Lincbrain WebKNOSSOS upstream sync #15
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* make login, registration and forgot password view more responsive to mobile devices - includes adding a link back to login for password reset view * make dashboard dataset view less awful * add changelog entry
* allow viewing a mapping * WIP: enable setting default active mappings in default view configuration * add default active mapping to default view configuration - add config settings to dataset settings default view config tab - auto load initial default mapping * fix bottom margin of layer settings - was broken in view mode with multiple segmentation layers; the "Save View Config..." Button had no spacing to towards * fix having the mapping settings enabled for layers with default mapping * WIP: move default mapping store proeprty to dataset layer config - undo moving mapping selection to a shared component * moved default active mapping from separate select to view config layer config - Also added validation check whether the mapping exists in the dataset view config settings * allow saving no default active mapping from view mode & model init to new dataset config version * rename defaultMapping to mapping * cache available mappings fetched from backend when checking config in dataset settings * remove logging statements * clean up * add changelog entry * apply pr feedback
* fix animation modal color layer validation * changelog * rename variable * apply pr feedback * improve error message of uint24 layers in animation modal --------- Co-authored-by: Michael Büßemeyer <[email protected]>
* validate BB size to be larger then 0 * changelog * appy PR feedback
Co-authored-by: MichaelBuessemeyer <[email protected]>
* default state wording to indicate loading * update nml tests --------- Co-authored-by: Michael Büßemeyer <[email protected]>
* Remove suggestion route * Remove WKWDataFormat * Lint * wip remove in frontend * unify readInboxDataSource * remove datasource suggestion - but keep isEditMode prop due to onboarding process needing this prop * remove left over code line linking to dataset import and clean up code * remove unused imports in backend * always show edit settings for datasets the user can edit * remove unused type * er-add dataset actions (show error & delete dataset) for broken datasets in dataset table * adapt wording in messages * add changelog entry * update migrationguide,changelog,docs --------- Co-authored-by: Florian M <[email protected]> Co-authored-by: Michael Büßemeyer <[email protected]> Co-authored-by: Florian M <[email protected]>
… split-off segments (scalableminds#7877) * combine custom names of merged agglomerates & transfer custom name to split off segment * add changelog entry * also keep custom name in split from all neighbors action * Update CHANGELOG.unreleased.md Co-authored-by: Philipp Otto <[email protected]> --------- Co-authored-by: Philipp Otto <[email protected]>
…calableminds#7887) * correctly use base mapping in FullMeshRequest when forwarding from TS to DS * changelog --------- Co-authored-by: MichaelBuessemeyer <[email protected]>
…7889) * Fix dataset composition when only one dataset is used * update changelog
* WIP: adding unit setting to datasource settings * WIP: backend: voxel size as object * WIP: Adding unit to dataset scale [ci skip] - make keep the base unit internally to nm - use configured unit for 3d space / voxel space - WIP: post fix all relevant function with Nm or Vx depending on their unit to make this as explicit as possible * finish migrating to new datasetscale format [ci skip] - current state: broken; nothing is rendered * adjust nml schema to backend changes * Fix initial dataset loading with scale in mircometers - add a lot of debugging output for testing [ci skip] * Fix td viewport camera init ( calulate in datasource unit not always in nm) - [ci skip] - Dont ignore far plane calculation * undo accidental semantic change * support conversion between larger and smaller units in 1d-3d - Full support for uncommon units is missing for 2d and 3d * format 1d length units in datasource unit to avoid precision loss * WIP: Support formatting for 2d and 3d values without always converting to nm [ci skip] * unify format function to work with multi dimensional values and not only in 1d && fix lots of tests [ci skip] * finish writing more tests for format utils * include all unit format in the datasource json validation in the frontend * Add support to convert to cm - WIP: Fix tests now that cm is supported * Add tests for uncommon units [ci skip] * rename "datasourceUnit" to "unit" everywhere * WIP: remove complex tests and add example based tests [ci skip] * add more format utils tests and fix some tests * fix / remove introduced todos of this pr * remove debugging console.logs * fix datasets e2e test * redo: use shorter decimals in scalebar * WIP: voxel unit support backend * fix vx distance calculation of shortest path between nodes * improve previous vx length calculation fix * use voxel size unit in more spots * schema, evolutions * snapshots * rename LengthUnit to Unit in frontend * further clean up of frontend code * more code cleanup frontend * update datasource json frontend validation * add changelog entry * log warning in case a mesh is loaded whose scale does not match the dataset's scale * bump api version to 7, drop 1 and 2 * document that ad-hoc meshing uses voxel size factor only * unused imports * WIP: use ngff units during explore * read ngff voxel size unit during explore * implement backend pr feedback part 1 * update nml spec snapshot * report unit in ngff streaming. change composeRequest to expect full voxel size with unit * format * unused import * Fix uploading zipped tiff (should set needsConversion=true) * changelog * rephrase code comment * WIP apply feedback * Add unit to params of wkw conversion job for dataset upload * apply pr feedback * fix adhoc mesh computation * rename datasetScale to voxelSize in frontend And remove datasetScale/voxelSize uniform from shaders as it was unused * power-of-two check on all mag dimensions * adapt voxelSize to nanometer for worker for now * use term REST API in changelog after all * use long lengthUnit names as default format * snapshots * migrate frontend to use long unit names except for format utils * rename UnitShortMap to LongUnitToShortUnitMap * fix flycam reducer tests --------- Co-authored-by: Florian M <[email protected]> Co-authored-by: Florian M <[email protected]>
* move bbox context menus to container * close context menu after actions * open context menu upon click anywhere on bb entry * add comment * fix that second scroll bar is rendered * add changelog * actually fix scroll bar in skeleton tab
* Add nd support for tiff export job * remove nd warning from tiff export modal * add nd info to zarr2 streaming metadata * add changelog entry * transform input bbox & additionalCoordinates to nd bounding box for worker input * format backend * apply feedback * fix rendering of new nd bounding box tiff export job arg in jobs list --------- Co-authored-by: Michael Büßemeyer <[email protected]> Co-authored-by: Florian M <[email protected]> Co-authored-by: Florian M <[email protected]>
…leminds#8085) * Remove superfluous _type field when writing zarr3 codec jsons * rename to highlight that keys are removed recursively
…lableminds#8082) * mag register all segments for bbox feature mag aware * remove console.logs * add error toasts for missing mag or segmentation layer * add changelog * improve changelog * move line * bubble up API error to open toast in view * fix mag-related edge case * register segments for segmentation layers without volume annotation layers * add warning toast if segmentation layer isnt editable
Co-authored-by: MichaelBuessemeyer <[email protected]>
* WIP: user-defined key-value properties for skeletons * adapt UpdateNode test * also for trees,segments. add to backend NMLWriter * parse string list values too * allow to create string tags for segments; styling tweaks * don't use inline tags; instead use a resizable two-split-pane and a table * tweak layout so that the details pane only occupies as much space as needed and not more than the user-specified (via drag) height * allow to edit values in segment details table * refactor * add property UI to skeleton trees * add missing file * fix tests * fix spinner margin in dashboard * allow user to resize pane larger than needed * fix styling in light theme * filter duplicate keys in action creator * implement NML parsing and serialization of user defined properties for trees * adapt parser and serialize for userDefinedProperties; add test * start unifying metadata tables * remove superfluous type wrapper * integrate dashboards metadata table into tree hierarchy view (styling + string-based props) * also integrate with segments tab * make adding and removing properties work properly * also support number and string array as property types * format * re-order props * extract InputWithUpdateOnBlur to fix cyclic dependency * temporarily disable ci * fix metadata editing for segments * change trash to close icon in dashboard * give metadata table rounded corners * warn user when keys are not unique; avoid frequent rerenders via memo * iterate on validation, styling and tag input * try to fix stringListValue: [] error * don't save duplicate keys in case the user ignores the validation errors * auto-focus just added key fields * remove context-menu way for adding metadata; iterate on icon in segment and tree list * change dashboard metadata table style * also adapt validation styling * make some props optional * move multiple-trees-selected note into details pane * make fields read only if no update permissions exist * fix theader style for segments tab * store height for details pane in local storage * fix lost highlighting of segments that are hovered in the data viewports * also print statistic of previous runs in wk dev benchmark * move isCentered logic into SegmentListItem to avoid rerenders * fix type error * fix linting * rename UserDefinedProperty to MetadataEntry * wrap metadata in parent tag in nml * rename userDefinedProperty/ies to metadata and metadata entry * clean up * rename metadata-table-wrapper class * more renaming * remove debug code * clarify comments * delete unused InputNumberWithUpdateOnBlur * minor clean up * re-enable ci * fix compact_toggle_actions.spec.ts and make it type check * update snapshots * remove todo comment * make tooltip color consistent orange * add tooltip to tag icon * Update frontend/stylesheets/_variables.less Co-authored-by: MichaelBuessemeyer <[email protected]> * integrate feedback * rename record to entry * adapt parseTimestamp to defaultValue options interface * also adapt _parseTreeType * rename MetadataEntry to MetadataEntryProto * also rename APIMetadata to APIMetadataEntry and add comments about the distinction * fix e2e tests * deduplicate metadata entries when applying update actions * changelog, deduplicate for segments too * remove unused imports in frontend code * integrate backend pr feedback * refresh snapshots * readd border around empty metadata placeholder in dashboard --------- Co-authored-by: Philipp Otto <[email protected]> Co-authored-by: Philipp Otto <[email protected]> Co-authored-by: MichaelBuessemeyer <[email protected]> Co-authored-by: Michael Büßemeyer <[email protected]>
…minds#8094) * Fix padding for 3D view buttons and temporarily trigger nightlies on this branch * Temporarily run screenshot tests on this branch * update screenshots * Revert "Temporarily run screenshot tests on this branch" This reverts commit c8a27a2. * revert triggering nightlies
* bump sbt plugin versions+protobuf, run codespell * Update conf/evolutions/120-remove-old-organization-id.sql Co-authored-by: Daniel <[email protected]> --------- Co-authored-by: Daniel <[email protected]>
* implement train-model for multiple annotations (WIP) * further refactoring of train model form * make onFinish work for multi-annotation training * clean up * fix annotationId and csv validation * fix training model from annotation view * clean up * WIP: Apply feedback - includes extending bbox validation * make bbox checking work while not refetching tracings * some cleanup * apply missing pr feedback * improve ai modal csv input parsing * Update frontend/javascripts/oxalis/view/jobs/train_ai_model.tsx Co-authored-by: Daniel <[email protected]> * apply feedback - add comment about why AnnotationInfoForAIJob is so complex - filter out dataset segmentation layers that are used as fallback layers of other volume tracing layers of an annotation * Update frontend/javascripts/oxalis/view/jobs/train_ai_model.tsx Co-authored-by: Daniel <[email protected]> --------- Co-authored-by: Michael Büßemeyer <[email protected]> Co-authored-by: MichaelBuessemeyer <[email protected]> Co-authored-by: Daniel <[email protected]>
* Fix dataset upload for absolute binaryData paths * changelog, fix message key
* disable proofreading actions for meshfiles that were created for a mapping * add changelog * address review --------- Co-authored-by: Florian M <[email protected]>
* add summary row to time tracking * add changelog * remove whitespace
Co-authored-by: bulldozer-boy[bot] <53086266+bulldozer-boy[bot]@users.noreply.github.com>
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