new
> > > > fields.
> > > > > (and get rid of depreciated fields)
> > > > > -with the GUI we can enforce required/suggested/optional
> > > > > -we already have a list fields that we'd like to add that brendon
> > > worked
> > > > > on pretty extensively, can be refined as we go
> > > > >
> > > > > —
> > > > > You are receiving this because you were assigned.
> > > > > Reply to this email directly, view it on GitHub
> > > > > <#86#
> > > issuecomment-323215077
> > > > >,
> > > > > or mute the thread
> > > > > <https://github.com/notifications/unsubscribe-
> > auth/ANnfgOEUI0bC6Mhswv-
> > > > DfOCsRSqhaMewks5sZMOpgaJpZM4O62X5>
> > > > > .
> > > > >
> > > >
> > > > —
> > > > You are receiving this because you were assigned.
> > > >
> > > >
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> > > > <#86#
> > issuecomment-323215392
> > > >,
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> > > zRG3fbo6s0IuhjduUd6ks5sZMQagaJpZM4O62X5>
> > > > .
> > > >
> > >
> > > —
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Import function is very good. I can't say what's good for data collection, and obviously we should do what needs to be done to make that process work well. But I think GUI is necessary for any metadata added post-recording during analysis. I.e. adding badchannels or other channel tags. Or for perusing recordings in a database. Also anything we do needs to be able to import from the old xmls so we can import the metadata from all the legacy datasets |
|
Also the system needs to be robust/flexible enough that it can still work if you're not doing the precise data collection pipeline imagined, as I'm sure others will have different needs |
|
any who - I think if we had a good GUI for the .mat, which automatically produced and synced an xml, that could work |
|
Just what I am thinking now, as I need to go over more dataset folders to
see how each lab member fills out the metadata.
We need to figure out what are the common properties and unique properties
of each session.
For common properties, we may need to setup a rule to unify user inputs.
Otherwise, it will require a bunch of data cleaning afterwards, as SQL will
recognize Bob and Robert as two different persons.
On Thu, Aug 17, 2017 at 7:26 PM, samamckenzie <[email protected]>
wrote:
… how do you update the metadata for the unique properties of a session? here
a prepopulated GUI would be nice
On Thu, Aug 17, 2017 at 7:15 PM, Brendon Watson ***@***.***>
wrote:
> As it is now, the .SessionMetadata includes the animal metadata so they
are
> unified.
>
> Furthermore I made it so .xml is not redundant but is BASED on the .mats,
> so no risk of mistakes. Making the animal metadata lets you create the
> .xml from it... which I wrote code for. So you can record that way on day
> 1 before you have a session to make metadata for. So you make animal
> metadata once and make the .xml from that so it's NOT redundant, but
> the.mat is more primary... which is how it should be
>
> Then when making session metadata you can just incorporate that animal
> metadata
>
> Finally, I think GUIs are fine but actually very inefficient as far as
> time... ie every single day you have to open the GUI. So if you do that
> then make it so there's another way to do it for people who find text
more
> efficient than GUI... in my case I just have a .m file that's a script
for
> creating the SessionMetadata.mat
>
>
>
>
>
> On Thu, Aug 17, 2017 at 6:52 PM samamckenzie ***@***.***>
> wrote:
>
> > I have been talking with June about this. I think we should make one
> *.mat
> > file that has everything we want and then build a GUI to populate it.
> This
> > should be in addition to and somewhat redundant with the XML for now
and
> > perhaps one day we drop the XML, or the *.mat, but for now I think we
> need
> > both
> >
> > On Thu, Aug 17, 2017 at 6:50 PM, Dan Levenstein <
> ***@***.***>
> > wrote:
> >
> > > -I think we need something that is GUI based
> > > -An update to the .xml would be ideal - the xml already works with
> > > neuroscope and has a gui editor. All we need to do is add the fields
we
> > > need, update the GUI, and improve LoadParameters to reflect the new
> > fields.
> > > (and get rid of depreciated fields)
> > > -with the GUI we can enforce required/suggested/optional
> > > -we already have a list fields that we'd like to add that brendon
> worked
> > > on pretty extensively, can be refined as we go
> > >
> > > —
> > > You are receiving this because you were assigned.
> > > Reply to this email directly, view it on GitHub
> > > <#86#
> issuecomment-323215077
> > >,
> > > or mute the thread
> > > <https://github.com/notifications/unsubscribe-
auth/ANnfgOEUI0bC6Mhswv-
> > DfOCsRSqhaMewks5sZMOpgaJpZM4O62X5>
> > > .
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maybe we can give a lot of things dropdown menus, with the ability to add new options that then gets added to everyone's dropdown menu (via buzcode) when they make a new metadata file this would be especially good for region, experimenter etc as a side note, for region we probably need like 3 fields: Gross Anatomical Region (HPC,CTX), Region (CA1, mPFC), SubRegion(L5,Pyramidal Layer, etc). I think this matches what they have at Allen... we could even just use the Allen map regions |
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Sorry if I was overly attached to my previous setup. I like it but not
everyone will. We just need something that works - hopefully from all
angles
As for June's question - Has anyone used the metadata other than me? I
would try to get my data to June but with Ratgers2 down I can't. Maybe Dan
L has some in the william dataset?
What I at least attempted to do was to set up both a system that works now
but which is also sitting inside a general framework that will allow future
users to add new classes of information. I also tried to tie into the flow
of actually recording data.
If June or anyone wants me to walk you through what I've done I'm happy to
do so.
…On Thu, Aug 17, 2017 at 8:00 PM Dan Levenstein ***@***.***> wrote:
maybe we can give a lot of things dropdown menus, with the ability to add
new options that then gets added to everyone's dropdown menu (via buzcode)
when they make a new metadata file
this would be especially good for region etc
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This was referenced Aug 29, 2017
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This is really more of a place to start discussion than code production. Currently, we have two places where metadata is stored at the individual session level (animal metadata is duplicated elsewhere) 1) the .xml and 2) the *.sessionInfo.mat file. Going forward we should establish a single internal lab format that is easy for newcomers to adopt and extensible to new data types (imaging, opto, patch, etc).
Some things we should figure out:
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