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Create a layer for each channel of NGFF-Zarr datasets #6609

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merged 14 commits into from
Nov 10, 2022
Merged

Create a layer for each channel of NGFF-Zarr datasets #6609

merged 14 commits into from
Nov 10, 2022

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frcroth
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@frcroth frcroth commented Nov 4, 2022 •
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URL of deployed dev instance (used for testing):

Steps to test:

Not tested: Importing zarr datasets with only one channel. This should result in only one layer.

Issues:

(Please delete unneeded items, merge only when none are left open)

@frcroth frcroth changed the title WIP: Create layers for channels Create layers for channels Nov 9, 2022
@frcroth frcroth requested a review from fm3 November 9, 2022 09:30
@frcroth frcroth marked this pull request as ready for review November 9, 2022 09:31
@fm3 fm3 changed the title Create layers for channels Create a layer for each channel of NGFF-Zarr datasets Nov 9, 2022
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Looking good, and works for me! Please see my two small refactoring suggestions.

Also: could you add the passing of the channelIndex also for the N5Array (at N5BucketProvider)? The N5 explorer does not currently support inferring channel metadata (which is fine for now), but if added manually to the datasource-properties.json, this should also work.

app/models/binary/explore/NgffExplorer.scala Outdated Show resolved Hide resolved
app/models/binary/explore/NgffExplorer.scala Outdated Show resolved Hide resolved
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frcroth commented Nov 10, 2022

Also: could you add the passing of the channelIndex also for the N5Array (at N5BucketProvider)? The N5 explorer does not currently support inferring channel metadata (which is fine for now), but if added manually to the datasource-properties.json, this should also work.

I don't exactly know what you intend for the N5Array. Should the N5Array have another property channelIndex?

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fm3 commented Nov 10, 2022

I don't exactly know what you intend for the N5Array. Should the N5Array have another property channelIndex?

Yes, and pass it to its superclass (that should be enough)

@frcroth frcroth requested a review from fm3 November 10, 2022 09:24
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fm3 commented Nov 10, 2022

…sorry, should have been more clear 😇 The N5BucketProvider calls N5Array.open, and there the channelIndex should be passed through, analogous to what happens in the ZarrBucketProvider and ZarrArray.open

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🎉

@frcroth frcroth merged commit 2fb50d6 into master Nov 10, 2022
@frcroth frcroth deleted the channelIndex branch November 10, 2022 10:31
hotzenklotz added a commit that referenced this pull request Nov 11, 2022
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Merge branch 'master' of github.com:scalableminds/webknossos into pri…
cb094d4 
…cing

* 'master' of github.com:scalableminds/webknossos:
  Fix parsing failure during import of ngff zarr datasets with translation transforms (#6621)
  Fix rerender after each layer name keypress in dataset import view (#6628)
  Create a layer for each channel of NGFF-Zarr datasets (#6609)
  Fix screenshot tests (#6623)
  Fix importing a dataset from disk (#6615)
  Allow deleting annotation layers (#6593)
  Rephrased Error Messages (#6616)
normanrz added a commit to normanrz/ome-ngff-tools that referenced this pull request Nov 11, 2022
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Multichannels now work in webKnossos
1293d6d 
scalableminds/webknossos#6609 has been merged and deployed yesterday.
@normanrz normanrz mentioned this pull request Nov 11, 2022
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@fm3 fm3 mentioned this pull request Nov 11, 2022
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Add ChannelIndex to MagLocator, adapt Zarr Import for Multichannel datasets
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