Code

Auto-Select via SAM#7051

Code

Merged

philippotto merged 83 commits intomasterscalableminds/webknossos:masterfrom samscalableminds/webknossos:samCopy head branch name to clipboardMay 17, 2023

+1,853-1,039

Commits

Commits on May 4, 2023

• WIP: Auto-Select via SAM

  fm3

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  dd5fd1a

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• load data from datastore

  fm3

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  f069f52

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• send element class to sam server

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Commits on May 5, 2023

• mag handling

  fm3

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  3df1b35

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• rough sam integration into frontend

  philippotto

  committed
  6d985ef

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• Merge branch 'sam' of github.com:scalableminds/webknossos into sam

  philippotto

  committed
  1ab28af

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• use embedding route from backend instead of fetching precomputed embedding

  philippotto

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Commits on May 8, 2023

• small unrelated bug fix for canceling poll under certain race condition

  philippotto

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  1992858

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• switch for dynamic vs hardcoded embedding

  philippotto

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• better error handling and disable fetching of hardcoded embedding

  philippotto

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• only use user-requested bbox when applying results for better performance

  philippotto

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• request embedding for actual user position

  philippotto

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  14c40d9

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• implement caching and reuse of embedding

  philippotto

  committed
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• temporarily disable most CI checks

  philippotto

  committed
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• restore application.conf setting for slick and swagger; add another comment to explain impact on dev instances

  philippotto

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  d87c3c3

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• make it work in arbitrary mags

  philippotto

  committed
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• integrate mag into embedding cache

  philippotto

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• show busy indicator when loading embedding

  philippotto

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  e88bc82

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• remove the entire heuristic-based quickselect code

  philippotto

  committed
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• refactor and clean up so that ML and heuristic based quick select are both usable

  philippotto

  committed
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• allow to select AI or not for quick select in UI

  philippotto

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• fix inverted style

  philippotto

  committed
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Commits on May 9, 2023

• only allow quick-select with SAM on wkorg

  philippotto

  committed
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• make sam select compatible with other viewports

  philippotto

  committed
  bacc9fc

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• refactor embedding request

  philippotto

  committed
  205d0dc

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• fix linting

  philippotto

  committed
  c9760c5

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• Revert "temporarily disable most CI checks"

  Show description for 13bafd4
  philippotto

  committed
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• prefetch embedding as soon as user presses mouse down

  philippotto

  committed
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• use segmentAnythingEnabled instead of isWkorgInstance

  philippotto

  committed
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• update snapshots

  philippotto

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• also prefetch ORT session

  philippotto

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• use camel case in infer code

  philippotto

  committed
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• optimize extraction of mask

  philippotto

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• rename some vars

  philippotto

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• adapt analytics event

  philippotto

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• update changelog

  philippotto

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• Merge branch 'master' into sam

  philippotto

  authored
  2ec15cd

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• update docs

  philippotto

  committed
  988d212

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• fix some deprecations

  philippotto

  committed
  158f627

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• Merge branch 'sam' of github.com:scalableminds/webknossos into sam

  philippotto

  committed
  8f6b70a

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• don't cache failed embeddings; only support uint8 in ai mode

  philippotto

  committed
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Commits on May 10, 2023

• Merge branch 'master' into sam

  fm3

  committed
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• re-add assertion, disable in conf by default

  fm3

  committed
  36c6ed9

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• update snapshot (segmentAnything disabled by default)

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  8d74ea5

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• don't clamp min coord of bounding boxes to 0

  philippotto

  committed
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• remove unnecessary V3.max calls

  philippotto

  committed
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• pr feedback

  philippotto

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• catch error better if wasm cannot be loaded

  philippotto

  committed
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• avoid redundant error toast

  philippotto

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  5b2cc11

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• further simplication for bbox

  philippotto

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• add assertion for bbox < 1024**2

  philippotto

  committed
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• slice cache when adding to it instead of when accessing it

  philippotto

  committed
  2b6bbcf

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• remove time measurement code

  philippotto

  committed
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• align user bbox to mag before using it to ai-select

  philippotto

  committed
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Commits on May 11, 2023

• more bbox alignment (except for geometry)

  philippotto

  committed
  df37965

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• fix onnxCoord interpretation for yz viewport

  philippotto

  committed
  b940e28

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• fix mag-alignment logic by rewriting the alignWithMag function to provide more strategies

  philippotto

  committed
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• fix usage of wrong cache entries because of zero-volume bounding boxes that led to positive containment checks

  philippotto

  committed
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• fix that QuickSelectGeometry would be invisible when the third dimension's fractional was below 0.5

  philippotto

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• extrude bounding boxes by correctly mag-adapted depth

  philippotto

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• add comments to inference code

  philippotto

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Commits on May 12, 2023

• prefetch session as soon as quick select tool is activated

  philippotto

  committed
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• allow to cancel quick select with escape while drawing rectangle

  philippotto

  committed
  f30c90b

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• fix invisible geometry

  philippotto

  committed
  e8606a1

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• clean up console.logs

  philippotto

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  84046a3

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• fix linting

  philippotto

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Commits on May 15, 2023

• Merge branch 'master' into sam

  normanrz

  authored
  a1ef7ee

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Commits on May 16, 2023

• include intensity min/max and element class in byte array sent to sam server

  fm3

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  1eb5585

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• Merge branch 'master' of github.com:scalableminds/webknossos into sam

  philippotto

  committed
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• assert min/max intensity is supplied if element class is float or double

  fm3

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  6b25b11

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• fix frontend typecheck

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• send intensity range to embedding endpoint if layer is not uint8

  philippotto

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  910495c

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• Merge branch 'sam' of github.com:scalableminds/webknossos into sam

  philippotto

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• backend error messages

  fm3

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• use 4 bytes each for min/max of intensity range, not 8

  fm3

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• only show center marker when using old quick-select mode; fix scale of center marker

  philippotto

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  b19c0cf

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• Merge branch 'sam' of github.com:scalableminds/webknossos into sam

  philippotto

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• add comment

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• send metadata with correct endianness

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• Merge branch 'sam' of github.com:scalableminds/webknossos into sam

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  1ae7278

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• take layer name into account when caching embedding

  philippotto

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• Merge branch 'sam' of github.com:scalableminds/webknossos into sam

  philippotto

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Commits on May 17, 2023

• Merge branch 'master' into sam

  fm3

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