-
Notifications
You must be signed in to change notification settings - Fork 39
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Zarr sink metadata management #1508
base: master
Are you sure you want to change the base?
Conversation
annehaley
commented
Apr 17, 2024
•
edited
edited
- Resolves In zarr sink, set mm_x, mm_y #1482
- Resolves In zarr sink, set image description #1483
- Resolves In zarr sink, set channel names #1484
- Resolves In zarr sink, support adding associated images #1485
@@ -653,6 +648,111 @@ def addTile(self, tile, x=0, y=0, mask=None, axes=None, **kwargs): | |||
self.levels = int(max(1, math.ceil(math.log(max( | |||
self.sizeX / self.tileWidth, self.sizeY / self.tileHeight)) / math.log(2)) + 1)) | |||
|
|||
def addAssociatedImage(self, image): |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
We should change this method signature to def addAssociatedImage(self, image, imageKey=None)
, where imageKey is an optional string that we store and can use to identify what this associated image is used for.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Note that you couldn't set the imageKey in the vips sink (we could go back and add it eventually).
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
We don't currently read in the imageKey when finding associated images in zarr files. If we used the key as the zarr group OR used associated_, then we could use the group name on read (this means changing https://github.com/girder/large_image/blob/master/sources/zarr/large_image_source_zarr/__init__.py#L323-L324 and associated areas).
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Ok, I made this change in 8976f3d. We now store self._associatedImages
as a dict.