Merge branch 'master' into add-y-scale-to-histogram

CHANGELOG.md

@@ -16,7 +16,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.md).
 -
 
 ### Fixed
--
+- Fixed an issue where webKnossos would complain in certain scenarios when resolutions of datasets were not complete. [#4344](https://github.com/scalableminds/webknossos/pull/4344)
 
 ### Removed
 -
@@ -37,10 +37,12 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.md).
 
 ### Changed
 - Some user actions, like deleting a group with all subtrees, resulted in lots of entries in the undo stack (one for each deleted tree). Those actions are now handled as a single atomic change and can be undone with a single undo invocation. [#4312](https://github.com/scalableminds/webknossos/pull/4312)
+- The "Find Data" feature will jump to the center of the layer's bounding box, if no data could be found. The "Find Data" feature can be found next to each layer's name in the dataset settings tab. [#4346](https://github.com/scalableminds/webknossos/pull/4346)
 
 ### Fixed
 - Fixed broken sorting in the dataset table of the dashboard. [#4318](https://github.com/scalableminds/webknossos/pull/4318)
 - Fixed annotation access to match the text in the modal. [#4314](https://github.com/scalableminds/webknossos/pull/4314)
+- Fixed that the brush tool could be selected in an read-only tracing. [#4345](https://github.com/scalableminds/webknossos/pull/4345)
 - Fixed the name of downloaded annotation zips. [#4330](https://github.com/scalableminds/webknossos/pull/4330)
 
 

frontend/javascripts/libs/toast.js

@@ -78,7 +78,7 @@ const Toast = {
 
     if (type === "error") {
       toastConfig = Object.assign(toastConfig, {
-        icon: <Icon type="cross-circle-o" className="alert-wiggle" style={{ color: "#a94442" }} />,
+        icon: <Icon type="close-circle-o" className="alert-wiggle" style={{ color: "#a94442" }} />,
         style: {
           backgroundColor: "#f2dede",
           borderColor: "#ebccd1",

frontend/javascripts/oxalis/model/reducers/volumetracing_reducer.js

@@ -54,10 +54,16 @@ function VolumeTracingReducer(state: OxalisState, action: VolumeTracingAction):
     .map(volumeTracing => {
       switch (action.type) {
         case "SET_TOOL": {
+          if (!state.tracing.restrictions.allowUpdate) {
+            return state;
+          }
           return setToolReducer(state, volumeTracing, action.tool);
         }
 
         case "CYCLE_TOOL": {
+          if (!state.tracing.restrictions.allowUpdate) {
+            return state;
+          }
           const tools = Object.keys(VolumeToolEnum);
           const currentToolIndex = tools.indexOf(volumeTracing.activeTool);
           const newTool = tools[(currentToolIndex + 1) % tools.length];

frontend/javascripts/oxalis/model/sagas/root_saga.js

@@ -11,6 +11,7 @@ import {
   pushAnnotationAsync,
   saveTracingAsync,
   collectUndoStates,
+  toggleErrorHighlighting,
 } from "oxalis/model/sagas/save_saga";
 import {
   warnAboutSegmentationOpacity,
@@ -55,6 +56,7 @@ function* restartableSaga(): Saga<void> {
   } catch (err) {
     console.error(err);
     ErrorHandling.notify(err, {});
+    toggleErrorHighlighting(true);
     alert(`\
 Internal error.
 Please reload the page to avoid losing data.

frontend/javascripts/oxalis/model_initialization.js

@@ -308,13 +308,14 @@ function initializeDataset(
   Store.dispatch(setDatasetAction(dataset));
 }
 
-function ensureDenseLayerResolutions(dataset: APIDataset) {
+export function ensureDenseLayerResolutions(dataset: APIDataset) {
+  const mostExtensiveResolutions = convertToDenseResolution(getMostExtensiveResolutions(dataset));
   for (const layer of dataset.dataSource.dataLayers) {
-    layer.resolutions = convertToDenseResolution(layer.resolutions);
+    layer.resolutions = convertToDenseResolution(layer.resolutions, mostExtensiveResolutions);
   }
 }
 
-function ensureMatchingLayerResolutions(dataset: APIDataset): void {
+export function ensureMatchingLayerResolutions(dataset: APIDataset): void {
   const mostExtensiveResolutions = getMostExtensiveResolutions(dataset);
   for (const layer of dataset.dataSource.dataLayers) {
     for (const resolution of layer.resolutions) {
@@ -325,7 +326,10 @@ function ensureMatchingLayerResolutions(dataset: APIDataset): void {
   }
 }
 
-function convertToDenseResolution(resolutions: Array<Vector3>) {
+export function convertToDenseResolution(
+  resolutions: Array<Vector3>,
+  fallbackDenseResolutions?: Array<Vector3>,
+): Array<Vector3> {
   // Each resolution entry can be characterized by it's greatest resolution dimension.
   // E.g., the resolution array [[1, 1, 1], [2, 2, 1], [4, 4, 2]] defines that
   // a log zoomstep of 2 corresponds to the resolution [2, 2, 1] (and not [4, 4, 2]).
@@ -339,11 +343,13 @@ function convertToDenseResolution(resolutions: Array<Vector3>) {
   }
   const paddedResolutionCount = 1 + Math.log2(_.max(resolutions.map(v => _.max(v))));
   const resolutionsLookUp = _.keyBy(resolutions, _.max);
+  const fallbackResolutionsLookUp = _.keyBy(fallbackDenseResolutions || [], _.max);
 
   return _.range(0, paddedResolutionCount).map(exp => {
     const resPower = 2 ** exp;
-    // If the resolution does not exist, use a fallback resolution
-    return resolutionsLookUp[resPower] || [resPower, resPower, resPower];
+    // If the resolution does not exist, use either the given fallback resolution or an isotropic fallback
+    const fallback = fallbackResolutionsLookUp[resPower] || [resPower, resPower, resPower];
+    return resolutionsLookUp[resPower] || fallback;
   });
 }
 

frontend/javascripts/oxalis/view/action-bar/volume_actions_view.js

@@ -46,7 +46,8 @@ class VolumeActionsView extends PureComponent<Props> {
         </RadioGroup>
         <ButtonGroup>
           <ButtonComponent onClick={this.handleCreateCell}>
-            New <span style={{ textDecoration: "underline" }}>C</span>ell
+            New&nbsp;
+            <span style={{ textDecoration: "underline" }}>C</span>ell
           </ButtonComponent>
         </ButtonGroup>
       </div>

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

@@ -8,6 +8,7 @@ import type { Dispatch } from "redux";
 import { connect } from "react-redux";
 import * as React from "react";
 import _ from "lodash";
+import { V3 } from "libs/mjs";
 
 import type { APIDataset, APIHistogramData } from "admin/api_flow_types";
 import { AsyncIconButton } from "components/async_clickables";
@@ -20,7 +21,11 @@ import {
 import { findDataPositionForLayer, getHistogramForLayer } from "admin/admin_rest_api";
 import { getGpuFactorsWithLabels } from "oxalis/model/bucket_data_handling/data_rendering_logic";
 import { getMaxZoomValueForResolution } from "oxalis/model/accessors/flycam_accessor";
-import { hasSegmentation, getElementClass } from "oxalis/model/accessors/dataset_accessor";
+import {
+  hasSegmentation,
+  getElementClass,
+  getLayerBoundaries,
+} from "oxalis/model/accessors/dataset_accessor";
 import { setPositionAction, setZoomStepAction } from "oxalis/model/actions/flycam_actions";
 import {
   updateDatasetSettingAction,
@@ -307,7 +312,13 @@ class DatasetSettings extends React.PureComponent<DatasetSettingsProps, State> {
       layerName,
     );
     if (!position || !resolution) {
-      Toast.warning(`Couldn't find data within layer "${layerName}."`);
+      const { upperBoundary, lowerBoundary } = getLayerBoundaries(dataset, layerName);
+      const centerPosition = V3.add(lowerBoundary, upperBoundary).map(el => el / 2);
+
+      Toast.warning(
+        `Couldn't find data within layer "${layerName}." Jumping to the center of the layer's bounding box.`,
+      );
+      this.props.onSetPosition(centerPosition);
       return;
     }
 

frontend/javascripts/test/model/model_resolutions.spec.js

@@ -0,0 +1,41 @@
+// @noflow
+import test from "ava";
+
+import {
+  ensureDenseLayerResolutions,
+  ensureMatchingLayerResolutions,
+  convertToDenseResolution,
+} from "oxalis/model_initialization";
+
+test("Simple convertToDenseResolution", t => {
+  const denseResolutions = convertToDenseResolution([[2, 2, 1], [4, 4, 2]]);
+  t.deepEqual(denseResolutions, [[1, 1, 1], [2, 2, 1], [4, 4, 2]]);
+});
+
+test("Complex convertToDenseResolution", t => {
+  const dataset = {
+    dataSource: {
+      dataLayers: [
+        {
+          resolutions: [[2, 2, 1], [4, 4, 1], [8, 8, 1], [16, 16, 2], [32, 32, 4]],
+        },
+        {
+          resolutions: [[32, 32, 4]],
+        },
+      ],
+    },
+  };
+  ensureDenseLayerResolutions(dataset);
+  ensureMatchingLayerResolutions(dataset);
+  const expectedResolutions = [
+    [1, 1, 1],
+    [2, 2, 1],
+    [4, 4, 1],
+    [8, 8, 1],
+    [16, 16, 2],
+    [32, 32, 4],
+  ];
+
+  t.deepEqual(dataset.dataSource.dataLayers[0].resolutions, expectedResolutions);
+  t.deepEqual(dataset.dataSource.dataLayers[1].resolutions, expectedResolutions);
+});