Make mappings work with 8 and 16 bit segmentations

CHANGELOG.md

@@ -14,6 +14,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.md).
 - webKnossos now comes with a list of sample datasets that can be automatically downloaded and imported from the menu. [#3725](https://github.com/scalableminds/webknossos/pull/3725)
 - Added a shortcut (Q) and button in the actions dropdown to screenshot the tracing views. The screenshots will contain everything that is visible in the tracing views, so feel free to disable the crosshairs in the settings or toggle the tree visibility using the (1) and (2) shortcuts before triggering the screenshot. [#3834](https://github.com/scalableminds/webknossos/pull/3834)
 - Neuroglancer precomputed datasets can now be added to webKnossos using the webknossos-connect (wk-connect) service. To setup a wk-connect datastore follow the instructions in the [Readme](https://github.com/scalableminds/webknossos-connect). Afterwards, datasets can be added through "Add Dataset" - "Add Dataset via wk-connect". [#3843](https://github.com/scalableminds/webknossos/pull/3843)
+- Added support for mappings for 8-bit and 16-bit segmentation layers. [#3953](https://github.com/scalableminds/webknossos/pull/3953)
 - The dataset settings within the tracing view allow to select between different loading strategies now ("best quality first" and "progressive quality"). Additionally, the rendering can use different magnifications as a fallback (instead of only one magnification). [#3801](https://github.com/scalableminds/webknossos/pull/3801)
 - The mapping selection dropbown is now sorted alphabetically. [#3864](https://github.com/scalableminds/webknossos/pull/3864)
 - Added the possibility to filter datasets in the dashboard according to their availability. By default, datasets which are missing on disk (e.g., when the datastore was deleted) are not shown anymore. This behavior can be configured via the settings icon next to the search box in the dashboard. [#3883](https://github.com/scalableminds/webknossos/pull/3883)

frontend/javascripts/oxalis/model/bucket_data_handling/data_rendering_logic.js

@@ -44,8 +44,10 @@ export function validateMinimumRequirements(specs: GpuSpecs): void {
 export type DataTextureSizeAndCount = { textureSize: number, textureCount: number };
 
 export function getPackingDegree(byteCount: number) {
-  // If the layer only holds one byte per voxel, we can pack 4 bytes using rgba channels
-  return byteCount === 1 ? 4 : 1;
+  // If the layer holds less than 4 byte per voxel, we can pack multiple voxels using rgba channels
+  if (byteCount === 1) return 4;
+  if (byteCount === 2) return 2;
+  return 1;
 }
 
 function getNecessaryVoxelCount() {

frontend/javascripts/oxalis/model/bucket_data_handling/texture_bucket_manager.js

@@ -6,6 +6,7 @@ import { DataBucket, bucketDebuggingFlags } from "oxalis/model/bucket_data_handl
 import { createUpdatableTexture } from "oxalis/geometries/materials/plane_material_factory_helpers";
 import { getBaseBucketsForFallbackBucket } from "oxalis/model/helpers/position_converter";
 import { getMaxZoomStepDiff } from "oxalis/model/bucket_data_handling/loading_strategy_logic";
+import { getPackingDegree } from "oxalis/model/bucket_data_handling/data_rendering_logic";
 import { getRenderer } from "oxalis/controller/renderer";
 import { getResolutions } from "oxalis/model/accessors/dataset_accessor";
 import { waitForCondition } from "libs/utils";
@@ -57,7 +58,7 @@ export default class TextureBucketManager {
   constructor(textureWidth: number, dataTextureCount: number, bytes: number) {
     // If there is one byte per voxel, we pack 4 bytes into one texel (packingDegree = 4)
     // Otherwise, we don't pack bytes together (packingDegree = 1)
-    this.packingDegree = bytes === 1 ? 4 : 1;
+    this.packingDegree = getPackingDegree(bytes);
 
     this.maximumCapacity =
       (this.packingDegree * dataTextureCount * textureWidth ** 2) / constants.BUCKET_SIZE;

frontend/javascripts/oxalis/shaders/segmentation.glsl.js

@@ -78,6 +78,15 @@ export const getSegmentationId: ShaderModule = {
 
       <% if (isMappingSupported) { %>
         if (isMappingEnabled) {
+          // Depending on the packing degree, the returned volume color contains extra values
+          // which would make the binary search fail
+
+          <% if (segmentationPackingDegree === "4.0") { %>
+            volume_color = vec4(volume_color.r, 0.0, 0.0, 0.0);
+          <% } else if (segmentationPackingDegree === "2.0") { %>
+            volume_color = vec4(volume_color.r, volume_color.g, 0.0, 0.0);
+          <% } %>
+
           float index = binarySearchIndex(
             <%= segmentationName %>_mapping_lookup_texture,
             mappingSize,

frontend/javascripts/oxalis/shaders/texture_access.glsl.js

@@ -207,6 +207,18 @@ export const getColorForCoords: ShaderModule = {
 
       float rgbaIndex = linearizeVec3ToIndexWithMod(offsetInBucket, bucketWidth, packingDegree);
 
+      if (packingDegree == 2.0) {
+        // It's essentially irrelevant what we return as the 3rd and 4th value here as we only have 2 byte of information.
+        // The caller needs to unpack this vec4 according to the packingDegree, see getSegmentationId for an example.
+        // The same goes for the following code where the packingDegree is 4 and we only have 1 byte of information.
+        if (rgbaIndex == 0.0) {
+          return vec4(bucketColor.r, bucketColor.g, bucketColor.r, bucketColor.g);
+        } else if (rgbaIndex == 1.0) {
+          return vec4(bucketColor.b, bucketColor.a, bucketColor.b, bucketColor.a);
+        }
+      }
+
+      // The following code deals with packingDegree == 4.0
       if (rgbaIndex == 0.0) {
         return vec4(bucketColor.r);
       } else if (rgbaIndex == 1.0) {

frontend/javascripts/oxalis/view/settings/user_settings_view.js

@@ -18,6 +18,7 @@ import {
 } from "oxalis/view/settings/setting_input_views";
 import type { UserConfiguration, OxalisState, Tracing } from "oxalis/store";
 import type { APIDataset } from "admin/api_flow_types";
+import { hasSegmentation } from "oxalis/model/accessors/dataset_accessor";
 import {
   enforceSkeletonTracing,
   getActiveNode,
@@ -239,10 +240,7 @@ class UserSettingsView extends PureComponent<UserSettingsViewProps, State> {
       const activeNodeRadius = getActiveNode(skeletonTracing)
         .map(activeNode => activeNode.radius)
         .getOrElse(0);
-      const isMergerModeSupported =
-        (this.props.dataset.dataSource.dataLayers || []).find(
-          layer => layer.category === "segmentation" && layer.elementClass === "uint32",
-        ) != null;
+      const isMergerModeSupported = hasSegmentation(this.props.dataset);
       panels.push(
         <Panel header="Nodes & Trees" key="3a">
           <NumberInputSetting
@@ -301,7 +299,7 @@ class UserSettingsView extends PureComponent<UserSettingsViewProps, State> {
             disabled={!isMergerModeSupported}
             tooltipText={
               !isMergerModeSupported
-                ? "The merger mode is only available for datasets with uint32 segmentations."
+                ? "The merger mode is only available for datasets with a segmentation layer."
                 : null
             }
           />