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Refine Examples/Demos #486

Merged
merged 12 commits into from
Dec 8, 2021
Merged

Refine Examples/Demos #486

merged 12 commits into from
Dec 8, 2021

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hotzenklotz
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@hotzenklotz hotzenklotz commented Nov 22, 2021 •
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Description:

  • PR updates the included examples slightly. Mostly adds more comments to make them even easier to understand.
  • Swap cell demo dataset to a 3D version (fluorescence microscopy) to fit our clients use cases better and showcase the 3D aspects of webKnossos
  • switched example URLs to use webKnossos.org, since this is the primary wK source for most people

@hotzenklotz hotzenklotz self-assigned this Nov 22, 2021
@hotzenklotz
fix formatting
f31c772
@hotzenklotz
fixed formatting, add more comments
58c65a5
@hotzenklotz
added link to github to docs
76f5892
@hotzenklotz
Merge branch 'master' of github.com:scalableminds/webknossos-libs int…
99cf7b6 
…o update_demos

* 'master' of github.com:scalableminds/webknossos-libs:
  Update changelogs for release v0.8.23 (#493)
  Resolve path when symlinking layer and make_relative is False (#492)
  Globalize Floodfill Script (#461)
  Bump pillow from 8.2.0 to 8.3.2 in /wkcuber (#488)
  Add websites metadata to pyproject.toml (#485)
@hotzenklotz
fixed more tests
c720a07
hotzenklotz
hotzenklotz commented Nov 30, 2021
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webknossos/examples/dataset_usage.py Outdated
)
# Link a layer of the initial dataset to the copy:
sym_layer = copy_of_dataset.add_symlink_layer(new_layer)
if __name__ == "__main__":
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Required or otherwise example crashed because of spawning issues with the cluster tools...

@philippotto I much prefer to have an example without this. I don't think we can expect our users to always call the wk-libs methods from a module.

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@hotzenklotz I merged in the newest master and fixed the tests (e.g. allowing skimage to request the cell3d data). I undid your removal of mag.get_view() in the learned segmenter, because this changes the semantic and would read the wrong data. Is this PR review-ready then @hotzenklotz? Then maybe @philippotto could have another look, from my impression this is fine 👍

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@jstriebel Thanks! I don't want to add any more changes and from my point of view the PR is ready.

@jstriebel jstriebel marked this pull request as ready for review December 7, 2021 16:07
@jstriebel jstriebel requested a review from philippotto December 7, 2021 16:07
philippotto
philippotto reviewed Dec 7, 2021
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jstriebel approved these changes Dec 8, 2021
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👍

@hotzenklotz hotzenklotz enabled auto-merge (squash) December 8, 2021 14:27
@hotzenklotz hotzenklotz merged commit ae30458 into master Dec 8, 2021
@hotzenklotz hotzenklotz deleted the update_demos branch December 8, 2021 14:45
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@jstriebel jstriebel jstriebel approved these changes

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