Code

Connectome Tab#5894

Code

Merged

philippotto merged 108 commits intomasterscalableminds/webknossos:masterfrom connectome-viewingscalableminds/webknossos:connectome-viewingCopy head branch name to clipboardFeb 28, 2022

+3,207-278

Commits

Commits on Nov 30, 2021

• initial version of connectome viewer using mocked data

  daniel-wer

  committed
  0c5b319

Commits on Dec 1, 2021

• remove self-synapses from mock data, load agglomerate on check

  daniel-wer

  committed
  8a7f739

• merge master

  daniel-wer

  committed
  a1ba30f

• allow to render multiple Skeletons (skeleton.js)

  daniel-wer

  committed
  087c99f

Commits on Dec 2, 2021

• refactor and unify restrictions handling in skeletontracing reducer, avoid indentation

  daniel-wer

  committed
  244c099

• allow merger mode if allowUpdate is false

  daniel-wer

  committed
  1967f28

• Merge branch 'master' of github.com:scalableminds/webknossos into connectome-viewing

  daniel-wer

  committed
  e1277d3

Commits on Dec 6, 2021

• Merge branch 'master' into better-restrictions-handling

  daniel-wer

  authored
  6877dda

• Merge branch 'better-restrictions-handling' of github.com:scalableminds/webknossos into connectome-viewing

  daniel-wer

  committed
  9c08b1b

• load agglomerates from connectome tab into separate section of the store, but still display them

  daniel-wer

  committed
  b3b48fa

Commits on Dec 7, 2021

• Merge branch 'master' of github.com:scalableminds/webknossos into connectome-viewing

  daniel-wer

  committed
  44c3d60

• remove skeletons when unchecking agglomerates

  daniel-wer

  committed
  c664bec

Commits on Dec 8, 2021

• Add stubs for connectome file backend routes

  fm3

  committed
  8fbe06b

• validate POST parameters in backend routes

  fm3

  committed
  66d68fc

• adapt frontend api routes according to backend route draft, request synapse types and display as Tag next to synapse

  daniel-wer

  committed
  1db626e

• Merge branch 'connectome-viewing' of github.com:scalableminds/webknossos into connectome-viewing

  daniel-wer

  committed
  c7478f5

• remove obsolete BasicSkeletonTracing and fix tests

  daniel-wer

  committed
  784c456

• add synapses as single-node trees, use synapse type for node color, dynamically diff connectome data and add/delete synapse trees accordingly, add reset button

  daniel-wer

  committed
  b4f1334

• lazy load agglomerate skeletons and toggle visibility otherwise, remove agglomerate skeletons if they are no longer part of the connectome data

  daniel-wer

  committed
  26a7b9d

Commits on Dec 9, 2021

• Merge branch 'master' into connectome-viewing

  fm3

  committed
  8269e5e

• merge master

  fm3

  committed
  d961de3

• Implement single-id case for synapses route

  fm3

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  90998fb

• implement synaptic partner lookup

  fm3

  committed
  5361d77

• include mapping name with connectome file list

  fm3

  committed
  1f39467

• positions for synapses

  fm3

  committed
  af11e42

• add synapse types

  fm3

  committed
  974bdf5

• add basic filter ui and filter connectome tree, prepare filtering at state level to remove filtered synapse trees as well

  daniel-wer

  committed
  f19edc3

• Merge branch 'connectome-viewing' of github.com:scalableminds/webknossos into connectome-viewing

  daniel-wer

  committed
  6f13909

• fix agglomerateIds key, mock typeToString in connectome_view until backend sends correct mapping

  daniel-wer

  committed
  fde5cc2

Commits on Dec 10, 2021

• Fix index reading for synapses by agglomerate

  fm3

  committed
  facffab

• Merge branch 'connectome-viewing' of github.com:scalableminds/webknossos into connectome-viewing

  fm3

  committed
  60d5e06

Commits on Dec 13, 2021

• filter both the connectome tab view and the synapses/agglomerates displayed in the viewports

  daniel-wer

  committed
  fd2b461

• read synapse types from json

  fm3

  committed
  230ee37

• Merge branch 'connectome-viewing' of github.com:scalableminds/webknossos into connectome-viewing

  fm3

  committed
  26c558b

• fix empty array case in hdf reading

  fm3

  committed
  c54ccbe

• naming things

  fm3

  committed
  bccc033

• dynamically add/remove/show/hide agglomerate skeletons based on filters and checked nodes, enhance filter UI

  daniel-wer

  committed
  a9ca8b4

• Merge branch 'connectome-viewing' of github.com:scalableminds/webknossos into connectome-viewing

  daniel-wer

  committed
  2a2d9b4

• replace synapseTypes mock with an error toast if no json file was found and mock types only then

  daniel-wer

  committed
  3c6ad57

• enable virtual scroll for antd tree to boost performance

  daniel-wer

  committed
  4f7eb78

Commits on Dec 14, 2021

• reliably expand all nodes when selecting new agglomerate

  daniel-wer

  committed
  70904c6

• only hide/show synapse trees if they are filtered

  daniel-wer

  committed
  a63afc6

Commits on Dec 15, 2021

• Merge branch 'master' of github.com:scalableminds/webknossos into connectome-viewing

  daniel-wer

  committed
  60eb217

• prepare specification of multiple agglomerate ids

  daniel-wer

  committed
  f93d6f3

• small refactorings, properly persist available connectome files in store, allow to select connectome file

  daniel-wer

  committed
  e725acc

Commits on Dec 20, 2021

• run importjs

  daniel-wer

  committed
  2882cc6

• Merge branch 'master' of github.com:scalableminds/webknossos into connectome-viewing

  daniel-wer

  committed
  2c06dc7

• fix automatic merge

  daniel-wer

  committed
  3d61c2c

• implement hotlinking of agglomerates in the connectome tab so that they are automatically loaded when opening a link

  daniel-wer

  committed
  96175d7

Commits on Dec 21, 2021

• add synapse direction filter

  daniel-wer

  committed
  847bfdb

• increase performance of hiding/showing/deleting synapses, 10x faster to filter now

  daniel-wer

  committed
  2323325

Commits on Dec 27, 2021

• Merge branch 'master' of github.com:scalableminds/webknossos into connectome-viewing

  daniel-wer

  committed
  4685032

• implement getVisibleOrLastSegmentationLayer, update caniuse-lite

  daniel-wer

  committed
  04f3f42

Commits on Jan 3, 2022

• fix number NaN parsing and reset

  daniel-wer

  committed
  9dc31d6

Commits on Jan 4, 2022

• query synapses between agglomerate set from connectome file (#5907)

  Show description for b13ad1b
  

  fm3

  and

  daniel-wer

  authored
  b13ad1b

• improve filtering and small refactorings

  daniel-wer

  committed
  748b9c5

• refactor connectomeData data format to be more flat so it's easier to reason about and work with

  daniel-wer

  committed
  e49e5cb

Commits on Jan 5, 2022

• allow hotlinking to synapses even if the connectome tab is not visible, lazy-load synapse tree DOM nodes

  daniel-wer

  committed
  edc060c

• do not automatically activate mapping for connectome tab, show info alert to activate

  daniel-wer

  committed
  2b5d8a8

• clean up skeleton when switching segmentation layer in connectome tab

  daniel-wer

  committed
  e1402e5

• use native flatMap

  daniel-wer

  committed
  ddfbac1

• add context menu to second-level segments with the option to show all synapses for them, can be used to 'walk' the connectome

  daniel-wer

  committed
  132436e

Commits on Jan 6, 2022

• fix synapse direction filtering, fix initial loading performance which was caused by temporarily disabled virtualization

  daniel-wer

  committed
  f4c1ed3

• fix synapse type filtering for real and simplify code

  daniel-wer

  committed
  cadce45

• remove connectome mock data

  daniel-wer

  committed
  064cd86

Commits on Jan 10, 2022

• Merge branch 'master' of github.com:scalableminds/webknossos into connectome-viewing

  daniel-wer

  committed
  c6c8176

• apply PR feedback, use all antd preset colors for synapse types instead of only the first 8

  daniel-wer

  committed
  6311e88

• extract SynapseTree into its own component

  daniel-wer

  committed
  3f55a34

• extract ConnectomeFilters and ConnectomeSettings into their own components

  daniel-wer

  committed
  99dba6f

• fix agglomerate filtering if synapse direction was filtered

  daniel-wer

  committed
  4a14495

Commits on Jan 11, 2022

• fix initial auto-expand of all keys

  daniel-wer

  committed
  adf0b95

• decrease size of expandedKeys array to only contain valid entries

  daniel-wer

  committed
  00018b4

• check and uncheck all trees representing the same agglomerate

  daniel-wer

  committed
  702842a

• update docs, clean up when switching connectome file

  daniel-wer

  committed
  293b04d

• fix bug where store updates could be swallowed if the update was triggered by a store listener

  daniel-wer

  committed
  5fe62e1

• fix tooltips

  daniel-wer

  committed
  6c7ee34

• add some more comments

  daniel-wer

  committed
  a0fb8da

Commits on Jan 12, 2022

• keep activeAgglomerateIds if the connectome file is changed, always delete/add synapse trees instead of hiding/showing since it is faster, less complex, and less error-prone

  daniel-wer

  committed
  b8b18ff

• fix race condition during connectome activation

  daniel-wer

  committed
  82a4678

• fix connectome initialization if the tab is not visible, add screenshot test and snapshot

  daniel-wer

  committed
  ad6aa0d

Commits on Jan 17, 2022

• Merge branch 'master' of github.com:scalableminds/webknossos into connectome-viewing

  daniel-wer

  committed
  54a4dd3

• fix typo

  daniel-wer

  committed
  640b395

• apply PR feedback #1

  daniel-wer

  committed
  bf6b686

• apply PR feedback #2

  daniel-wer

  committed
  ef153e9

• highlight hovered segment ID when hovering in connectome tab

  daniel-wer

  committed
  203f1c5

Commits on Jan 18, 2022

• add entry to load synapses for agglomerate to context menu, fix mapping activation with subsequent mesh loading, unify segmentation id access

  daniel-wer

  committed
  d756742

• allow to load synapses for agglomerates in view mode, refactor agglomerate skeleton loading to different actions for normal tracing and connectome to account for different initialization and access…

  Show description for 1668340
  daniel-wer

  committed
  1668340

Commits on Jan 25, 2022

• Merge branch 'master' of github.com:scalableminds/webknossos into connectome-viewing

  daniel-wer

  committed
  2fd1a05

• agglomerate can have too many nodes or too many edges

  daniel-wer

  committed
  bd054aa

Commits on Feb 22, 2022

• Merge branch 'master' of github.com:scalableminds/webknossos into connectome-viewing

  daniel-wer

  committed
  a6ec3d7

• fix error in type definition that popped up after lodash type improvement

  daniel-wer

  committed
  675f27f

• move reset logic to componentDidUpdate and add comment

  daniel-wer

  committed
  0760ecd

• add particleSize slider to connectome settings since it would otherwise not be available if there is no skeleton tracing, tweak setting styles to make full use of antd grid without any custom margi…

  Show description for 86a26ff
  daniel-wer

  committed
  86a26ff

• avoid permanent node selection to fix that every second click didn't jump to the synapse position

  daniel-wer

  committed
  7ab8c36

• tune instructions on how to get started with the connectome tab

  daniel-wer

  committed
  15f39fb

• update changelog

  daniel-wer

  committed
  ee4f997

• temporarily enable nightly tests and renew connectome dataset screenshot

  daniel-wer

  committed
  74999f4

• use dev deployment for nightly tests

  daniel-wer

  committed
  5b08f11

Commits on Feb 23, 2022

• Merge branch 'master' of github.com:scalableminds/webknossos into connectome-viewing

  daniel-wer

  committed
  ddb8c85

• revert enabling nightly tests for this branch

  daniel-wer

  committed
  60cde4f

Commits on Feb 24, 2022

• add method to find the ultimatelyRenderedZoomStepAtPosition in contrast to the currentlyRenderedZoomStepAtPosition by waiting until buckets are loaded before checking whether the zoomStep is render…

  Show description for d91ca6d
  daniel-wer

  committed
  d91ca6d

• Merge branch 'master' of github.com:scalableminds/webknossos into connectome-viewing

  daniel-wer

  committed
  c070542

Commits on Feb 25, 2022

• control visibility of connectome tab via feature flag in application.conf

  philippotto

  committed
  7954613

• temporarily enable Connectome tab via application.conf

  philippotto

  committed
  828acab

• unbump currentLayoutVersion since the connectome tab can be added ad-hoc now

  philippotto

  committed
  5184d5f

• Merge branch 'connectome-viewing' of github.com:scalableminds/webknossos into connectome-viewing

  philippotto

  committed
  178c8c3

Commits on Feb 28, 2022

• Apply suggestions from code review

  philippotto

  authored
  772a924

• Merge branch 'master' into connectome-viewing

  philippotto

  authored
  5d50471