Comments (9)
unidesigner
commented on May 24, 2024
1
@chrisj It seems like there is agreement between @jbms and @william-silversmith about the hidden attribute. Would you care about submitting a PR to implement this as you are very familiar with the neuroglancer codebase? Thank you!
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jbms
commented on May 24, 2024
How about setting their shape to [0,0,0]?
Although if it is the first level that would be problematic.
…On Thu, Mar 2, 2023, 15:43 William Silversmith ***@***.***> wrote:
Hi Jeremy,
My lab has been using "placeholder" mips to keep different versions of
datasets numerically aligned in "mip" sequence. Recently, an improvement to
neuroglancer made it so that these placeholders with no data display black.
796cc7d
<796cc7d>
Would it be possible to support either toggling off the fill value or
alternatively, supporting a "hidden": true attribute on scales to avoid
displaying them in Neuroglancer? @chrisj <https://github.com/chrisj>
brought this to my attention.
Thank you so much!
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william-silversmith
commented on May 24, 2024
Unfortunately it is the first mip level 😅
Why would that be more problematic than higher levels?
On Thu, Mar 2, 2023, 6:49 PM Jeremy Maitin-Shepard ***@***.***>
wrote:
… How about setting their shape to [0,0,0]?
Although if it is the first level that would be problematic.
On Thu, Mar 2, 2023, 15:43 William Silversmith ***@***.***>
wrote:
> Hi Jeremy,
>
> My lab has been using "placeholder" mips to keep different versions of
> datasets numerically aligned in "mip" sequence. Recently, an improvement
to
> neuroglancer made it so that these placeholders with no data display
black.
>
> 796cc7d
> <
796cc7d
>
>
> Would it be possible to support either toggling off the fill value or
> alternatively, supporting a "hidden": true attribute on scales to avoid
> displaying them in Neuroglancer? @chrisj <https://github.com/chrisj>
> brought this to my attention.
>
> Thank you so much!
>
> —
> Reply to this email directly, view it on GitHub
> <#446>, or unsubscribe
> <
https://github.com/notifications/unsubscribe-auth/ABAEJ2TICLT3WN6C5ZQYNW3W2EWCBANCNFSM6AAAAAAVN7423I
>
> .
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> ID: ***@***.***>
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jbms
commented on May 24, 2024
The first level is used by Neuroglancer to determine the clip bounds, so if it has a shape of [0,0,0] then that won't work.
I think a hidden attribute would be fine.
Do you want it to completely ignore the scale, e.g. basically behave as if the scale did not exist, or still use the first scale (even if hidden) to determine clip bounds and units to use for the global coordinate space by default?
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william-silversmith
commented on May 24, 2024
Other than occupying the mip number, the scale should not exist (except for
the first level which would provide clip bounds as that would be backwards
compatible with how we've been using it).
…On Fri, Mar 3, 2023 at 3:59 PM Jeremy Maitin-Shepard < ***@***.***> wrote:
The first level is used by Neuroglancer to determine the clip bounds, so
if it has a shape of [0,0,0] then that won't work.
I think a hidden attribute would be fine.
Do you want it to completely ignore the scale, e.g. basically behave as if
the scale did not exist, or still use the first scale (even if hidden) to
determine clip bounds and units to use for the global coordinate space by
default?
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jbms
commented on May 24, 2024
I think it would be most natural in Neuroglancer to just have "hidden" mean completely ignored, in which case the clip bounds would instead come from the first visible scale. Presumably that would only differ by a small amount. Do you think that would work for you?
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william-silversmith
commented on May 24, 2024
I think one thing we want from this is for Neuroglancer to display the coordinates as hidden mip 0 coordinates, but display the image from mip 1. This way we can easily convert between different datasets. For example, sometimes an aligned dataset is rendered at mip 2 but we want to be able to cross reference between layers easily.
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jbms
commented on May 24, 2024
Okay, sounds reasonable. Would you care to create a pull request to implement this?
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chrisj
commented on May 24, 2024
This issue is discussing the same problem #444
I have a commit to fix this seung-lab@a7edadd#diff-048ab67a423ce920e92e4cff52db026f6361491c6b7189eb558f3a7c42e14759R208
Not sure if it is an appropriate place to put it but seems to work. Also needs to be updated if we swap to using the hidden attribute.
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