@vitessce/config 3.1.2 → 3.2.0

package/dist/index.js

@@ -3,8 +3,10 @@ const ViewType$1 = {
   STATUS: "status",
   SCATTERPLOT: "scatterplot",
   SPATIAL: "spatial",
+  SPATIAL_BETA: "spatialBeta",
   HEATMAP: "heatmap",
   LAYER_CONTROLLER: "layerController",
+  LAYER_CONTROLLER_BETA: "layerControllerBeta",
   GENOMIC_PROFILES: "genomicProfiles",
   GATING: "gating",
   FEATURE_LIST: "featureList",
@@ -16,20 +18,24 @@ const ViewType$1 = {
 const DataType$1 = {
   OBS_LABELS: "obsLabels",
   OBS_EMBEDDING: "obsEmbedding",
-  OBS_LOCATIONS: "obsLocations",
   OBS_FEATURE_MATRIX: "obsFeatureMatrix",
   OBS_SETS: "obsSets",
   FEATURE_LABELS: "featureLabels",
   IMAGE: "image",
   OBS_SEGMENTATIONS: "obsSegmentations",
   NEIGHBORHOODS: "neighborhoods",
-  GENOMIC_PROFILES: "genomic-profiles"
+  GENOMIC_PROFILES: "genomic-profiles",
+  OBS_SPOTS: "obsSpots",
+  OBS_POINTS: "obsPoints",
+  OBS_LOCATIONS: "obsLocations"
 };
 const FileType$1 = {
   // Joint file types
   ANNDATA_ZARR: "anndata.zarr",
   // Atomic file types
   OBS_EMBEDDING_CSV: "obsEmbedding.csv",
+  OBS_SPOTS_CSV: "obsSpots.csv",
+  OBS_POINTS_CSV: "obsPoints.csv",
   OBS_LOCATIONS_CSV: "obsLocations.csv",
   OBS_LABELS_CSV: "obsLabels.csv",
   FEATURE_LABELS_CSV: "featureLabels.csv",
@@ -42,6 +48,8 @@ const FileType$1 = {
   OBS_FEATURE_MATRIX_ANNDATA_ZARR: "obsFeatureMatrix.anndata.zarr",
   OBS_SETS_ANNDATA_ZARR: "obsSets.anndata.zarr",
   OBS_EMBEDDING_ANNDATA_ZARR: "obsEmbedding.anndata.zarr",
+  OBS_SPOTS_ANNDATA_ZARR: "obsSpots.anndata.zarr",
+  OBS_POINTS_ANNDATA_ZARR: "obsPoints.anndata.zarr",
   OBS_LOCATIONS_ANNDATA_ZARR: "obsLocations.anndata.zarr",
   OBS_SEGMENTATIONS_ANNDATA_ZARR: "obsSegmentations.anndata.zarr",
   OBS_LABELS_ANNDATA_ZARR: "obsLabels.anndata.zarr",
@@ -50,6 +58,8 @@ const FileType$1 = {
   OBS_FEATURE_MATRIX_MUDATA_ZARR: "obsFeatureMatrix.mudata.zarr",
   OBS_SETS_MUDATA_ZARR: "obsSets.mudata.zarr",
   OBS_EMBEDDING_MUDATA_ZARR: "obsEmbedding.mudata.zarr",
+  OBS_SPOTS_MUDATA_ZARR: "obsSpots.mudata.zarr",
+  OBS_POINTS_MUDATA_ZARR: "obsPoints.mudata.zarr",
   OBS_LOCATIONS_MUDATA_ZARR: "obsLocations.mudata.zarr",
   OBS_SEGMENTATIONS_MUDATA_ZARR: "obsSegmentations.mudata.zarr",
   OBS_LABELS_MUDATA_ZARR: "obsLabels.mudata.zarr",
@@ -93,10 +103,8 @@ const FileType$1 = {
   ANNDATA_EXPRESSION_MATRIX_ZARR: "anndata-expression-matrix.zarr"
 };
 const CoordinationType$1 = {
-  // Meta coordination scopes
   META_COORDINATION_SCOPES: "metaCoordinationScopes",
   META_COORDINATION_SCOPES_BY: "metaCoordinationScopesBy",
-  // Other coordination scopes
   DATASET: "dataset",
   // Entity types
   OBS_TYPE: "obsType",
@@ -122,6 +130,7 @@ const CoordinationType$1 = {
   SPATIAL_TARGET_X: "spatialTargetX",
   SPATIAL_TARGET_Y: "spatialTargetY",
   SPATIAL_TARGET_Z: "spatialTargetZ",
+  SPATIAL_TARGET_T: "spatialTargetT",
   SPATIAL_ROTATION_X: "spatialRotationX",
   SPATIAL_ROTATION_Y: "spatialRotationY",
   SPATIAL_ROTATION_Z: "spatialRotationZ",
@@ -159,7 +168,46 @@ const CoordinationType$1 = {
   GATING_FEATURE_SELECTION_X: "gatingFeatureSelectionX",
   GATING_FEATURE_SELECTION_Y: "gatingFeatureSelectionY",
   FEATURE_VALUE_TRANSFORM_COEFFICIENT: "featureValueTransformCoefficient",
-  TOOLTIPS_VISIBLE: "tooltipsVisible"
+  TOOLTIPS_VISIBLE: "tooltipsVisible",
+  FILE_UID: "fileUid",
+  IMAGE_LAYER: "imageLayer",
+  IMAGE_CHANNEL: "imageChannel",
+  SEGMENTATION_LAYER: "segmentationLayer",
+  SEGMENTATION_CHANNEL: "segmentationChannel",
+  SPATIAL_TARGET_C: "spatialTargetC",
+  SPATIAL_LAYER_VISIBLE: "spatialLayerVisible",
+  SPATIAL_LAYER_OPACITY: "spatialLayerOpacity",
+  SPATIAL_LAYER_COLORMAP: "spatialLayerColormap",
+  SPATIAL_LAYER_TRANSPARENT_COLOR: "spatialLayerTransparentColor",
+  SPATIAL_LAYER_MODEL_MATRIX: "spatialLayerModelMatrix",
+  SPATIAL_SEGMENTATION_FILLED: "spatialSegmentationFilled",
+  SPATIAL_SEGMENTATION_STROKE_WIDTH: "spatialSegmentationStrokeWidth",
+  SPATIAL_CHANNEL_COLOR: "spatialChannelColor",
+  SPATIAL_CHANNEL_VISIBLE: "spatialChannelVisible",
+  SPATIAL_CHANNEL_OPACITY: "spatialChannelOpacity",
+  SPATIAL_CHANNEL_WINDOW: "spatialChannelWindow",
+  PHOTOMETRIC_INTERPRETATION: "photometricInterpretation",
+  // For 3D volume rendering
+  SPATIAL_RENDERING_MODE: "spatialRenderingMode",
+  VOLUMETRIC_RENDERING_ALGORITHM: "volumetricRenderingAlgorithm",
+  SPATIAL_TARGET_RESOLUTION: "spatialTargetResolution",
+  // For clipping plane sliders
+  SPATIAL_SLICE_X: "spatialSliceX",
+  SPATIAL_SLICE_Y: "spatialSliceY",
+  SPATIAL_SLICE_Z: "spatialSliceZ",
+  // For spatial spot and point layers
+  SPOT_LAYER: "spotLayer",
+  POINT_LAYER: "pointLayer",
+  SPATIAL_SPOT_RADIUS: "spatialSpotRadius",
+  SPATIAL_SPOT_FILLED: "spatialSpotFilled",
+  SPATIAL_SPOT_STROKE_WIDTH: "spatialSpotStrokeWidth",
+  SPATIAL_LAYER_COLOR: "spatialLayerColor",
+  PIXEL_HIGHLIGHT: "pixelHighlight",
+  TOOLTIP_CROSSHAIRS_VISIBLE: "tooltipCrosshairsVisible",
+  LEGEND_VISIBLE: "legendVisible",
+  SPATIAL_CHANNEL_LABELS_VISIBLE: "spatialChannelLabelsVisible",
+  SPATIAL_CHANNEL_LABELS_ORIENTATION: "spatialChannelLabelsOrientation",
+  SPATIAL_CHANNEL_LABEL_SIZE: "spatialChannelLabelSize"
 };
 var commonjsGlobal = typeof globalThis !== "undefined" ? globalThis : typeof window !== "undefined" ? window : typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : {};
 function getDefaultExportFromCjs(x) {
@@ -8913,6 +8961,8 @@ const annDataObsSets = z.array(z.object({
   ]),
   scorePath: z.string().optional().describe("The location in the AnnData store for the set confidence scores, like 'obs/celltype_prediction_score.'")
 }));
+const annDataObsSpots = annDataObsm;
+const annDataObsPoints = annDataObsm;
 const annDataObsLocations = annDataObsm;
 const annDataObsEmbedding = annDataObsm;
 const annDataObsSegmentations = annDataObs;
@@ -8939,10 +8989,21 @@ z.object({
 z.object({
   obsIndex: z.string(),
   obsEmbedding: z.array(z.string()).length(2)
+  // TODO: support 3D?
+});
+z.object({
+  obsIndex: z.string(),
+  obsSpots: z.array(z.string()).length(2)
+  // TODO: support 3D?
+});
+z.object({
+  obsIndex: z.string(),
+  obsPoints: z.array(z.string()).length(3)
 });
 z.object({
   obsIndex: z.string(),
   obsLocations: z.array(z.string()).length(2)
+  // TODO: support 3D?
 });
 z.object({
   obsIndex: z.string(),
@@ -8974,6 +9035,8 @@ z.object({
   ]),
   obsFeatureMatrix: annDataObsFeatureMatrix,
   obsSets: annDataObsSets,
+  obsSpots: annDataObsSpots,
+  obsPoints: annDataObsPoints,
   obsLocations: annDataObsLocations,
   obsSegmentations: annDataObsSegmentations,
   obsEmbedding: z.union([
@@ -15609,7 +15672,7 @@ class VitessceConfigDataset {
     };
   }
 }
-function useComplexCoordinationHelper(scopes, coordinationScopes, coordinationScopesBy) {
+function useCoordinationByObjectHelper(scopes, coordinationScopes, coordinationScopesBy) {
   function processLevel(parentType, parentScope, levelType, levelVal) {
     var _a, _b;
     if (Array.isArray(levelVal)) {
@@ -15711,14 +15774,20 @@ class VitessceConfigView {
     });
     return this;
   }
-  useComplexCoordination(scopes) {
+  /**
+   * Attach potentially multi-level coordination scopes to this view.
+   * @param {object} scopes A value returned by `VitessceConfig.addCoordinationByObject`.
+   * Not intended to be a manually-constructed object.
+   * @returns {VitessceConfigView} This, to allow chaining.
+   */
+  useCoordinationByObject(scopes) {
     if (!this.view.coordinationScopes) {
       this.view.coordinationScopes = {};
     }
     if (!this.view.coordinationScopesBy) {
       this.view.coordinationScopesBy = {};
     }
-    const [nextCoordinationScopes, nextCoordinationScopesBy] = useComplexCoordinationHelper(
+    const [nextCoordinationScopes, nextCoordinationScopesBy] = useCoordinationByObjectHelper(
       scopes,
       this.view.coordinationScopes,
       this.view.coordinationScopesBy
@@ -15800,7 +15869,20 @@ function vconcat(...views) {
 class CoordinationLevel {
   constructor(value) {
     this.value = value;
+    this.cachedValue = null;
+  }
+  setCached(processedLevel) {
+    this.cachedValue = processedLevel;
+  }
+  getCached() {
+    return this.cachedValue;
   }
+  isCached() {
+    return this.cachedValue !== null;
+  }
+}
+function CL(value) {
+  return new CoordinationLevel(value);
 }
 class VitessceConfigCoordinationScope {
   /**
@@ -15854,14 +15936,21 @@ class VitessceConfigMetaCoordinationScope {
     this.metaScope.setValue(metaScopesVal);
     return this;
   }
-  useComplexCoordination(scopes) {
+  /**
+   * Attach potentially multi-level coordination scopes to this meta coordination
+   * scope instance.
+   * @param {object} scopes A value returned by `VitessceConfig.addCoordinationByObject`.
+   * Not intended to be a manually-constructed object.
+   * @returns {VitessceConfigView} This, to allow chaining.
+   */
+  useCoordinationByObject(scopes) {
     if (!this.metaScope.cValue) {
       this.metaScope.setValue({});
     }
     if (!this.metaByScope.cValue) {
       this.metaByScope.setValue({});
     }
-    const [metaScopesVal, metaByScopesVal] = useComplexCoordinationHelper(
+    const [metaScopesVal, metaByScopesVal] = useCoordinationByObjectHelper(
       scopes,
       this.metaScope.cValue,
       this.metaByScope.cValue
@@ -15870,15 +15959,6 @@ class VitessceConfigMetaCoordinationScope {
     this.metaByScope.setValue(metaByScopesVal);
     return this;
   }
-  /**
-   * Set the coordination value of the coordination scope.
-   * @param {any} cValue The value to set.
-   * @returns {VitessceConfigCoordinationScope} This, to allow chaining.
-   */
-  setValue(cValue) {
-    this.cValue = cValue;
-    return this;
-  }
 }
 class VitessceConfig {
   /**
@@ -16001,6 +16081,11 @@ class VitessceConfig {
     });
     return result;
   }
+  /**
+   * Initialize a new meta coordination scope in the coordination space,
+   * and get a reference to it in the form of a meta coordination scope instance.
+   * @returns {VitessceConfigMetaCoordinationScope} A new meta coordination scope instance.
+   */
   addMetaCoordination() {
     const prevMetaScopes = this.config.coordinationSpace[CoordinationType$1.META_COORDINATION_SCOPES] ? Object.keys(this.config.coordinationSpace[CoordinationType$1.META_COORDINATION_SCOPES]) : [];
     const prevMetaByScopes = this.config.coordinationSpace[CoordinationType$1.META_COORDINATION_SCOPES_BY] ? Object.keys(this.config.coordinationSpace[CoordinationType$1.META_COORDINATION_SCOPES_BY]) : [];
@@ -16018,14 +16103,29 @@ class VitessceConfig {
     this.config.coordinationSpace[CoordinationType$1.META_COORDINATION_SCOPES_BY][metaContainer.metaByScope.cScope] = metaContainer.metaByScope;
     return metaContainer;
   }
-  addComplexCoordination(input) {
+  /**
+   * Set up the initial values for multi-level coordination in the coordination space.
+   * Get a reference to these values to pass to the `useCoordinationByObject` method
+   * of either view or meta coordination scope instances.
+   * @param {object} input A (potentially nested) object with coordination types as keys
+   * and values being either the initial coordination value, a `VitessceConfigCoordinationScope`
+   * instance, or a `CoordinationLevel` instance.
+   * The CL function takes an array of objects as its argument, and returns a CoordinationLevel
+   * instance, to support nesting.
+   * @returns {object} A (potentially nested) object with coordination types as keys and values
+   * being either { scope }, { scope, children }, or an array of these. Not intended to be
+   * manipulated before being passed to a `useCoordinationByObject` function.
+   */
+  addCoordinationByObject(input) {
     const processLevel = (level) => {
       const result = {};
       Object.entries(level).forEach(([cType, nextLevelOrInitialValue]) => {
         if (nextLevelOrInitialValue instanceof CoordinationLevel) {
           const nextLevel = nextLevelOrInitialValue.value;
-          if (Array.isArray(nextLevel)) {
-            result[cType] = nextLevel.map((nextEl) => {
+          if (nextLevelOrInitialValue.isCached()) {
+            result[cType] = nextLevelOrInitialValue.getCached();
+          } else if (Array.isArray(nextLevel)) {
+            const processedLevel = nextLevel.map((nextEl) => {
               const [dummyScope] = this.addCoordination(cType);
               dummyScope.setValue("__dummy__");
               return {
@@ -16033,14 +16133,28 @@ class VitessceConfig {
                 children: processLevel(nextEl)
               };
             });
+            nextLevelOrInitialValue.setCached(processedLevel);
+            result[cType] = processedLevel;
           } else {
-            throw new Error("Expected CoordinationLevel.value to be an array.");
+            const nextEl = nextLevel;
+            const [dummyScope] = this.addCoordination(cType);
+            dummyScope.setValue("__dummy__");
+            const processedLevel = {
+              scope: dummyScope,
+              children: processLevel(nextEl)
+            };
+            nextLevelOrInitialValue.setCached(processedLevel);
+            result[cType] = processedLevel;
           }
         } else {
           const initialValue = nextLevelOrInitialValue;
-          const [scope] = this.addCoordination(cType);
-          scope.setValue(initialValue);
-          result[cType] = { scope };
+          if (initialValue instanceof VitessceConfigCoordinationScope) {
+            result[cType] = { scope: initialValue };
+          } else {
+            const [scope] = this.addCoordination(cType);
+            scope.setValue(initialValue);
+            result[cType] = { scope };
+          }
         }
       });
       return result;
@@ -16070,6 +16184,33 @@ class VitessceConfig {
     }
     return this;
   }
+  /**
+   * A convenience function for setting up multi-level and meta-coordination scopes
+   * across a set of views.
+   * @param {VitessceConfigView[]} views An array of view objects to link together.
+   * @param {object} input A (potentially nested) object with coordination types as keys
+   * and values being either the initial coordination value, a `VitessceConfigCoordinationScope`
+   * instance, or a `CoordinationLevel` instance.
+   * The CL function takes an array of objects as its argument, and returns a CoordinationLevel
+   * instance, to support nesting.
+   * @param {boolean} meta Should meta-coordination be used? Optional. By default, true.
+   * @returns {VitessceConfig} This, to allow chaining.
+   */
+  linkViewsByObject(views, input, meta = true) {
+    const scopes = this.addCoordinationByObject(input);
+    if (meta) {
+      const metaScope = this.addMetaCoordination();
+      metaScope.useCoordinationByObject(scopes);
+      views.forEach((view) => {
+        view.useMetaCoordination(metaScope);
+      });
+    } else {
+      views.forEach((view) => {
+        view.useCoordinationByObject(scopes);
+      });
+    }
+    return this;
+  }
   /**
    * Set the layout of views.
    * @param {VitessceConfigView|VitessceConfigViewHConcat|VitessceConfigViewVConcat} viewConcat A
@@ -16770,6 +16911,7 @@ async function generateConfig(fileUrls, hintTitle = null) {
   });
 }
 export {
+  CL as CoordinationLevel,
   HINTS_CONFIG,
   HINT_TYPE_TO_FILE_TYPE_MAP,
   VitessceConfig,

package/dist-tsc/VitessceConfig.d.ts

@@ -108,7 +108,13 @@ export class VitessceConfigView {
      * @returns {VitessceConfigView} This, to allow chaining.
      */
     useCoordination(...args: VitessceConfigCoordinationScope[]): VitessceConfigView;
-    useComplexCoordination(scopes: any): VitessceConfigView;
+    /**
+     * Attach potentially multi-level coordination scopes to this view.
+     * @param {object} scopes A value returned by `VitessceConfig.addCoordinationByObject`.
+     * Not intended to be a manually-constructed object.
+     * @returns {VitessceConfigView} This, to allow chaining.
+     */
+    useCoordinationByObject(scopes: object): VitessceConfigView;
     /**
      * Attach meta coordination scopes to this view.
      * @param {VitessceConfigMetaCoordinationScope} metaScope A meta coordination scope instance.
@@ -189,14 +195,14 @@ export class VitessceConfigMetaCoordinationScope {
      * @returns {VitessceConfigMetaCoordinationScope} This, to allow chaining.
      */
     useCoordination(...args: VitessceConfigCoordinationScope[]): VitessceConfigMetaCoordinationScope;
-    useComplexCoordination(scopes: any): VitessceConfigMetaCoordinationScope;
     /**
-     * Set the coordination value of the coordination scope.
-     * @param {any} cValue The value to set.
-     * @returns {VitessceConfigCoordinationScope} This, to allow chaining.
+     * Attach potentially multi-level coordination scopes to this meta coordination
+     * scope instance.
+     * @param {object} scopes A value returned by `VitessceConfig.addCoordinationByObject`.
+     * Not intended to be a manually-constructed object.
+     * @returns {VitessceConfigView} This, to allow chaining.
      */
-    setValue(cValue: any): VitessceConfigCoordinationScope;
-    cValue: any;
+    useCoordinationByObject(scopes: object): VitessceConfigView;
 }
 /**
  * Class representing a Vitessce view config.
@@ -271,8 +277,26 @@ export class VitessceConfig {
      * @returns {VitessceConfigCoordinationScope[]} An array of coordination scope instances.
      */
     addCoordination(...args: string[]): VitessceConfigCoordinationScope[];
+    /**
+     * Initialize a new meta coordination scope in the coordination space,
+     * and get a reference to it in the form of a meta coordination scope instance.
+     * @returns {VitessceConfigMetaCoordinationScope} A new meta coordination scope instance.
+     */
     addMetaCoordination(): VitessceConfigMetaCoordinationScope;
-    addComplexCoordination(input: any): {};
+    /**
+     * Set up the initial values for multi-level coordination in the coordination space.
+     * Get a reference to these values to pass to the `useCoordinationByObject` method
+     * of either view or meta coordination scope instances.
+     * @param {object} input A (potentially nested) object with coordination types as keys
+     * and values being either the initial coordination value, a `VitessceConfigCoordinationScope`
+     * instance, or a `CoordinationLevel` instance.
+     * The CL function takes an array of objects as its argument, and returns a CoordinationLevel
+     * instance, to support nesting.
+     * @returns {object} A (potentially nested) object with coordination types as keys and values
+     * being either { scope }, { scope, children }, or an array of these. Not intended to be
+     * manipulated before being passed to a `useCoordinationByObject` function.
+     */
+    addCoordinationByObject(input: object): object;
     /**
      * A convenience function for setting up new coordination scopes across a set of views.
      * @param {VitessceConfigView[]} views An array of view objects to link together.
@@ -282,6 +306,19 @@ export class VitessceConfig {
      * @returns {VitessceConfig} This, to allow chaining.
      */
     linkViews(views: VitessceConfigView[], cTypes: string[], cValues?: any[]): VitessceConfig;
+    /**
+     * A convenience function for setting up multi-level and meta-coordination scopes
+     * across a set of views.
+     * @param {VitessceConfigView[]} views An array of view objects to link together.
+     * @param {object} input A (potentially nested) object with coordination types as keys
+     * and values being either the initial coordination value, a `VitessceConfigCoordinationScope`
+     * instance, or a `CoordinationLevel` instance.
+     * The CL function takes an array of objects as its argument, and returns a CoordinationLevel
+     * instance, to support nesting.
+     * @param {boolean} meta Should meta-coordination be used? Optional. By default, true.
+     * @returns {VitessceConfig} This, to allow chaining.
+     */
+    linkViewsByObject(views: VitessceConfigView[], input: object, meta?: boolean): VitessceConfig;
     /**
      * Set the layout of views.
      * @param {VitessceConfigView|VitessceConfigViewHConcat|VitessceConfigViewVConcat} viewConcat A
@@ -298,6 +335,10 @@ export class VitessceConfig {
 declare class CoordinationLevel {
     constructor(value: any);
     value: any;
+    cachedValue: any;
+    setCached(processedLevel: any): void;
+    getCached(): any;
+    isCached(): boolean;
 }
 export {};
 //# sourceMappingURL=VitessceConfig.d.ts.map

package/dist-tsc/VitessceConfig.d.ts.map

@@ -1 +1 @@
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