Refactor TreeMap to DiffableMap (#8626)

* allow to toggle visibility of each segment via custom segment colors

* allow to toggle segments and groups

* linting

* backend: add UpdateSegmentVisibilityVolumeAction, UpdateSegmentGroupVisibilityVolumeAction

* integrate updateSegmentVisibility update action

* implement toggle compaction and integrate updateSegmentGroupVisibilityVolumeAction

* warn user when too many custom segment colors exist; don't show checkboxes if selective visibility is active

* move titleRender to own method

* implement hideUnregisteredSegments and only-show-this-segment etc in context menu

* fix saving of hideUnregisteredSegments

* fix typing

* remove unlisted segments group prototype again

* expose hide unlisted segments in left sidebar and add show-all-segments in context menu of data viewports

* remove -2 handling for unlisted group stuff

* fix visibility when removing segment from list; refactor toggling

* hide checkboxes when proofreading and selectiveVisibilityInProofreading is active; fix screenshot tests

* write and parse tree and segment isVisible in NMLs

* fix support for view only

* add missing volumetracing_action_helpers.ts module

* fix warning because of non-string value in radio button component for tool bar

* use fast tooltip to avoid findDOMNode warning

* fmt backend

* fix warning when opening context menu by restructuring hooks

* refactor context info in context menu

* lint

* add some position when a segment is registered by toggling its visibility

* update screenshots (the selective rendering is done via hovering where
the opacity is a bit different now)

* implement benchmark for segment list scrolling; improve perf a little bit

* clean up unnecessary isChecked property

* use extracted vars

* add comments

* linting

* integrate some code rabbit feedback

* format

* added docstrings to DiffableMap

* extended unit tests for diffable map

* add missing type to merge

* WIP refactor treemap as diffablemap

* delete commented code

* merge defaultDatasetViewConfiguration with defaultDatasetViewConfigurationOrNull

* incorporate feedback

* WIP refactor Treemaps as diffablemaps

* WIP more refactoring

* WIP more refactoring

* WIP even more refactoring

* fixed more stuff

* update changelog

* fix more tests

* fix more tests

* fix more tests and types

* fix remaining tests

* unify proto property setting using withIsVisible

* fix array buffer related TS problems

* fix remaining type errors

* formatting

* add Toast.info to global mocks

* fix incorrect copy of TypedArray (buffer offsets may differ; slice is simpler anyway)

* changelog

* fix tree visibility toggle

* fix tree group toggling

* Update frontend/javascripts/viewer/view/right-border-tabs/connectome_tab/connectome_view.tsx

Co-authored-by: Philipp Otto <philippotto@users.noreply.github.com>

* Update frontend/javascripts/libs/diffable_map.ts

Co-authored-by: Philipp Otto <philippotto@users.noreply.github.com>

* Update frontend/javascripts/viewer/view/right-border-tabs/connectome_tab/connectome_view.tsx

Co-authored-by: Philipp Otto <philippotto@users.noreply.github.com>

* Update frontend/javascripts/viewer/model/reducers/skeletontracing_reducer.ts

Co-authored-by: Philipp Otto <philippotto@users.noreply.github.com>

* Update frontend/javascripts/libs/diffable_map.ts

Co-authored-by: Philipp Otto <philippotto@users.noreply.github.com>

* update can-i-use / browser capabilites list

* add PR feedback

* move tree type definitions into separate file to avoid cyclic dependency

* misc fixes

* clean unused code

* add warnings to the mutable methods of diffable map

* fix Object.values(props.trees) in three places, which TS did not complain about

* more fixes

* forbid usage of Object.keys/values/entries on DiffableMap and EdgeCollection to prevent errors

* use toArray

* use toArray instead of Array.from

* convert more foreach to for loops

* two more foreach -> for loop

* use clone and mutableSet instead of repeated immutable sets

* refactor chain reducer a bit

* add reducer tests for toggling of trees and fix them

* simplify chain reduce in tests

* avoid ts-expect error

---------

Co-authored-by: Philipp Otto <philipp.4096@gmail.com>
Co-authored-by: Florian M <florian@scm.io>
Co-authored-by: Philipp Otto <philippotto@users.noreply.github.com>

Author: 3 people

CHANGELOG.unreleased.md

@@ -30,6 +30,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Updated to Typescript from version `5.5` to `5.8`. [#8613](https://github.com/scalableminds/webknossos/pull/8613)
 - Updated Voxelytics log streaming to also include the `log_path` attribute. [#8615](https://github.com/scalableminds/webknossos/pull/8615)
 - When creating or uploading a non-task volume annotation layer with a fallback segmentation layer, the annotation layer’s bounding box will now be limited to that layer’s, instead of the whole dataset’s. [#7580](https://github.com/scalableminds/webknossos/pull/7580)
+- Refactored the `skeletonTracing.TreeMap` structure to use `DiffableMap` type. [#8626](https://github.com/scalableminds/webknossos/pull/8626)
 
 ### Fixed
 - When selecting a skeleton node in a viewport, its tree is focused and scrolled to in the skeleton tab, even if its parent group was collapsed before. [#8585](https://github.com/scalableminds/webknossos/pull/8585)

frontend/javascripts/admin/dataset/composition_wizard/02_upload_files.tsx

@@ -6,7 +6,6 @@ import ErrorHandling from "libs/error_handling";
 import { readFileAsText } from "libs/read_file";
 import Toast from "libs/toast";
 import { SoftError } from "libs/utils";
-import * as Utils from "libs/utils";
 import _ from "lodash";
 import type { Vector3 } from "viewer/constants";
 import { parseNml } from "viewer/model/helpers/nml_helpers";
@@ -175,13 +174,19 @@ async function parseNmlFiles(fileList: FileList): Promise<Partial<WizardContext>
     throw new SoftError("Could not extract dataset names.");
   }
 
-  if (Object.keys(trees1).length !== Object.keys(trees2).length) {
+  if (trees1.keys().toArray().length !== trees2.keys().toArray().length) {
     throw new SoftError("The two NML files should have the same tree count.");
   }
 
   for (const [tree1, tree2] of _.zip(
-    Utils.values(trees1).sort((a, b) => a.treeId - b.treeId),
-    Utils.values(trees2).sort((a, b) => a.treeId - b.treeId),
+    trees1
+      .values()
+      .toArray()
+      .sort((a, b) => a.treeId - b.treeId),
+    trees2
+      .values()
+      .toArray()
+      .sort((a, b) => a.treeId - b.treeId),
   )) {
     if (tree1 == null || tree2 == null) {
       // Satisfy TS. This should not happen, as we checked before that both tree collections

frontend/javascripts/libs/browser_feature_check.tsx

@@ -8,6 +8,7 @@ export default function checkBrowserFeatures() {
     Object.fromEntries([]);
     new BigUint64Array(1);
     "hello".replaceAll("l", "k");
+    new Map([[1, 2]]).values().map((v) => v);
     [].at(0);
   } catch (exception) {
     Toast.warning(

frontend/javascripts/libs/cuckoo/abstract_cuckoo_table.ts

@@ -14,7 +14,7 @@ let cachedNullTexture: UpdatableTexture | undefined;
 export abstract class AbstractCuckooTable<K, V, Entry extends [K, V]> {
   entryCapacity: number;
   entryCount: number = 0;
-  protected table!: Uint32Array;
+  protected table!: Uint32Array<ArrayBuffer>;
   protected seeds!: number[];
   protected seedSubscribers: Array<SeedSubscriberFn> = [];
   _texture: UpdatableTexture;