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Multi-Resolution Volume Tracings #4755

Merged
merged 157 commits into from
Nov 9, 2020
Merged

Multi-Resolution Volume Tracings #4755

merged 157 commits into from
Nov 9, 2020

Commits on Jul 31, 2020

  1. keep fixed zoom during td rotation to planes

    @MichaelBuessemeyer
    MichaelBuessemeyer committed Jul 31, 2020
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Commits on Aug 3, 2020

  1. refactor 3d rotation method to keep the zoom and simplify it

    @MichaelBuessemeyer
    MichaelBuessemeyer committed Aug 3, 2020
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  2. fix position and up vector not getting interpolated correctly

    @MichaelBuessemeyer
    MichaelBuessemeyer committed Aug 3, 2020
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  3. add changelog entry

    @MichaelBuessemeyer
    MichaelBuessemeyer committed Aug 3, 2020
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Commits on Aug 5, 2020

  1. Merge branch 'master' into keep-zoom-during-td-button-rotation

    @MichaelBuessemeyer
    MichaelBuessemeyer authored Aug 5, 2020
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Commits on Aug 6, 2020

  1. Apply suggestions from code review 

    Co-authored-by: Daniel <[email protected]>
    @MichaelBuessemeyer @daniel-wer
    MichaelBuessemeyer and daniel-wer authored Aug 6, 2020
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  2. remove zReductionFactor

    @MichaelBuessemeyer
    MichaelBuessemeyer committed Aug 6, 2020
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  3. Merge branch 'keep-zoom-during-td-button-rotation' of github.com:scal… 

    …ableminds/webknossos into keep-zoom-during-td-button-rotation
    @MichaelBuessemeyer
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  4. backend: support anisotropic resolutions in volume bucket keys

    @fm3
    fm3 committed Aug 6, 2020
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Commits on Aug 7, 2020

  1. fix 3d rotation preset

    @MichaelBuessemeyer
    MichaelBuessemeyer committed Aug 7, 2020
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  2. remove useless check for valid values

    @MichaelBuessemeyer
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Commits on Aug 10, 2020

  1. remove reassignment of width and height

    @MichaelBuessemeyer
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Commits on Aug 11, 2020

  1. do volume annotation in all resolutions

    @MichaelBuessemeyer
    MichaelBuessemeyer committed Aug 11, 2020
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  2. Update frontend/javascripts/oxalis/controller/camera_controller.js 

    Co-authored-by: Philipp Otto <[email protected]>
    @MichaelBuessemeyer @philippotto
    MichaelBuessemeyer and philippotto authored Aug 11, 2020
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  3. Merge branch 'master' into keep-zoom-during-td-button-rotation

    @MichaelBuessemeyer
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  4. made code pretty

    @MichaelBuessemeyer
    MichaelBuessemeyer committed Aug 11, 2020
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  5. reduce max brush size

    @MichaelBuessemeyer
    MichaelBuessemeyer committed Aug 11, 2020
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  6. disallow trace tool in higher resolutions

    @MichaelBuessemeyer
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  7. Merge branch 'keep-zoom-during-td-button-rotation' into multires-volumes

    @MichaelBuessemeyer
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  8. enable brushing in high again

    @MichaelBuessemeyer
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Commits on Aug 12, 2020

  1. do not block resolution loading

    @fm3
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  2. Merge branch 'master' of github.com:scalableminds/webknossos into mul… 

    …tires-volumes
    @MichaelBuessemeyer
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  3. annotate z many slices at once when z resolution is > 1

    @MichaelBuessemeyer
    MichaelBuessemeyer committed Aug 12, 2020
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Commits on Aug 13, 2020

  1. Merge branch 'master' into multires-volumes

    @MichaelBuessemeyer
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  2. fixing a few tests

    @MichaelBuessemeyer
    MichaelBuessemeyer committed Aug 13, 2020
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  3. hopefully fixed all tests

    @MichaelBuessemeyer
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  4. Merge branch 'multires-volumes' of github.com:scalableminds/webknosso… 

    …s into multires-volumes
    @MichaelBuessemeyer
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Commits on Aug 25, 2020

  1. Merge branch 'master' of github.com:scalableminds/webknossos into mul… 

    …tires-volumes
    @MichaelBuessemeyer
    MichaelBuessemeyer committed Aug 25, 2020
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  2. Add info about annotating multiple slices

    @MichaelBuessemeyer
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Commits on Aug 27, 2020

  1. limit area that gets autofilled

    @MichaelBuessemeyer
    MichaelBuessemeyer committed Aug 27, 2020
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Commits on Aug 28, 2020

  1. Merge branch 'master' of github.com:scalableminds/webknossos into mul… 

    …tires-volumes
    Youri K committed Aug 28, 2020
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Commits on Aug 31, 2020

  1. [WIP] lazy downscaling of volume buckets

    Youri K committed Aug 31, 2020
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Commits on Sep 2, 2020

  1. merge master into multires-volumes

    @fm3
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Commits on Sep 7, 2020

  1. lookup-based live downsampling

    @fm3
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  2. [WIP] downsample volume tracings on upload

    @fm3
    fm3 committed Sep 7, 2020
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  3. merge master

    @fm3
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  4. [WIP] downscale during upload

    @fm3
    fm3 committed Sep 7, 2020
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  5. fix offsets, switch to mode

    @fm3
    fm3 committed Sep 7, 2020
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Commits on Sep 8, 2020

  1. determine which mags to downsample

    @fm3
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  2. adapt nml unit test suite

    @fm3
    fm3 committed Sep 8, 2020
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  3. fix backend dummy tracing

    @fm3
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  4. Merge branch 'master' of github.com:scalableminds/webknossos into mul… 

    …tires-volumes
    @MichaelBuessemeyer
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Commits on Sep 9, 2020

  1. move function to get number of slices to accessor

    @MichaelBuessemeyer
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  2. WIP: applying flood fill to all resolutions

    @MichaelBuessemeyer
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Commits on Sep 10, 2020

  1. [WIP] track mags in volumetracing object

    @fm3
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  2. fix calculating error during downsampling

    @MichaelBuessemeyer
    MichaelBuessemeyer committed Sep 10, 2020
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  3. fix flood fill for all source resolutions

    @MichaelBuessemeyer
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  4. Merge branch 'multires-volumes' of github.com:scalableminds/webknosso… 

    …s into multires-volumes
    @MichaelBuessemeyer
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  5. fixed flood fill for all resolutions

    @MichaelBuessemeyer
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Commits on Sep 11, 2020

  1. handle differing resolutions during volume merging + upload

    @fm3
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  2. Merge branch 'multires-volumes' of github.com:scalableminds/webknosso… 

    …s into multires-volumes
    @fm3
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  3. add up and downsampling of LabeledVoxelsMap

    @MichaelBuessemeyer
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  4. Merge branch 'multires-volumes' of github.com:scalableminds/webknosso… 

    …s into multires-volumes
    @MichaelBuessemeyer
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Commits on Sep 14, 2020

  1. add unlinkFallback route

    @fm3
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  2. changelog

    @fm3
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  3. cleanup backend code

    @fm3
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  4. fixed up and downsampling and added tests

    @MichaelBuessemeyer
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  5. Merge branch 'multires-volumes' of github.com:scalableminds/webknosso… 

    …s into multires-volumes
    @MichaelBuessemeyer
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  6. added method to apply a voxel map

    @MichaelBuessemeyer
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  7. fixed upsampling and added regression test

    @MichaelBuessemeyer
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  8. add comments to sampling methods

    @MichaelBuessemeyer
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  9. make copylayer work in multi resolutions

    @MichaelBuessemeyer
    MichaelBuessemeyer committed Sep 14, 2020
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  10. while upsampling annotate mutliple slices

    @MichaelBuessemeyer
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Commits on Sep 15, 2020

  1. Add todo about refactoring labeling voxels

    @MichaelBuessemeyer
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  2. adjusted voxel labeling method to label in all resolutions the segmen… 

    …tation layer has
    @MichaelBuessemeyer
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  3. added some comments with todos

    @MichaelBuessemeyer
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Commits on Sep 23, 2020

  1. Update frontend/javascripts/oxalis/model/accessors/volumetracing_acce… 

    …ssor.js
    @philippotto
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  2. always label in all resolutions when using api; show stack-icon when … 

    …multi-slice-annotating
    @philippotto
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  3. Merge branch 'multires-volumes' of github.com:scalableminds/webknosso… 

    …s into multires-volumes
    @philippotto
    philippotto committed Sep 23, 2020
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  4. more comments

    @philippotto
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  5. replace old unlinkFallbackLayer with new API for that (keep old Updat… 

    …eAction for backwards compatibility)
    @philippotto
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Commits on Sep 24, 2020

  1. fix wrong parameter format

    @philippotto
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  2. refactor resolution handling to deal with sparse resolutions better (… 

    …WIP/1)
    @philippotto
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  3. undo temporary new_resolutions change

    @philippotto
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Commits on Sep 25, 2020

  1. continue refactoring resolution handling to deal with sparse resoluti… 

    …ons better (WIP/2) --> brush, paint-bucket and copy-segmentation tool seem to work
    @philippotto
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  2. fix picking segment color when being in a not-existing segmentation mag

    @philippotto
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  3. ensure that prefetch saga, bucket picker and pull queue don't try to … 

    …load buckets for not existing mags
    @philippotto
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  4. ensure legacy getResolutions method provides dense resolution set; cl… 

    …ean up
    @philippotto
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  5. fix initialization and volume annotation sampling spec

    @philippotto
    philippotto committed Sep 25, 2020
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  6. fix CI

    @philippotto
    philippotto committed Sep 25, 2020
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  7. update snapshots

    @philippotto
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Commits on Sep 28, 2020

  1. tune warning text

    @philippotto
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  2. make merger mode work in higher resolutions

    @philippotto
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Commits on Sep 29, 2020

  1. show a status indicator in the viewports if a layer cannot be rendere… 

    …d due to the zoom step
    @philippotto
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  2. reduce tooltip rerenderings by making styles constant

    @philippotto
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  3. fix enabled 'Render Missing Data Black' for missing mags

    @philippotto
    philippotto committed Sep 29, 2020
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  4. add issue links to todo comments

    @philippotto
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Commits on Sep 30, 2020

  1. implement some feedback

    @philippotto
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  2. Apply suggestions from code review 

    Co-authored-by: Daniel <[email protected]>
    @philippotto @daniel-wer
    philippotto and daniel-wer authored Sep 30, 2020
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  3. more PR feedback

    @philippotto
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  4. Merge branch 'multires-volumes' of github.com:scalableminds/webknosso… 

    …s into multires-volumes
    @philippotto
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  5. merge master with backend files

    Youri K committed Sep 30, 2020
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  6. also implement getIndexOrClosestHigherIndex for ResolutionInfo and us… 

    …e where appropriate
    @philippotto
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  7. return true in isVolumeTraceToolDisallowed if no volume tracing exists

    @philippotto
    philippotto committed Sep 30, 2020
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  8. fix front-end merge conflicts

    @philippotto
    philippotto committed Sep 30, 2020
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  9. Merge branch 'multires-volume-merge' into multires-volumes

    @philippotto
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  10. reduce usages of getResolutionByIndexWithFallback and make that funct… 

    …ion correct (remove isotropic fallback in favor of failing for unclear cases
    @philippotto
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  11. simplify is2DVoxelInsideBucket method in Bucket

    @philippotto
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Commits on Oct 2, 2020

  1. Apply suggestions from code review 

    Co-authored-by: Daniel <[email protected]>
    @philippotto @daniel-wer
    philippotto and daniel-wer authored Oct 2, 2020
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  2. integrate more PR feedback; resolve merge conflict in changelog; rena… 

    …me missing to unrenderable etc
    @philippotto
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  3. Merge branch 'multires-volumes' of github.com:scalableminds/webknosso… 

    …s into multires-volumes
    @philippotto
    philippotto committed Oct 2, 2020
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  4. refactor applyLabeledVoxelMapToAllMissingResolutions

    @philippotto
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  5. further refactoring of applyLabeledVoxelMapToAllMissingResolutions

    @philippotto
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  6. Merge branch 'master' of github.com:scalableminds/webknossos into mul… 

    …tires-volumes
    @philippotto
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  7. remove unused import

    @philippotto
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  8. fix flow after upgrade

    @philippotto
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  9. improve comment for LabeledVoxelsMap

    @philippotto
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  10. fix uniform definion

    @philippotto
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  11. fix getDataValue for missing resolution

    @philippotto
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Commits on Oct 6, 2020

  1. Merge branch 'master' into multires-volumes

    @philippotto
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Commits on Oct 7, 2020

  1. Improve performance of volume annotation tools (#4848) 

    * tmp: use LabeledVoxelsMap for brushing and TypedArray for brushing map (first measurements yield 20x better performance)

* restore all of the brush functionality; create LabeledVoxelMap in current mag; further performance optimizations

* clean up VoxelIterator a bit

* more clean up

* clean up and fix CI

* further clean up

* remove todo

* use unzoomed centroid when updating direction

* fix contour drawing in mag > 1

* fix flow

* fix circle-drawing for anisotropic mags

* update changelog

* rename VoxelIterator to VoxelBuffer2D

* optimize draw circle method by comparing squared dist with squared radius

* rename variables and change comment for bx and by

* remove obsolete comment

* add another comment to fillCircle call
    @philippotto
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  2. ensure that rendered volume magnification is also the mag in which is 

    annotated

- also ensure that the volume toolbar is disabled properly when the
segmentation cannot be rendered for some reason
    @philippotto
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  3. Update frontend/javascripts/oxalis/model/sagas/volumetracing_saga.js 

    Co-authored-by: Daniel <[email protected]>
    @philippotto @daniel-wer
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  4. Resolve Merge Conflicts and Merge branch 'master' of github.com:scala… 

    …bleminds/webknossos into multires-volumes
    @philippotto
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  5. fix issues from merging master

    @philippotto
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  6. Merge branch 'multires-volumes' of github.com:scalableminds/webknosso… 

    …s into multires-volumes
    @philippotto
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  7. fix upload/download

    @fm3
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  8. Merge branch 'multires-volumes' of github.com:scalableminds/webknosso… 

    …s into multires-volumes
    @fm3
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  9. fix issues after merge

    @fm3
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  10. disable continuous drawing for now since its performance needs to be … 

    …adapted to the multi-resolution feature
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  11. Merge branch 'multires-volumes' of github.com:scalableminds/webknosso… 

    …s into multires-volumes
    @philippotto
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  12. fix linting

    @philippotto
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  13. adapt headline in import modal

    @philippotto
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  14. change tracing to annotation

    @philippotto
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  15. change magnification to resolution in user-facing strings and some in… 

    …ternal ones
    @philippotto
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  16. make resolution-warning less verbose

    @philippotto
    philippotto committed Oct 7, 2020
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  17. try to fix e.trigger is not a function

    @philippotto
    philippotto committed Oct 7, 2020
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  18. fix linting

    @philippotto
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  19. fix bug in applyLabeledVoxelMap

    @philippotto
    philippotto committed Oct 7, 2020
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  20. fix flow

    @philippotto
    philippotto committed Oct 7, 2020
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  21. show fallback-not-included warning only when there is fallback data

    @philippotto
    philippotto committed Oct 7, 2020
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Commits on Oct 8, 2020

  1. fix anisotropic bucket adresses

    @fm3
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  2. treat empty resolution list as no resolution list

    @fm3
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  3. change Boolean() to != null

    @philippotto
    philippotto committed Oct 8, 2020
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  4. fix flow in model initialization

    @philippotto
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  5. ensure volume layer is saved before reloading; fixes #4857

    @philippotto
    philippotto committed Oct 8, 2020
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  6. format

    @philippotto
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  7. disable copy-segmentation feature for higher mags due to performance

    @philippotto
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  8. merge master

    @fm3
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Commits on Oct 19, 2020

  1. merge master

    @fm3
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Commits on Oct 22, 2020

  1. Merge branch 'master' into multires-volumes

    @philippotto
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  2. Merge branch 'master' of github.com:scalableminds/webknossos into mul… 

    …tires-volumes
    @philippotto
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  3. fix some merge-related problems

    @philippotto
    philippotto committed Oct 22, 2020
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Commits on Oct 23, 2020

  1. fix styling of multi-slice-icon

    @philippotto
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  2. throw an exception if the resolution could not be looked up instead o… 

    …f defaulting to 0,0,0
    @philippotto
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  3. look up volume bucket resolution by zoom step ** 2 rather than index

    @fm3
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  4. merge

    @fm3
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  5. fix that toolbar rerendered on every state change

    @philippotto
    philippotto committed Oct 23, 2020
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  6. improve handling of volume-is-disabled case in toolbar

    @philippotto
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  7. Merge branch 'multires-volumes' of github.com:scalableminds/webknosso… 

    …s into multires-volumes
    @philippotto
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Commits on Oct 26, 2020

  1. replace exception by fox.failure if volume resolution lookup fails

    @fm3
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  2. show data type and resolutions of layer in tooltip next to layer name… 

    … (therefore, the dtype tag is removed)
    @philippotto
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  3. Merge branch 'multires-volumes' of github.com:scalableminds/webknosso… 

    …s into multires-volumes
    @philippotto
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Commits on Nov 3, 2020

  1. Merge branch 'master' of github.com:scalableminds/webknossos into mul… 

    …tires-volumes
    @philippotto
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  2. fix syntax error

    @philippotto
    philippotto committed Nov 3, 2020
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Commits on Nov 5, 2020

  1. Merge branch 'master' into multires-volumes

    @fm3
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  2. Enforce TaskType Resolution Restrictions for Multi-Res Volume Tasks (#… 

    …4891)

* [WIP] enforce task type magnification settings in tasks

* pass allowedMagnifications to rpc methods

* pass magnifications as query string

* respect resolution restrictions for volume tracings.

* add option to downsample existing volume tracing

* remove outdated assertion, update resolution list after downsampling

* sleep 10s

* remove sleep and bump dev-proxy-timeout to 5 min

* fix task creation with resolution restrictions

* use inclusive check

* when uploading zips with differing resolution sets, fail

* remove unused import

* refresh snapshots (tracings contain organization name)

* write header.wkw to every mag in volume download, fix anisotropic directory names

* add resolution-samenss assertion in volume dnd import. fix flow types

* fix restriction passing in initial data

* Add button to trigger downsampling of volume annotation.

The reload button next to the active-resolution-indicator only appears
for explorative annotations with volume data. It opens a modal which
explains the action and its consequences. While the operation is
running, the modal blocks further usages of webKnossos. After the
operation has completed, the complete page is reloaded.

* fix parameter passing in duplicate rpc

* avoid undefined behavior of bucket iterator by checking hasNext. do not relabel when “merging” only one volume

* make tasktype resolution restrictions immutable. sort resolution list

* update migration guide

* remove debug output

* improve initiate-volume-downsampling modal and move its button to the layer settings

* show toast when mag-restriction is violated instead of prohibiting the zoom change in the first place

* don't allow editing mag-restrictions in already created tasktype

* remove some more debug output, unify variable names

* forbid creating new nodes or using volume tools when the current mag was forbidden by the task type

* clean up

* Update MIGRATIONS.unreleased.md

Co-authored-by: Philipp Otto <[email protected]>

* fix styling of button-link

* use ListBuffer instead of HashSet as per pr feedback

* integrate some feedback

* Apply suggestions from code review

Co-authored-by: Daniel <[email protected]>

* remove unnecessary SET_TOOL dependence

* do map ids if initialLargestSegmentId != 0

Co-authored-by: Philipp Otto <[email protected]>
Co-authored-by: Philipp Otto <[email protected]>
Co-authored-by: Daniel <[email protected]>
    @fm3 @philippotto @daniel-wer
    4 people authored Nov 5, 2020
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