Fix displayed segment (#4480)

* use corect resolution for segment id look up * fix flow * add individual resolution to mouse position and put resolution in own column * rename resolution column, add changelog entry
scalableminds · Mar 24, 2020 · e224316 · e224316
1 parent b1db834
commit e224316
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,15 +10,17 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.md).
 [Commits](https://github.com/scalableminds/webknossos/compare/20.04.0...HEAD)
 
  ### Added
--
+- Added the magnification used for determining the segment ids in the segmentation tab to the table of the tab [#4480](https://github.com/scalableminds/webknossos/pull/4480)  
 
  ### Changed
 - Reported datasets can now overwrite existing ones that are reported as missing, this ignores the isScratch precedence. [#4465](https://github.com/scalableminds/webknossos/pull/4465)
 
  ### Fixed
 - Users only get tasks of datasets that they can access. [#4488](https://github.com/scalableminds/webknossos/pull/4488)
+- Fixed the displayed segment ids in segmentation tab when "Render Missing Data Black" is turned off. [#4480](https://github.com/scalableminds/webknossos/pull/4480)
 
  ### Removed
+
 -
 
 

diff --git a/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.js b/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.js
@@ -368,6 +368,10 @@ class DataCube {
     }
   }
 
+  hasDataAtPositionAndZoomStep(voxel: Vector3, zoomStep: number = 0) {
+    return this.getBucket(this.positionToZoomedAddress(voxel, zoomStep)).hasData();
+  }
+
   getDataValue(voxel: Vector3, mapping: ?Mapping, zoomStep: number = 0): number {
     const bucket = this.getBucket(this.positionToZoomedAddress(voxel, zoomStep));
     const voxelIndex = this.getVoxelIndex(voxel, zoomStep);

diff --git a/frontend/javascripts/oxalis/view/right-menu/mapping_info_view.js b/frontend/javascripts/oxalis/view/right-menu/mapping_info_view.js
@@ -16,7 +16,7 @@ import type { OxalisState, Mapping } from "oxalis/store";
 import { calculateGlobalPos } from "oxalis/controller/viewmodes/plane_controller";
 import { getMappingsForDatasetLayer } from "admin/admin_rest_api";
 import { getPosition, getRequestLogZoomStep } from "oxalis/model/accessors/flycam_accessor";
-import { getSegmentationLayer } from "oxalis/model/accessors/dataset_accessor";
+import { getSegmentationLayer, getResolutions } from "oxalis/model/accessors/dataset_accessor";
 import { getVolumeTracing } from "oxalis/model/accessors/volumetracing_accessor";
 import { setLayerMappingsAction } from "oxalis/model/actions/dataset_actions";
 import { setMappingEnabledAction } from "oxalis/model/actions/settings_actions";
@@ -45,6 +45,7 @@ type StateProps = {|
   activeViewport: OrthoView,
   activeCellId: number,
   isMergerModeEnabled: boolean,
+  renderMissingDataBlack: boolean,
 |};
 type Props = {| ...OwnProps, ...StateProps |};
 
@@ -126,24 +127,74 @@ class MappingInfoView extends React.Component<Props, State> {
   }
 
   renderIdTable() {
+    const {
+      mapping,
+      isMappingEnabled,
+      mappingColors,
+      activeViewport,
+      mousePosition,
+      zoomStep,
+      position,
+      dataset,
+      segmentationLayer,
+      renderMissingDataBlack,
+    } = this.props;
     const cube = this.getSegmentationCube();
-    const hasMapping = this.props.mapping != null;
-    const customColors = this.props.isMappingEnabled ? this.props.mappingColors : null;
+    const hasMapping = mapping != null;
+    const customColors = isMappingEnabled ? mappingColors : null;
 
     let globalMousePosition;
-    if (this.props.mousePosition && this.props.activeViewport !== OrthoViews.TDView) {
-      const [x, y] = this.props.mousePosition;
+    if (mousePosition && activeViewport !== OrthoViews.TDView) {
+      const [x, y] = mousePosition;
       globalMousePosition = calculateGlobalPos({ x, y });
     }
 
-    const getIdForPos = pos => pos && cube.getDataValue(pos, null, this.props.zoomStep);
+    const flycamPosition = position;
+    const resolutions = getResolutions(dataset);
+    // While render missing data black is not active and there is no segmentation for the current zoom step,
+    // the segmentation of a higher zoom step is shown. Here we determine the the next zoom step of the
+    // displayed segmentation data to get the correct segment ids for the camera and the mouse position.
+    const getNextUsableZoomStepForPosition = pos => {
+      let usableZoomStep = zoomStep;
+      while (
+        pos &&
+        usableZoomStep < resolutions.length - 1 &&
+        !cube.hasDataAtPositionAndZoomStep(pos, usableZoomStep)
+      ) {
+        usableZoomStep++;
+      }
+      return usableZoomStep;
+    };
+
+    const usableZoomStepForCameraPosition = renderMissingDataBlack
+      ? zoomStep
+      : getNextUsableZoomStepForPosition(flycamPosition);
+    const usableZoomStepForMousePosition =
+      renderMissingDataBlack || globalMousePosition == null
+        ? zoomStep
+        : getNextUsableZoomStepForPosition(globalMousePosition);
+
+    const getResolutionOfZoomStepAsString = usedZoomStep => {
+      const usedResolution = segmentationLayer ? segmentationLayer.resolutions[usedZoomStep] : null;
+      return usedResolution
+        ? `${usedResolution[0]}-${usedResolution[1]}-${usedResolution[2]}`
+        : "Not available";
+    };
+    const getIdForPos = (pos, usableZoomStep) =>
+      pos && cube.getDataValue(pos, null, usableZoomStep);
 
     const tableData = [
-      { name: "Active ID", key: "active", unmapped: this.props.activeCellId },
       {
-        name: "ID at current position",
+        name: "Active ID",
+        key: "active",
+        unmapped: this.props.activeCellId,
+        resolution: "",
+      },
+      {
+        name: "ID at the center",
         key: "current",
-        unmapped: getIdForPos(this.props.position),
+        unmapped: getIdForPos(flycamPosition, usableZoomStepForCameraPosition),
+        resolution: getResolutionOfZoomStepAsString(usableZoomStepForCameraPosition),
       },
       {
         name: (
@@ -160,7 +211,10 @@ class MappingInfoView extends React.Component<Props, State> {
           </span>
         ),
         key: "mouse",
-        unmapped: getIdForPos(globalMousePosition),
+        unmapped: getIdForPos(globalMousePosition, usableZoomStepForMousePosition),
+        resolution: globalMousePosition
+          ? getResolutionOfZoomStepAsString(usableZoomStepForMousePosition)
+          : "Not available",
       },
     ]
       .map(idInfo => ({
@@ -170,23 +224,40 @@ class MappingInfoView extends React.Component<Props, State> {
       .map(idInfo => ({
         ...idInfo,
         unmapped: (
-          <span style={{ background: convertCellIdToCSS(idInfo.unmapped) }}>{idInfo.unmapped}</span>
+          <span
+            style={{
+              background: convertCellIdToCSS(idInfo.unmapped),
+            }}
+          >
+            {idInfo.unmapped}
+          </span>
         ),
         mapped: (
-          <span style={{ background: convertCellIdToCSS(idInfo.mapped, customColors) }}>
+          <span
+            style={{
+              background: convertCellIdToCSS(idInfo.mapped, customColors),
+            }}
+          >
             {idInfo.mapped}
           </span>
         ),
       }));
 
-    const columnHelper = (title, dataIndex) => ({ title, dataIndex });
+    const columnHelper = (title, dataIndex) => ({
+      title,
+      dataIndex,
+    });
     const idColumns =
       hasMapping && this.props.isMappingEnabled
         ? // Show an unmapped and mapped id column if there's a mapping
           [columnHelper("Unmapped", "unmapped"), columnHelper("Mapped", "mapped")]
         : // Otherwise, only show an ID column
           [columnHelper("ID", "unmapped")];
-    const columns = [columnHelper("", "name"), ...idColumns];
+    const columns = [
+      columnHelper("", "name"),
+      ...idColumns,
+      columnHelper("Magnification", "resolution"),
+    ];
     return (
       <Table
         size="small"
@@ -328,6 +399,7 @@ function mapStateToProps(state: OxalisState) {
       .map(tracing => tracing.activeCellId)
       .getOrElse(0),
     isMergerModeEnabled: state.temporaryConfiguration.isMergerModeEnabled,
+    renderMissingDataBlack: state.datasetConfiguration.renderMissingDataBlack,
   };
 }