Merge remote-tracking branch 'origin/master' into isosurface

* origin/master: Add debugging methods to visualize wireframe of buckets (#3402) fixed bug that selects a just removed layout (#3379) Added button to revoke admin rights in frontend (#3378) Revert "Add REST API versioning support (#3385)" (#3404) Add REST API versioning support (#3385) limit number of tasks to be created in one api request (#3386) Use correct volume download route in TracingStoreRpcClient (#3403) clearer error message when uploading nml for inaccessible dataset (#3390) Refactored dropdown item events (#3383) Show dataset extent in right menu tab (#3371)
scalableminds · Oct 26, 2018 · ed670e3 · ed670e3
2 parents 8f16f9e + 8238820
commit ed670e3
Show file tree

Hide file tree

Showing 21 changed files with 281 additions and 139 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,7 +14,9 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.md).
 - Added support for duplicate dataset names for different organizations [#3137](https://github.com/scalableminds/webknossos/pull/3137)
 - Extended the version restore view and added a view to restore older versions of a volume tracing. Access it through the dropdown next to the Save button. [#3349](https://github.com/scalableminds/webknossos/pull/3349)
 - Added support to watch additional dataset directories, automatically creating symbolic links to the main directory [#3330](https://github.com/scalableminds/webknossos/pull/3330)
+- Added a button to the users list view that revokes admin rights from all selected users. [#3378](https://github.com/scalableminds/webknossos/pull/3378)
 - A User can now have multiple layouts for tracing views. [#3299](https://github.com/scalableminds/webknossos/pull/3299)
+- The info tab in tracing views now displays the extent of the current dataset. [#3371](https://github.com/scalableminds/webknossos/pull/3371).
 
 ### Changed
 

diff --git a/app/assets/javascripts/admin/task/task_annotation_view.js b/app/assets/javascripts/admin/task/task_annotation_view.js
@@ -113,41 +113,32 @@ class TaskAnnotationView extends React.PureComponent<Props & StateProps, State>
           <a href={`/annotations/Task/${annotation.id}`}>{label}</a>
         </Item>
 
-        <Item key={`${annotation.id}-transfer`}>
-          <span
-            onClick={() =>
-              this.setState({ currentAnnotation: annotation, isTransferModalVisible: true })
-            }
-          >
-            <Icon type="team" />Transfer
-          </span>
+        <Item
+          key={`${annotation.id}-transfer`}
+          onClick={() =>
+            this.setState({ currentAnnotation: annotation, isTransferModalVisible: true })
+          }
+        >
+          <Icon type="team" />Transfer
         </Item>
         <Item key={`${annotation.id}-download`}>
           <a href={`/api/annotations/Task/${annotation.id}/download`}>
             <Icon type="download" />Download
           </a>
         </Item>
-        <Item key={`${annotation.id}-reset`}>
-          <span onClick={() => this.resetAnnotation(annotation)}>
-            <Icon type="rollback" />Reset
-          </span>
+        <Item key={`${annotation.id}-reset`} onClick={() => this.resetAnnotation(annotation)}>
+          <Icon type="rollback" />Reset
         </Item>
-        <Item key={`${annotation.id}-delete`}>
-          <span onClick={() => this.deleteAnnotation(annotation)}>
-            <Icon type="delete" />Reset and Cancel
-          </span>
+        <Item key={`${annotation.id}-delete`} onClick={() => this.deleteAnnotation(annotation)}>
+          <Icon type="delete" />Reset and Cancel
         </Item>
         {annotation.state === "Finished" ? (
-          <Item key={`${annotation.id}-reopen`}>
-            <span onClick={() => this.reOpenAnnotation(annotation)}>
-              <Icon type="folder-open" />Reopen
-            </span>
+          <Item key={`${annotation.id}-reopen`} onClick={() => this.reOpenAnnotation(annotation)}>
+            <Icon type="folder-open" />Reopen
           </Item>
         ) : (
-          <Item key={`${annotation.id}-finish`}>
-            <span onClick={() => this.finishAnnotation(annotation)}>
-              <Icon type="check-circle-o" />Finish
-            </span>
+          <Item key={`${annotation.id}-finish`} onClick={() => this.finishAnnotation(annotation)}>
+            <Icon type="check-circle-o" />Finish
           </Item>
         )}
       </Menu>

diff --git a/app/assets/javascripts/admin/user/user_list_view.js b/app/assets/javascripts/admin/user/user_list_view.js
@@ -170,11 +170,11 @@ class UserListView extends React.PureComponent<Props, State> {
     });
   };
 
-  grantAdminRights = async () => {
+  setAdminRightsTo = async (isAdmin: boolean) => {
     if (this.props.activeUser.isAdmin) {
       const newUserPromises = this.state.users.map(user => {
         if (this.state.selectedUserIds.includes(user.id)) {
-          const newUser = Object.assign({}, user, { isAdmin: true });
+          const newUser = Object.assign({}, user, { isAdmin });
 
           return updateUser(newUser);
         }
@@ -305,22 +305,40 @@ class UserListView extends React.PureComponent<Props, State> {
           Change Experience
         </Button>
         {this.props.activeUser.isAdmin ? (
-          <Button
-            onClick={() =>
-              Modal.confirm({
-                title: messages["users.grant_admin_rights_title"],
-                content: messages["users.grant_admin_rights"]({
-                  numUsers: this.state.selectedUserIds.length,
-                }),
-                onOk: this.grantAdminRights,
-              })
-            }
-            icon="rocket"
-            disabled={!hasRowsSelected}
-            style={marginRight}
-          >
-            Grant Admin Rights
-          </Button>
+          <React.Fragment>
+            <Button
+              onClick={() =>
+                Modal.confirm({
+                  title: messages["users.grant_admin_rights_title"],
+                  content: messages["users.grant_admin_rights"]({
+                    numUsers: this.state.selectedUserIds.length,
+                  }),
+                  onOk: () => this.setAdminRightsTo(true),
+                })
+              }
+              icon="rocket"
+              disabled={!hasRowsSelected}
+              style={marginRight}
+            >
+              Grant Admin Rights
+            </Button>
+            <Button
+              onClick={() =>
+                Modal.confirm({
+                  title: messages["users.revoke_admin_rights_title"],
+                  content: messages["users.revoke_admin_rights"]({
+                    numUsers: this.state.selectedUserIds.length,
+                  }),
+                  onOk: () => this.setAdminRightsTo(false),
+                })
+              }
+              icon="rollback"
+              disabled={!hasRowsSelected}
+              style={marginRight}
+            >
+              Revoke Admin Rights
+            </Button>
+          </React.Fragment>
         ) : null}
         <InviteUsersPopover
           organizationName={this.props.activeUser.organization}

diff --git a/app/assets/javascripts/dashboard/advanced_dataset/dataset_action_view.js b/app/assets/javascripts/dashboard/advanced_dataset/dataset_action_view.js
@@ -42,21 +42,13 @@ class DatasetActionView extends React.PureComponent<Props, State> {
 
     const menu = (
       <Menu>
-        <Menu.Item key="existing">
-          <a
-            href="#"
-            onClick={() => this.createTracing(dataset, "volume", true)}
-            title="Create volume tracing"
-          >
+        <Menu.Item key="existing" onClick={() => this.createTracing(dataset, "volume", true)}>
+          <a href="#" title="Create volume tracing">
             Use Existing Segmentation Layer
           </a>
         </Menu.Item>
-        <Menu.Item key="new">
-          <a
-            href="#"
-            onClick={() => this.createTracing(dataset, "volume", false)}
-            title="Create volume tracing"
-          >
+        <Menu.Item key="new" onClick={() => this.createTracing(dataset, "volume", false)}>
+          <a href="#" title="Create volume tracing">
             Use a New Segmentation Layer
           </a>
         </Menu.Item>

diff --git a/app/assets/javascripts/libs/utils.js b/app/assets/javascripts/libs/utils.js
@@ -5,6 +5,7 @@ import Maybe from "data.maybe";
 import window, { document, location } from "libs/window";
 import naturalSort from "javascript-natural-sort";
 import type { APIUser } from "admin/api_flow_types";
+import type { BoundingBoxObject } from "oxalis/store";
 
 export type Comparator<T> = (T, T) => -1 | 0 | 1;
 type UrlParams = { [key: string]: string };
@@ -129,6 +130,24 @@ export function computeArrayFromBoundingBox(bb: ?BoundingBoxType): ?Vector6 {
     : null;
 }
 
+export function aggregateBoundingBox(boundingBoxes: Array<BoundingBoxObject>): BoundingBoxType {
+  const allCoordinates = [0, 1, 2].map(index =>
+    boundingBoxes.map(box => box.topLeft[index]).concat(
+      boundingBoxes.map(box => {
+        const bottomRight = [
+          box.topLeft[0] + box.width,
+          box.topLeft[1] + box.height,
+          box.topLeft[2] + box.depth,
+        ];
+        return bottomRight[index];
+      }),
+    ),
+  );
+  const min = (([0, 1, 2].map(index => Math.min(...allCoordinates[index])): any): Vector3);
+  const max = (([0, 1, 2].map(index => Math.max(...allCoordinates[index])): any): Vector3);
+  return { min, max };
+}
+
 export function compareBy<T>(
   collectionForTypeInference: Array<T>, // this parameter is only used let flow infer the used type
   selector: T => number,

diff --git a/app/assets/javascripts/messages.js b/app/assets/javascripts/messages.js
@@ -185,6 +185,10 @@ In order to restore the current window, a reload is necessary.`,
   "users.grant_admin_rights": _.template(
     "You are about to grant admin privileges to <%- numUsers %> user(s) giving them access to all teams, datasets and annotations. Do you want to proceed?",
   ),
+  "users.revoke_admin_rights_title": "Do you really want to revoke admin rights?",
+  "users.revoke_admin_rights": _.template(
+    "You are about to revoke admin privileges from <%- numUsers %> user(s). Do you want to proceed?",
+  ),
   "users.change_email_title": "Do you really want to change the email?",
   "users.change_email": _.template(
     "Do you really want to change the email to '<%- newEmail %>' ? The corresponding user will be logged out and unsaved changes might be lost.",

diff --git a/app/assets/javascripts/oxalis/controller/scene_controller.js b/app/assets/javascripts/oxalis/controller/scene_controller.js
@@ -24,12 +24,17 @@ import Skeleton from "oxalis/geometries/skeleton";
 import Cube from "oxalis/geometries/cube";
 import ContourGeometry from "oxalis/geometries/contourgeometry";
 import Dimensions from "oxalis/model/dimensions";
-import { OrthoViews, OrthoViewValues, OrthoViewValuesWithoutTDView } from "oxalis/constants";
+import constants, {
+  OrthoViews,
+  OrthoViewValues,
+  OrthoViewValuesWithoutTDView,
+} from "oxalis/constants";
 import type { Vector3, OrthoView, OrthoViewMap, BoundingBoxType } from "oxalis/constants";
 import { listenToStoreProperty } from "oxalis/model/helpers/listener_helpers";
 import { getRenderer } from "oxalis/controller/renderer";
 import ArbitraryPlane from "oxalis/geometries/arbitrary_plane";
 import { getSomeTracing } from "oxalis/model/accessors/tracing_accessor";
+import window from "libs/window";
 
 const CUBE_COLOR = 0x999999;
 
@@ -80,6 +85,31 @@ class SceneController {
     this.rootGroup.scale.copy(new THREE.Vector3(...Store.getState().dataset.dataSource.scale));
     // Add scene to the group, all Geometries are then added to group
     this.scene.add(this.rootGroup);
+
+    this.setupDebuggingMethods();
+  }
+
+  setupDebuggingMethods() {
+    // These methods are attached to window, since we would run into circular import errors
+    // otherwise.
+    window.addBucketMesh = (position: Vector3, zoomStep: number, optColor?: string) => {
+      const bucketExtent = constants.BUCKET_WIDTH * 2 ** zoomStep;
+      const bucketSize = [bucketExtent, bucketExtent, bucketExtent];
+      const boxGeometry = new THREE.BoxGeometry(...bucketSize);
+      const edgesGeometry = new THREE.EdgesGeometry(boxGeometry);
+      const material = new THREE.LineBasicMaterial({
+        color: optColor || (zoomStep === 0 ? 0xff00ff : 0x00ffff),
+        linewidth: 1,
+      });
+      const cube = new THREE.LineSegments(edgesGeometry, material);
+      cube.position.x = position[0] + bucketSize[0] / 2;
+      cube.position.y = position[1] + bucketSize[1] / 2;
+      cube.position.z = position[2] + bucketSize[2] / 2;
+      this.rootNode.add(cube);
+      return cube;
+    };
+
+    window.removeBucketMesh = (mesh: THREE.LineSegments) => this.rootNode.remove(mesh);
   }
 
   addSTL(stlBuffer: ArrayBuffer): void {

diff --git a/app/assets/javascripts/oxalis/model/bucket_data_handling/bucket.js b/app/assets/javascripts/oxalis/model/bucket_data_handling/bucket.js
@@ -6,11 +6,15 @@
 import _ from "lodash";
 import BackboneEvents from "backbone-events-standalone";
 import type { Vector3, Vector4 } from "oxalis/constants";
+import * as THREE from "three";
 import constants from "oxalis/constants";
 import TemporalBucketManager from "oxalis/model/bucket_data_handling/temporal_bucket_manager";
 import * as Utils from "libs/utils";
 import window from "libs/window";
 import Toast from "libs/toast";
+import { getResolutions } from "oxalis/model/accessors/dataset_accessor";
+import Store from "oxalis/store";
+import { bucketPositionToGlobalAddress } from "oxalis/model/helpers/position_converter";
 
 export const BucketStateEnum = {
   UNREQUESTED: "UNREQUESTED",
@@ -31,6 +35,8 @@ export class DataBucket {
   BIT_DEPTH: number;
   BUCKET_LENGTH: number;
   BYTE_OFFSET: number;
+  visualizedMesh: ?Object;
+  visualizationColor: number;
 
   state: BucketStateEnumType;
   dirty: boolean;
@@ -322,6 +328,37 @@ export class DataBucket {
       }
     }
   }
+
+  // The following three methods can be used for debugging purposes.
+  // The bucket will be rendered in the 3D scene as a wireframe geometry.
+  visualize() {
+    if (this.visualizedMesh != null) {
+      return;
+    }
+    if (this.zoomedAddress[3] === 0 || this.zoomedAddress[3] === 1) {
+      const resolutions = getResolutions(Store.getState().dataset);
+      this.visualizedMesh = window.addBucketMesh(
+        bucketPositionToGlobalAddress(this.zoomedAddress, resolutions),
+        this.zoomedAddress[3],
+        this.visualizationColor,
+      );
+    }
+  }
+
+  unvisualize() {
+    if (this.visualizedMesh != null) {
+      window.removeBucketMesh(this.visualizedMesh);
+      this.visualizedMesh = null;
+    }
+  }
+
+  setVisualizationColor(colorDescriptor: string | number) {
+    const color = new THREE.Color(colorDescriptor);
+    this.visualizationColor = color;
+    if (this.visualizedMesh != null) {
+      this.visualizedMesh.material.color = color;
+    }
+  }
 }
 
 export class NullBucket {

diff --git a/app/assets/javascripts/oxalis/model/bucket_data_handling/texture_bucket_manager.js b/app/assets/javascripts/oxalis/model/bucket_data_handling/texture_bucket_manager.js
@@ -182,6 +182,7 @@ export default class TextureBucketManager {
         bucketHeightInTexture,
       );
       this.committedBucketSet.add(bucket);
+
       window.needsRerender = true;
       this.isRefreshBufferOutOfDate = true;
     }