Merge branch 'master' into supervoxel-naming

Author: MichaelBuessemeyer

app/models/job/Job.scala

@@ -73,7 +73,8 @@ case class Job(
             resultAnnotationLink
           }
         case JobCommand.infer_nuclei | JobCommand.infer_neurons | JobCommand.materialize_volume_annotation |
-            JobCommand.infer_with_model | JobCommand.infer_mitochondria | JobCommand.align_sections =>
+            JobCommand.infer_with_model | JobCommand.infer_mitochondria | JobCommand.align_sections |
+            JobCommand.infer_instances =>
           // There exist jobs with dataset name as return value, some with directoryName, and newest with datasetId
           // Construct links that work in either case.
           returnValue.map { datasetIdentifier =>

docs/data/neuroglancer_precomputed.md

@@ -35,10 +35,10 @@ my_dataset.precomputed             # One root folder per dataset
 └─ scale_n                  
 ```
 
-For details see the [Neuroglancer spec](https://github.com/google/neuroglancer/tree/master/src/neuroglancer/datasource/precomputed).
+For details see the [Neuroglancer spec](https://github.com/google/neuroglancer/blob/e13f1f4c62918f2ea07b12f2116bdcb6767b1499/src/datasource/precomputed/README.md).
 
 ## Performance Considerations
 To get the best streaming performance for Neuroglancer Precomputed datasets consider the following settings.
 
 - Use chunk sizes of 32 - 128 voxels^3
-- Enable sharding
+- Enable sharding

frontend/javascripts/viewer/view/action_bar_view.tsx

@@ -36,6 +36,7 @@ import TracingActionsView, {
 import ViewDatasetActionsView from "viewer/view/action-bar/view_dataset_actions_view";
 import ViewModesView from "viewer/view/action-bar/view_modes_view";
 import {
+  LayoutEvents,
   addNewLayout,
   deleteLayout,
   getLayoutConfig,
@@ -273,7 +274,7 @@ class ActionBarView extends React.PureComponent<Props, State> {
 
   handleResetLayout = () => {
     layoutEmitter.emit(
-      "resetLayout",
+      LayoutEvents.resetLayout,
       this.props.layoutProps.layoutKey,
       this.props.layoutProps.activeLayout,
     );

frontend/javascripts/viewer/view/context_menu.tsx

@@ -150,6 +150,7 @@ import {
   getVolumeRequestUrl,
   withMappingActivationConfirmation,
 } from "viewer/view/right-border-tabs/segments_tab/segments_view_helper";
+import { LayoutEvents, layoutEmitter } from "./layouting/layout_persistence";
 import { LoadMeshMenuItemLabel } from "./right-border-tabs/segments_tab/load_mesh_menu_item_label";
 
 type ContextMenuContextValue = React.MutableRefObject<HTMLElement | null> | null;
@@ -694,16 +695,16 @@ function getNodeContextMenuOptions({
       onClick: () => Store.dispatch(setActiveNodeAction(clickedNodeId)),
       label: "Select this Node",
     },
-    activeTreeId === clickedTree.treeId
-      ? {
-          key: "focus-tree",
-          onClick: () => {
-            Store.dispatch(expandParentGroupsOfTreeAction(clickedTree));
-            Store.dispatch(focusTreeAction(clickedTree));
-          },
-          label: "Focus Tree in Skeleton Tab",
-        }
-      : null,
+    {
+      key: "focus-tree",
+      onClick: () => {
+        Store.dispatch(setActiveNodeAction(clickedNodeId));
+        Store.dispatch(expandParentGroupsOfTreeAction(clickedTree));
+        Store.dispatch(focusTreeAction(clickedTree));
+        layoutEmitter.emit(LayoutEvents.showSkeletonTab);
+      },
+      label: "Activate & Focus Tree in Skeleton Tab",
+    },
     getMaybeMinCutItem(clickedTree, volumeTracing, userBoundingBoxes, isVolumeModificationAllowed),
     ...(allowUpdate
       ? [
@@ -1081,6 +1082,7 @@ function getNoNodeContextMenuOptions(props: NoNodeContextMenuProps): ItemType[]
     Store.dispatch(
       clickSegmentAction(clickedSegmentId, globalPosition, additionalCoordinates, layerName),
     );
+    layoutEmitter.emit(LayoutEvents.showSegmentsTab);
   };
 
   const onlyShowSegment = () => {

frontend/javascripts/viewer/view/layouting/flex_layout_wrapper.tsx

@@ -11,7 +11,7 @@ import messages from "messages";
 import * as React from "react";
 import { connect } from "react-redux";
 import type { Dispatch } from "redux";
-import type { OrthoView } from "viewer/constants";
+import type { BorderTabType, OrthoView } from "viewer/constants";
 import { ArbitraryViews, BorderTabs, OrthoViews } from "viewer/constants";
 import { setBorderOpenStatusAction } from "viewer/model/actions/ui_actions";
 import { setViewportAction } from "viewer/model/actions/view_mode_actions";
@@ -43,7 +43,7 @@ import {
   getMaximizedItemId,
   getPositionStatusOf,
 } from "./flex_layout_helper";
-import { getLayoutConfig, layoutEmitter } from "./layout_persistence";
+import { LayoutEvents, getLayoutConfig, layoutEmitter } from "./layout_persistence";
 
 const { Footer } = Layout;
 
@@ -118,21 +118,31 @@ class FlexLayoutWrapper extends React.PureComponent<Props, State> {
 
   addListeners() {
     this.unbindListeners.push(
-      layoutEmitter.on("resetLayout", () => {
+      layoutEmitter.on(LayoutEvents.resetLayout, () => {
         resetDefaultLayouts();
         this.rebuildLayout();
       }),
     );
     this.unbindListeners.push(
-      layoutEmitter.on("toggleBorder", (side) => {
+      layoutEmitter.on(LayoutEvents.toggleBorder, (side) => {
         this.toggleBorder(side);
       }),
     );
     this.unbindListeners.push(
-      layoutEmitter.on("toggleMaximize", () => {
+      layoutEmitter.on(LayoutEvents.toggleMaximize, () => {
         this.toggleMaximize();
       }),
     );
+    this.unbindListeners.push(
+      layoutEmitter.on(LayoutEvents.showSkeletonTab, () => {
+        this.openRightBorderTabById(BorderTabs.SkeletonTabView);
+      }),
+    );
+    this.unbindListeners.push(
+      layoutEmitter.on(LayoutEvents.showSegmentsTab, () => {
+        this.openRightBorderTabById(BorderTabs.SegmentsView);
+      }),
+    );
     this.unbindListeners.push(this.attachKeyboardShortcuts());
   }
 
@@ -147,6 +157,19 @@ class FlexLayoutWrapper extends React.PureComponent<Props, State> {
     return model;
   }
 
+  openRightBorderTabById(tabType: BorderTabType) {
+    const rightBorderId = "right-border-tab-container";
+    const node = this.state.model.getNodeById(rightBorderId);
+    if (!node || node.getType() !== "tab") return;
+
+    const isRightOpen = getBorderOpenStatus(this.state.model).right;
+    if (!isRightOpen) this.toggleBorder("right");
+
+    const rightBorderModel = (node as TabNode).getExtraData().model;
+    if (rightBorderModel == null) return;
+    rightBorderModel.doAction(FlexLayout.Actions.selectTab(tabType.id));
+  }
+
   adaptModelToConditionalTabs(model: Model) {
     /*
      * Currently, this method only adapts the visibility/existence of the

frontend/javascripts/viewer/view/layouting/floating_mobile_controls.tsx

@@ -7,7 +7,7 @@ import * as MoveHandlers from "viewer/controller/combinations/move_handlers";
 import { getMoveOffset, getMoveOffset3d } from "viewer/model/accessors/flycam_accessor";
 import { moveFlycamAction } from "viewer/model/actions/flycam_actions";
 import { Store } from "viewer/singletons";
-import { layoutEmitter } from "viewer/view/layouting/layout_persistence";
+import { LayoutEvents, layoutEmitter } from "viewer/view/layouting/layout_persistence";
 import ButtonComponent from "../components/button_component";
 
 const moveForward = (timeFactor: number, isFirst: boolean) =>
@@ -49,7 +49,7 @@ export function FloatingMobileControls() {
           type="primary"
           shape="circle"
           style={BUTTON_STYLE}
-          onClick={() => layoutEmitter.emit("toggleBorder", "left")}
+          onClick={() => layoutEmitter.emit(LayoutEvents.toggleBorder, "left")}
           icon={
             <img
               alt="Toggle left sidebar"
@@ -63,7 +63,7 @@ export function FloatingMobileControls() {
           type="primary"
           shape="circle"
           style={BUTTON_STYLE}
-          onClick={() => layoutEmitter.emit("toggleBorder", "right")}
+          onClick={() => layoutEmitter.emit(LayoutEvents.toggleBorder, "right")}
           icon={
             <img
               alt="Toggle right sidebar"
@@ -95,7 +95,7 @@ export function FloatingMobileControls() {
           type="primary"
           shape="circle"
           style={BUTTON_STYLE}
-          onClick={() => layoutEmitter.emit("toggleMaximize")}
+          onClick={() => layoutEmitter.emit(LayoutEvents.toggleMaximize)}
           icon={<ExpandAltOutlined style={{ transform: ICON_TRANSFORM_VALUE }} />}
         />
         {viewMode === "orthogonal" && (

frontend/javascripts/viewer/view/layouting/layout_persistence.ts

@@ -13,6 +13,13 @@ import getDefaultLayouts, {
   mapLayoutKeysToLanguage,
 } from "./default_layout_configs";
 export const layoutEmitter = createNanoEvents();
+export enum LayoutEvents {
+  resetLayout = "RESET_LAYOUT",
+  toggleBorder = "TOGGLE_BORDER",
+  toggleMaximize = "TOGGLE_MAXIMIZE",
+  showSkeletonTab = "SHOW_SKELETON_TAB",
+  showSegmentsTab = "SHOW_SEGMENTS_TAB",
+}
 // For debugging purposes:
 const disableLayoutPersistance = false;
 const localStorageKeys = {
@@ -92,7 +99,7 @@ function persistLayoutConfigs() {
   );
 }
 
-layoutEmitter.on("resetLayout", (layoutKey: LayoutKeys, activeLayout: string) => {
+layoutEmitter.on(LayoutEvents.resetLayout, (layoutKey: LayoutKeys, activeLayout: string) => {
   storeLayoutConfig(getDefaultLayouts()[layoutKey], layoutKey, activeLayout);
 });
 
@@ -185,8 +192,9 @@ export function setActiveLayout(layoutKey: LayoutKeys, activeLayout: string) {
     Store.dispatch(setStoredLayoutsAction(newLayouts));
     persistLayoutConfigsDebounced();
   } else {
-    throw new Error(`Active layout could not be set. The given layout ${layoutKey}  with name ${activeLayout}
-      // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message
-      was not found in layouts for ${mapLayoutKeysToLanguage[layoutKey]}.`);
+    throw new Error(
+      `Active layout could not be set. The given layout ${layoutKey} with name 
+      ${activeLayout} was not found in layouts for ${mapLayoutKeysToLanguage[layoutKey]}.`,
+    );
   }
 }

frontend/javascripts/viewer/view/layouting/tracing_layout_view.tsx

@@ -36,6 +36,7 @@ import {
   recalculateInputCatcherSizes,
 } from "viewer/view/input_catcher";
 import {
+  LayoutEvents,
   getLastActiveLayout,
   getLayoutConfig,
   layoutEmitter,
@@ -186,10 +187,10 @@ class TracingLayoutView extends React.PureComponent<PropsWithRouter, State> {
       // Simply assume mobile.
       const { left, right } = Store.getState().uiInformation.borderOpenStatus;
       if (left) {
-        layoutEmitter.emit("toggleBorder", "left");
+        layoutEmitter.emit(LayoutEvents.toggleBorder, "left");
       }
       if (right) {
-        layoutEmitter.emit("toggleBorder", "right");
+        layoutEmitter.emit(LayoutEvents.toggleBorder, "right");
       }
       // Immediately show mobile buttons
       this.handleTouch();

unreleased_changes/8897.md

@@ -0,0 +1,2 @@
+### Fixed
+- Fixed a bug where exploring remote datasets served by WEBKNOSSOS would yield invalid paths.

unreleased_changes/8917.md

@@ -0,0 +1,2 @@
+### Changed
+- Clicking `Focus Tree in Skeleton Tab` or `Focus in Segment List` will not only focus the clicked tree/segment, but also open the right tab if it was not open already.