Merge branch 'master' into suport-ngff-translate

Author: frcroth

CHANGELOG.unreleased.md

@@ -13,6 +13,10 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 ### Added
 - Added the total volume of a dataset to a tooltip in the dataset info tab. [#8229](https://github.com/scalableminds/webknossos/pull/8229)
 - Optimized performance of data loading with “fill value“ chunks. [#8271](https://github.com/scalableminds/webknossos/pull/8271)
+- The fill tool can now be adapted so that it only acts within a specified bounding box. Use the new "Restrict Floodfill" mode for that in the toolbar. [#8267](https://github.com/scalableminds/webknossos/pull/8267)
+- Added the option for "Selective Segment Visibility" for segmentation layers. Select this option in the left sidebar to only show segments that are currently active or hovered.  [#8281](https://github.com/scalableminds/webknossos/pull/8281)
+- A segment can be activated with doubleclick now. [#8281](https://github.com/scalableminds/webknossos/pull/8281)
+- It is now possible to select the magnification of the layers on which an AI model will be trained. [#8266](https://github.com/scalableminds/webknossos/pull/8266)
 - Added support for translations in OME NGFF zarr datasets (translation within coordinateTransformations on datasets). [#8311](https://github.com/scalableminds/webknossos/pull/8311)
 
 ### Changed
@@ -22,6 +26,7 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Improved the default colors for skeleton trees. [#8228](https://github.com/scalableminds/webknossos/pull/8228)
 - Allowed to train an AI model using differently sized bounding boxes. We recommend all bounding boxes to have equal dimensions or to have dimensions which are multiples of the smallest bounding box. [#8222](https://github.com/scalableminds/webknossos/pull/8222)
 - Within the bounding box tool, the cursor updates immediately after pressing `ctrl`, indicating that a bounding box can be moved instead of resized. [#8253](https://github.com/scalableminds/webknossos/pull/8253)
+- Improved the styling of active tools and modes in the toolbar. [#8295](https://github.com/scalableminds/webknossos/pull/8295)
 
 ### Fixed
 - Fixed that listing datasets with the `api/datasets` route without compression failed due to missing permissions regarding public datasets. [#8249](https://github.com/scalableminds/webknossos/pull/8249)
@@ -37,8 +42,12 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released
 - Fixed some layout issues in the upload view. [#8231](https://github.com/scalableminds/webknossos/pull/8231)
 - Fixed `FATAL: role "postgres" does not exist` error message in Docker compose. [#8240](https://github.com/scalableminds/webknossos/pull/8240)
 - Fixed the Zarr 3 implementation not accepting BytesCodec without "configuration" key. [#8282](https://github.com/scalableminds/webknossos/pull/8282)
+- Fixed that reloading the data of a volume annotation layer did not work properly. [#8298](https://github.com/scalableminds/webknossos/pull/8298)
+- Removed the magnification slider for the TIFF export within the download modal if only one magnification is available for the selected layer. [#8297](https://github.com/scalableminds/webknossos/pull/8297)
+- Fixed regression in styling of segment and skeleton tree tab. [#8307](https://github.com/scalableminds/webknossos/pull/8307)
 
 ### Removed
 - Removed support for HTTP API versions 3 and 4. [#8075](https://github.com/scalableminds/webknossos/pull/8075)
+- Removed that a warning is shown when a dataset is served from a datastore that was marked with isScratch=true. [#8296](https://github.com/scalableminds/webknossos/pull/8296)
 
 ### Breaking Changes

app/models/dataset/DataStore.scala

@@ -71,7 +71,6 @@ class DataStoreService @Inject()(dataStoreDAO: DataStoreDAO, jobService: JobServ
       Json.obj(
         "name" -> dataStore.name,
         "url" -> dataStore.publicUrl,
-        "isScratch" -> dataStore.isScratch,
         "allowsUpload" -> dataStore.allowsUpload,
         "jobsSupportedByAvailableWorkers" -> Json.toJson(jobsSupportedByAvailableWorkers),
         "jobsEnabled" -> jobsEnabled

docs/ui/layers.md

@@ -31,6 +31,7 @@ In addition to the general layer properties mentioned above, `color` and `segmen
 
 - `Color`: Every `color` layer can be re-colored to make it easily identifiable. By default, all layers have a white overlay, showing the true, raw black & white data. Clicking on the square color indicator brings up your system's color palette to choose from. Note, there is an icon button for inverting all color values in this layer.
 - `Pattern Opacity`: Adjust the visibility of the texture/pattern on each segment. To make segments easier to distinguish and more unique, a pattern is applied to each in addition to its base color. 0% hides the pattern. 100% makes the pattern very prominent. Great for increasing the visual contrast between segments.
+- `Selective Visibility`: When activated, only segments are shown that are currently active or hovered.
 - `ID Mapping`: WEBKNOSSOS supports applying pre-computed agglomerations/groupings of segmentation IDs for a given segmentation layer. This is a very powerful feature to explore and compare different segmentation strategies for a given segmentation layer. Mappings need to be pre-computed and stored together with a dataset for WEBKNOSSOS to download and apply. [Read more about this here](../proofreading/segmentation_mappings.md).
 
 

docs/volume_annotation/images/icon_restricted_floodfill.jpg

@@ -68,6 +68,8 @@ The following interactions and modes become available when working with some of
 ![3D Fill Modifier](./images/3d-modifier.jpg){align=left width="60"} 
 **2D/3D Fill**: Modifies the flood filling tool to work in 2D (in-plane only) or 3D (volumetric fill/re-labeling). 3D flood fill is constrained to a small, regional bounding box for performance reasons. Read more about [flood fills](#volume-flood-fills) below.
 
+![Restrict Fill](./images/icon_restricted_floodfill.jpg){align=left width="60"} 
+**Restrict Fill by Bounding Box**: When enabled, the fill operation will be restricted by the smallest bounding box that encloses the clicked position. This feature can be useful when correcting segmentation in a small bounding box (e.g., when curating training data).
 
 ## Quick-select tool
 The Quick Select tool offers AI-powered automatic segmentation, powered by [Segment Anything Model 2](https://ai.meta.com/blog/segment-anything-2/). Simply draw a selection around your target structure, and WEBKNOSSOS will automatically segment it for you.

docs/volume_annotation/tools.md

@@ -109,7 +109,7 @@ function TrainNewAiJobModal({ onClose }: { onClose: () => void }) {
     AnnotationInfoForAIJob<APIAnnotation>[]
   >([]);
 
-  const getMagForSegmentationLayer = async (annotationId: string, layerName: string) => {
+  const getMagsForSegmentationLayer = (annotationId: string, layerName: string) => {
     // The layer name is a human-readable one. It can either belong to an annotationLayer
     // (therefore, also to a volume tracing) or to the actual dataset.
     // Both are checked below. This won't be ambiguous because annotationLayers must not
@@ -130,10 +130,10 @@ function TrainNewAiJobModal({ onClose }: { onClose: () => void }) {
         (tracing) => tracing.tracingId === annotationLayer.tracingId,
       );
       const mags = volumeTracingMags[volumeTracingIndex] || ([[1, 1, 1]] as Vector3[]);
-      return getMagInfo(mags).getFinestMag();
+      return getMagInfo(mags);
     } else {
       const segmentationLayer = getSegmentationLayerByName(dataset, layerName);
-      return getMagInfo(segmentationLayer.resolutions).getFinestMag();
+      return getMagInfo(segmentationLayer.resolutions);
     }
   };
 
@@ -152,7 +152,7 @@ function TrainNewAiJobModal({ onClose }: { onClose: () => void }) {
       maskClosable={false}
     >
       <TrainAiModelTab
-        getMagForSegmentationLayer={getMagForSegmentationLayer}
+        getMagsForSegmentationLayer={getMagsForSegmentationLayer}
         onClose={onClose}
         annotationInfos={annotationInfosForAiJob}
         onAddAnnotationsInfos={(newItems) => {

frontend/javascripts/admin/voxelytics/ai_model_list_view.tsx

@@ -1,4 +1,4 @@
-import { Button, type ButtonProps } from "antd";
+import { Button, ConfigProvider, type ButtonProps } from "antd";
 import { LoadingOutlined } from "@ant-design/icons";
 import * as React from "react";
 import FastTooltip from "./fast_tooltip";
@@ -47,9 +47,12 @@ export function AsyncButton(props: AsyncButtonProps) {
   const effectiveChildren = hideContentWhenLoading && isLoading ? null : children;
   return (
     <FastTooltip title={title}>
-      <Button {...rest} loading={isLoading} onClick={onClick}>
-        {effectiveChildren}
-      </Button>
+      {/* Avoid weird animation when icons swap */}
+      <ConfigProvider theme={{ token: { motion: false } }}>
+        <Button {...rest} loading={isLoading} onClick={onClick}>
+          {effectiveChildren}
+        </Button>
+      </ConfigProvider>
     </FastTooltip>
   );
 }

frontend/javascripts/components/async_clickables.tsx

@@ -32,7 +32,7 @@ import { Tooltip as ReactTooltip } from "react-tooltip";
 const ROOT_TOOLTIP_IDS = {
   DEFAULT: "main-tooltip",
   DYNAMIC: "main-tooltip-dynamic",
-};
+} as const;
 
 export type FastTooltipPlacement =
   | "top"

frontend/javascripts/components/fast_tooltip.tsx

@@ -8,6 +8,7 @@ type LayerSelectionProps<L extends { name: string }> = {
   getReadableNameForLayer: (layer: L) => string;
   fixedLayerName?: string;
   label?: string;
+  onChange?: (a: string) => void;
 };
 
 export function LayerSelection<L extends { name: string }>({
@@ -65,6 +66,7 @@ export function LayerSelectionFormItem<L extends { name: string }>({
   getReadableNameForLayer,
   fixedLayerName,
   label,
+  onChange,
 }: LayerSelectionProps<L>): JSX.Element {
   const layerType = chooseSegmentationLayer ? "segmentation" : "color";
   return (
@@ -85,6 +87,7 @@ export function LayerSelectionFormItem<L extends { name: string }>({
         fixedLayerName={fixedLayerName}
         layerType={layerType}
         getReadableNameForLayer={getReadableNameForLayer}
+        onChange={onChange}
       />
     </Form.Item>
   );

frontend/javascripts/components/layer_selection.tsx

@@ -0,0 +1,73 @@
+import { Form, Select } from "antd";
+import { V3 } from "libs/mjs";
+import { clamp } from "libs/utils";
+import type { Vector3 } from "oxalis/constants";
+import type { MagInfo } from "oxalis/model/helpers/mag_info";
+
+export function MagSelectionFormItem({
+  name,
+  magInfo,
+}: {
+  name: string | Array<string | number>;
+  magInfo: MagInfo | undefined;
+}): JSX.Element {
+  return (
+    <Form.Item
+      name={name}
+      label={"Magnification"}
+      rules={[
+        {
+          required: true,
+          message: "Please select the magnification.",
+        },
+      ]}
+    >
+      <MagSelection magInfo={magInfo} />
+    </Form.Item>
+  );
+}
+
+function MagSelection({
+  magInfo,
+  value,
+  onChange,
+}: {
+  magInfo: MagInfo | undefined;
+  value?: Vector3;
+  onChange?: (newValue: Vector3) => void;
+}): JSX.Element {
+  const allMags = magInfo != null ? magInfo.getMagList() : [];
+
+  const onSelect = (index: number | undefined) => {
+    if (onChange == null || index == null) return;
+    const newMag = allMags[index];
+    if (newMag != null) onChange(newMag);
+  };
+
+  return (
+    <Select
+      placeholder="Select a magnification"
+      value={
+        // Using the index of the mag *in the mag list* as value internally,
+        // this is different from the mag index.
+        value == null || magInfo == null
+          ? null
+          : clamp(
+              0,
+              allMags.findIndex((v) => V3.equals(v, value)),
+              allMags.length - 1,
+            )
+      }
+      onSelect={onSelect}
+    >
+      {allMags.map((mag, index) => {
+        const readableName = mag.join("-");
+        return (
+          <Select.Option key={index} value={index}>
+            {readableName}
+          </Select.Option>
+        );
+      })}
+    </Select>
+  );
+}