Support rendering more dtypes

.github/workflows/nightly.yml

@@ -14,11 +14,23 @@ jobs:
       - name: Checkout code
         uses: actions/checkout@v3
 
+      - name: Process and Log Branch Name
+        run: |
+          echo "BRANCH_NAME=${{ github.ref_name }}" >> $GITHUB_ENV
+          SUBDOMAIN=$(echo "${{ github.ref_name }}" | tr -dc '[:alpha:]' | tr '[:upper:]' '[:lower:]')
+          TAG_NAME=$(echo "${{ github.ref_name }}" | sed 's/[\/-]/_/g')
+
+          echo "SUBDOMAIN=$SUBDOMAIN" >> $GITHUB_ENV
+          echo "TAG_NAME=$TAG_NAME" >> $GITHUB_ENV
+
+          echo "Sanitized branch name: $SUBDOMAIN"
+          echo "Tag name: $TAG_NAME"
+
       - name: Remove dev-deployment
         run: |
           curl -X POST \
             -H "X-Auth-Token: ${{ secrets.RELEASE_API_TOKEN }}" \
-            https://kubernetix.scm.io/hooks/remove/webknossos/dev/master?user=CI+%28nightly%29
+            https://kubernetix.scm.io/hooks/remove/webknossos/dev/${{ env.TAG_NAME }}?user=CI+%28nightly%29
 
       - name: Wait 3 minutes
         run: sleep 180
@@ -27,32 +39,32 @@ jobs:
         run: |
           curl -X POST \
             -H "X-Auth-Token: ${{ secrets.RELEASE_API_TOKEN }}" \
-            https://kubernetix.scm.io/hooks/install/webknossos/dev/master?user=CI+%28nightly%29
+            https://kubernetix.scm.io/hooks/install/webknossos/dev/${{ env.TAG_NAME }}?user=CI+%28nightly%29
 
       - uses: actions/setup-node@v4
         with:
-            node-version: 18
+          node-version: 18
 
       - name: Install dependencies and wait
         run: |
-            corepack enable && yarn install --immutable & 
-            sleep 180 &
-            wait
+          corepack enable && yarn install --immutable &
+          sleep 180 &
+          wait
 
       - name: Refresh datasets
         run: |
-          curl -X POST --fail https://master.webknossos.xyz/data/triggers/checkInboxBlocking?token=${{ secrets.WK_AUTH_TOKEN }}
+          curl -X POST --fail https://${{ env.SUBDOMAIN }}.webknossos.xyz/data/triggers/checkInboxBlocking?token=${{ secrets.WK_AUTH_TOKEN }}
 
       - name: Run screenshot tests
         run: |
-          URL=https://master.webknossos.xyz/ \
+          URL=https://${{ env.SUBDOMAIN }}.webknossos.xyz/ \
           timeout 3000 \
           yarn test-screenshot
         env:
-          URL: https://master.webknossos.xyz/
+          URL: https://${{ env.SUBDOMAIN }}.webknossos.xyz/
           WK_AUTH_TOKEN: ${{ secrets.WK_AUTH_TOKEN }}
           BROWSERSTACK_USERNAME: ${{ secrets.BROWSERSTACK_USERNAME }}
-          BROWSERSTACK_ACCESS_KEY : ${{ secrets.BROWSERSTACK_ACCESS_KEY }}
+          BROWSERSTACK_ACCESS_KEY: ${{ secrets.BROWSERSTACK_ACCESS_KEY }}
 
       - name: Upload screenshots as artifact
         uses: actions/upload-artifact@v4

CHANGELOG.unreleased.md

@@ -11,6 +11,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 [Commits](https://github.com/scalableminds/webknossos/compare/25.02.1...HEAD)
 
 ### Added
+- Added support for datasets with the following data types: int8, int16, int32, uint32 (support for color was added, support for segmentation already existed before) and int64 (segmentation only). [#8325](https://github.com/scalableminds/webknossos/pull/8325)
 - Added a command palette that allows navigating between pages, switching tools and accessing some user settings via Ctrl+P. [#8447](https://github.com/scalableminds/webknossos/pull/8447/)
 - Failed jobs may be retried by super-users. [#8377](https://github.com/scalableminds/webknossos/pull/8377)
 
@@ -24,6 +25,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Fixed a bug that would lock a non-existing mapping to an empty segmentation layer under certain conditions. [#8401](https://github.com/scalableminds/webknossos/pull/8401)
 - Fixed the alignment of the button that allows restricting floodfill operations to a bounding box. [#8388](https://github.com/scalableminds/webknossos/pull/8388) 
 - Fixed rare bug where saving got stuck. [#8409](https://github.com/scalableminds/webknossos/pull/8409)
+- Fixed some rendering bugs for float datasets that used a large dynamic range. [#8325](https://github.com/scalableminds/webknossos/pull/8325)
 - Fixed a bug where reverting annotations could get stuck if some of its layers had been deleted in the meantime. [#8405](https://github.com/scalableminds/webknossos/pull/8405)
 - When removing a segment from the segment list, a corresponding precomputed mesh was not removed automatically. [#8428](https://github.com/scalableminds/webknossos/pull/8428)
 - Fixed a bug where newly added remote datasets would always appear in root folder, regardless of actual selected folder. [#8425](https://github.com/scalableminds/webknossos/pull/8425)

app/controllers/AnnotationController.scala

@@ -182,7 +182,7 @@ class AnnotationController @Inject()(
         dataset <- datasetDAO.findOne(datasetId) ?~> Messages("dataset.notFound", datasetId) ~> NOT_FOUND
         annotation <- annotationService.createExplorationalFor(
           request.identity,
-          dataset._id,
+          dataset,
           request.body
         ) ?~> "annotation.create.failed"
         _ = analyticsService.track(CreateAnnotationEvent(request.identity: User, annotation: Annotation))

app/controllers/AnnotationIOController.scala

@@ -327,18 +327,20 @@ class AnnotationIOController @Inject()(
     val bbox =
       if (volumeTracing.boundingBox.isEmpty) boundingBoxToProto(dataSource.boundingBox)
       else volumeTracing.boundingBox
-    val elementClass = fallbackLayerOpt
-      .map(layer => elementClassToProto(layer.elementClass))
-      .getOrElse(elementClassToProto(VolumeTracingDefaults.elementClass))
+
     for {
       tracingCanHaveSegmentIndex <- canHaveSegmentIndex(organizationId,
                                                         dataset.name,
                                                         fallbackLayerOpt.map(_.name),
                                                         remoteDataStoreClient)
+      elementClassProto <- fallbackLayerOpt
+        .map(layer => ElementClass.toProto(layer.elementClass))
+        .getOrElse(ElementClass.toProto(VolumeTracingDefaults.elementClass))
+        .toFox
     } yield
       volumeTracing.copy(
         boundingBox = bbox,
-        elementClass = elementClass,
+        elementClass = elementClassProto,
         fallbackLayer = fallbackLayerOpt.map(_.name),
         largestSegmentId = combineLargestSegmentIdsByPrecedence(volumeTracing.largestSegmentId,
                                                                 fallbackLayerOpt.map(_.largestSegmentId)),

app/models/annotation/AnnotationService.scala

@@ -141,6 +141,9 @@ class AnnotationService @Inject()(
           remoteDatastoreClient.hasSegmentIndexFile(datasetOrganizationId, dataSource.id.directoryName, layer.name)
         case None => Fox.successful(false)
       }
+      elementClassProto <- ElementClass
+        .toProto(fallbackLayer.map(layer => layer.elementClass).getOrElse(VolumeTracingDefaults.elementClass))
+        .toFox
     } yield
       VolumeTracing(
         None,
@@ -149,8 +152,7 @@ class AnnotationService @Inject()(
         dataSource.id.directoryName,
         vec3IntToProto(startPosition.getOrElse(dataSource.center)),
         vec3DoubleToProto(startRotation.getOrElse(vec3DoubleFromProto(VolumeTracingDefaults.editRotation))),
-        elementClassToProto(
-          fallbackLayer.map(layer => layer.elementClass).getOrElse(VolumeTracingDefaults.elementClass)),
+        elementClassProto,
         fallbackLayer.map(_.name),
         combineLargestSegmentIdsByPrecedence(fromNml = None, fromFallbackLayer = fallbackLayer.map(_.largestSegmentId)),
         0,
@@ -289,19 +291,18 @@ class AnnotationService @Inject()(
       _ <- tracingStoreClient.saveAnnotationProto(annotationId, annotationProto)
     } yield newAnnotationLayers
 
-  def createExplorationalFor(user: User,
-                             datasetId: ObjectId,
-                             annotationLayerParameters: List[AnnotationLayerParameters])(
+  def createExplorationalFor(user: User, dataset: Dataset, annotationLayerParameters: List[AnnotationLayerParameters])(
       implicit ctx: DBAccessContext,
-      m: MessagesProvider): Fox[Annotation] =
+      m: MessagesProvider): Fox[Annotation] = {
+    val newAnnotationId = ObjectId.generate
+    val datasetId = dataset._id
     for {
-      dataset <- datasetDAO.findOne(datasetId) ?~> "dataset.noAccessById"
-      newAnnotationId = ObjectId.generate
       annotationLayers <- createLayersForExplorational(dataset, newAnnotationId, annotationLayerParameters) ?~> "annotation.createTracings.failed"
       teamId <- selectSuitableTeam(user, dataset) ?~> "annotation.create.forbidden"
       annotation = Annotation(newAnnotationId, datasetId, None, teamId, user._id, annotationLayers)
       _ <- annotationDAO.insertOne(annotation)
     } yield annotation
+  }
 
   // WARNING: needs to be repeatable, might be called multiple times for an annotation
   def finish(annotation: Annotation, user: User, restrictions: AnnotationRestrictions)(

app/models/annotation/nml/NmlParser.scala

@@ -9,6 +9,7 @@ import com.scalableminds.util.tools.Fox.box2Fox
 import com.scalableminds.util.tools.JsonHelper.bool2Box
 import com.scalableminds.webknossos.datastore.SkeletonTracing._
 import com.scalableminds.webknossos.datastore.MetadataEntry.MetadataEntryProto
+import com.scalableminds.webknossos.datastore.VolumeTracing.VolumeTracing.ElementClassProto
 import com.scalableminds.webknossos.datastore.VolumeTracing.{Segment, SegmentGroup, VolumeTracing}
 import com.scalableminds.webknossos.datastore.geometry.{
   AdditionalAxisProto,
@@ -19,7 +20,6 @@ import com.scalableminds.webknossos.datastore.geometry.{
   Vec3IntProto
 }
 import com.scalableminds.webknossos.datastore.helpers.{NodeDefaults, ProtoGeometryImplicits, SkeletonTracingDefaults}
-import com.scalableminds.webknossos.datastore.models.datasource.ElementClass
 import com.scalableminds.webknossos.tracingstore.tracings.ColorGenerator
 import com.scalableminds.webknossos.tracingstore.tracings.skeleton.updating.TreeType
 import com.scalableminds.webknossos.tracingstore.tracings.skeleton.{MultiComponentTreeSplitter, TreeValidator}
@@ -75,7 +75,7 @@ class NmlParser @Inject()(datasetDAO: DatasetDAO) extends LazyLogging with Proto
             datasetName = dataset.name,
             editPosition = nmlParams.editPosition,
             editRotation = nmlParams.editRotation,
-            elementClass = ElementClass.uint32, // Note: this property may be adapted later in adaptPropertiesToFallbackLayer
+            elementClass = ElementClassProto.uint32, // Note: this property may be adapted later in adaptPropertiesToFallbackLayer
             fallbackLayer = v.fallbackLayerName,
             largestSegmentId = v.largestSegmentId,
             version = 0,

frontend/javascripts/admin/admin_rest_api.ts

@@ -8,7 +8,7 @@ import * as Utils from "libs/utils";
 import window, { location } from "libs/window";
 import _ from "lodash";
 import messages from "messages";
-import type { AnnotationTypeFilterEnum, LOG_LEVELS, Vector2, Vector3 } from "oxalis/constants";
+import type { AnnotationTypeFilterEnum, LOG_LEVELS, Vector3 } from "oxalis/constants";
 import Constants, { ControlModeEnum, AnnotationStateFilterEnum } from "oxalis/constants";
 import type BoundingBox from "oxalis/model/bucket_data_handling/bounding_box";
 import {
@@ -2234,7 +2234,7 @@ export async function getSamMask(
         pointY: number; // int, relative to topleft
       },
   additionalCoordinates: AdditionalCoordinate[],
-  intensityRange?: Vector2 | null,
+  intensityRange?: readonly [number, number] | null,
 ): Promise<Uint8Array> {
   const params = new URLSearchParams();
   if (intensityRange != null) {

frontend/javascripts/dashboard/dataset/dataset_settings_data_tab.tsx

@@ -26,7 +26,7 @@ import Toast from "libs/toast";
 import { jsonStringify, parseMaybe } from "libs/utils";
 import { BoundingBoxInput, Vector3Input } from "libs/vector_input";
 import { AllUnits, LongUnitToShortUnitMap, type Vector3 } from "oxalis/constants";
-import { getBitDepth } from "oxalis/model/accessors/dataset_accessor";
+import { getSupportedValueRangeForElementClass } from "oxalis/model/bucket_data_handling/data_rendering_logic";
 import type { BoundingBoxObject, OxalisState } from "oxalis/store";
 import * as React from "react";
 import { useSelector } from "react-redux";
@@ -362,7 +362,7 @@ function SimpleLayerForm({
   const dataLayers = Form.useWatch(["dataSource", "dataLayers"]);
   const category = Form.useWatch(["dataSource", "dataLayers", index, "category"]);
   const isSegmentation = category === "segmentation";
-  const bitDepth = getBitDepth(layer);
+  const valueRange = getSupportedValueRangeForElementClass(layer.elementClass);
 
   const mayLayerBeRemoved = dataLayers?.length > 1;
 
@@ -585,21 +585,23 @@ function SimpleLayerForm({
                   rules={[
                     {
                       validator: (_rule, value) =>
-                        value == null || value === "" || (value > 0 && value < 2 ** bitDepth)
+                        value == null ||
+                        value === "" ||
+                        (value >= valueRange[0] && value <= valueRange[1] && value !== 0)
                           ? Promise.resolve()
                           : Promise.reject(
                               new Error(
-                                `The largest segmentation ID must be greater than 0 and smaller than 2^${bitDepth}. You can also leave this field empty, but annotating this layer later will only be possible with manually chosen segment IDs.`,
+                                `The largest segmentation ID must be between ${valueRange[0]} and ${valueRange[1]} and not 0. You can also leave this field empty, but annotating this layer later will only be possible with manually chosen segment IDs.`,
                               ),
                             ),
                     },
                     {
                       warningOnly: true,
                       validator: (_rule, value) =>
-                        value != null && value === 2 ** bitDepth - 1
+                        value != null && value === valueRange[1]
                           ? Promise.reject(
                               new Error(
-                                `The largest segmentation ID has already reached the maximum possible value of 2^${bitDepth}-1. Annotations of this dataset cannot create new segments.`,
+                                `The largest segmentation ID has already reached the maximum possible value of ${valueRange[1]}. Annotations of this dataset cannot create new segments.`,
                               ),
                             )
                           : Promise.resolve(),

frontend/javascripts/libs/UpdatableTexture.ts

@@ -1,3 +1,4 @@
+import type { TypedArray } from "oxalis/constants";
 import * as THREE from "three";
 
 /* The UpdatableTexture class exposes a way to partially update a texture.
@@ -75,13 +76,7 @@ class UpdatableTexture extends THREE.Texture {
     return this.renderer.properties.get(this).__webglTexture != null;
   }
 
-  update(
-    src: Float32Array | Uint8Array | Uint32Array,
-    x: number,
-    y: number,
-    width: number,
-    height: number,
-  ) {
+  update(src: TypedArray, x: number, y: number, width: number, height: number) {
     if (originalTexSubImage2D == null) {
       // See explanation at declaration of originalTexSubImage2D.
       originalTexSubImage2D = this.gl.texSubImage2D.bind(this.gl);

frontend/javascripts/libs/cuckoo/abstract_cuckoo_table.ts

@@ -50,18 +50,12 @@ export abstract class AbstractCuckooTable<K, V, Entry extends [K, V]> {
     this._texture = createUpdatableTexture(
       textureWidth,
       textureWidth,
-      this.getClass().getTextureChannelCount(),
       this.getClass().getTextureType(),
       getRenderer(),
       this.getClass().getTextureFormat(),
+      this.getClass().getInternalFormat(),
     );
 
-    // The internal format has to be set manually, since ThreeJS does not
-    // derive this value by itself.
-    // See https://webgl2fundamentals.org/webgl/lessons/webgl-data-textures.html
-    // for a reference of the internal formats.
-    this._texture.internalFormat = this.getClass().getInternalFormat();
-
     this.entryCapacity = Math.floor(
       (textureWidth ** 2 * this.getClass().getTextureChannelCount()) /
         this.getClass().getElementsPerEntry(),
@@ -96,7 +90,6 @@ export abstract class AbstractCuckooTable<K, V, Entry extends [K, V]> {
       // Use 1x1 texture to avoid WebGL warnings.
       1,
       1,
-      this.getTextureChannelCount(),
       this.getTextureType(),
       getRenderer(),
       this.getTextureFormat(),

frontend/javascripts/libs/utils.ts

@@ -881,9 +881,11 @@ export function waitForElementWithId(elementId: string): Promise<any> {
 }
 
 export function convertDecToBase256(num: number): Vector4 {
+  const sign = Math.sign(num);
+
   const divMod = (n: number) => [Math.floor(n / 256), n % 256];
 
-  let tmp = num;
+  let tmp = Math.abs(num);
 
   let r: number, g: number, b: number, a: number;
   [tmp, r] = divMod(tmp);
@@ -895,11 +897,13 @@ export function convertDecToBase256(num: number): Vector4 {
   [tmp, a] = divMod(tmp);
 
   // Little endian
-  return [r, g, b, a];
+  return map4((el) => sign * el, [r, g, b, a]);
 }
 
 export function castForArrayType(uncastNumber: number, data: TypedArray): number | bigint {
-  return data instanceof BigUint64Array ? BigInt(uncastNumber) : uncastNumber;
+  return data instanceof BigUint64Array || data instanceof BigInt64Array
+    ? BigInt(uncastNumber)
+    : uncastNumber;
 }
 
 export function convertNumberTo64Bit(num: number | bigint | null): [Vector4, Vector4] {
@@ -915,12 +919,20 @@ export function convertNumberTo64BitTuple(num: number | bigint | null): [number,
   if (num == null || Number.isNaN(num)) {
     return [0, 0];
   }
+
+  let sign: number | null;
+  if (typeof num === "bigint") {
+    sign = num < 0n ? -1 : 1;
+  } else {
+    sign = Math.sign(num);
+  }
+
   // Cast to BigInt as bit-wise operations only work with 32 bits,
   // even though Number uses 53 bits.
-  const bigNum = BigInt(num);
+  const bigNum = BigInt(sign) * BigInt(num);
 
-  const bigNumLow = Number((2n ** 32n - 1n) & bigNum);
-  const bigNumHigh = Number(bigNum >> 32n);
+  const bigNumLow = sign * Number((2n ** 32n - 1n) & bigNum);
+  const bigNumHigh = sign * Number(bigNum >> 32n);
 
   return [bigNumHigh, bigNumLow];
 }

frontend/javascripts/messages.tsx

@@ -177,9 +177,12 @@ instead. Only enable this option if you understand its effect. All layers will n
     </span>
   ),
   "tracing.copy_cell_id": "Hit CTRL + I to copy the currently hovered segment id",
-  "tracing.segment_id_out_of_bounds": _.template(
-    "Cannot create a segment id larger than the segment layers maximum value of <%- maxSegmentId %>.",
-  ),
+  "tracing.segment_id_out_of_bounds": (
+    requestedId: number,
+    validRange: readonly [number, number],
+  ) =>
+    `Cannot create a segment with id=${requestedId} because it is not between ${validRange[0]} and ${validRange[1]}.`,
+
   "tracing.copy_maybe_mapped_cell_id":
     "Hit CTRL + I to copy the currently hovered segment id. Press CTRL + ALT + I if you want to copy the mapped id.",
   "tracing.no_more_branchpoints": "No more branchpoints",
@@ -365,8 +368,6 @@ instead. Only enable this option if you understand its effect. All layers will n
     `The layer "${layerName}" was defined as ${elementClass}. This format is not officially supported. Please convert the layer to a supported format.`,
   "dataset.unsupported_segmentation_class_uint24":
     "The segmentation layer was defined as uint24. This format is not supported for segmentations. Please convert the layer to a supported format.",
-  "dataset.unsupported_segmentation_class_int64":
-    "The segmentation layer was defined as int64. This format is not supported for segmentations. Please convert the layer to the unsigned uint64 format.",
   "dataset.is_scratch":
     "This dataset location is marked as 'scratch' and meant for testing only. Please move this dataset to a permanent storage location and reimport it.",
   "dataset.z1_downsampling_hint":

frontend/javascripts/oxalis/api/cross_origin_api.ts

@@ -147,7 +147,6 @@ function CrossOriginApi() {
   // biome-ignore lint/correctness/useExhaustiveDependencies: Rerun each time window.webknossos changes.
   useEffect(() => {
     if (window.webknossos && window.parent) {
-      // @ts-expect-error ts-migrate(2339) FIXME: Property 'webknossos' does not exist on type 'Wind... Remove this comment to see the full error message
       window.webknossos.apiReady().then(() => {
         window.parent.postMessage(
           {