@vitessce/config 3.3.1 → 3.3.3

package/dist/index.js

@@ -44,7 +44,9 @@ const FileType$1 = {
   OBS_SEGMENTATIONS_JSON: "obsSegmentations.json",
   OBS_SETS_CSV: "obsSets.csv",
   OBS_SETS_JSON: "obsSets.json",
+  // OME-Zarr
   IMAGE_OME_ZARR: "image.ome-zarr",
+  OBS_SEGMENTATIONS_OME_ZARR: "obsSegmentations.ome-zarr",
   // AnnData
   OBS_FEATURE_MATRIX_ANNDATA_ZARR: "obsFeatureMatrix.anndata.zarr",
   OBS_SETS_ANNDATA_ZARR: "obsSets.anndata.zarr",
@@ -645,6 +647,24 @@ function getNextScope(prevScopes) {
   } while (prevScopes.includes(nextScope));
   return nextScope;
 }
+function createPrefixedGetNextScopeNumeric(prefix) {
+  return (prevScopes) => {
+    let nextScopeInt = 0;
+    let nextScopeStr;
+    do {
+      nextScopeStr = `${prefix}${nextScopeInt}`;
+      nextScopeInt += 1;
+    } while (prevScopes.includes(nextScopeStr));
+    return nextScopeStr;
+  };
+}
+function getInitialCoordinationScopePrefix(datasetUid, dataType) {
+  return `init_${datasetUid}_${dataType}_`;
+}
+function getInitialCoordinationScopeName(datasetUid, dataType, i = null) {
+  const prefix = getInitialCoordinationScopePrefix(datasetUid, dataType);
+  return `${prefix}${i === null ? 0 : i}`;
+}
 let getRandomValues;
 const rnds8 = new Uint8Array(16);
 function rng() {
@@ -8990,30 +9010,39 @@ const omeCoordinateTransformations = z.array(z.union([
     scale: z.array(z.number())
   })
 ]));
-z.object({
+const imageOmeTiffSchema = z.object({
   offsetsUrl: z.string().optional(),
   coordinateTransformations: omeCoordinateTransformations.optional()
 });
+imageOmeTiffSchema.extend({
+  obsTypesFromChannelNames: z.boolean().optional()
+});
 const imageOmeZarrSchema = z.object({
   coordinateTransformations: omeCoordinateTransformations.optional()
 });
 imageOmeZarrSchema.extend({
+  obsTypesFromChannelNames: z.boolean().optional()
+});
+const imageSpatialdataSchema = imageOmeZarrSchema.extend({
   path: z.string()
 });
-z.object({
+const obsSegmentationsSpatialdataSchema = z.object({
+  // TODO: should this also extend the imageOmeZarrSchema?
+  // TODO: should this be renamed labelsSpatialdataSchema?
+  // TODO: support obsTypesFromChannelNames?
   path: z.string()
 });
 z.object({
   path: z.string()
 });
-z.object({
+const obsSpotsSpatialdataSchema = z.object({
   path: z.string(),
   tablePath: z.string().optional().describe("The path to a table which annotates the spots. If available but not specified, the spot identifiers may not be aligned with associated tabular data as expected.")
 });
-annDataObsFeatureMatrix.extend({
+const obsFeatureMatrixSpatialdataSchema = annDataObsFeatureMatrix.extend({
   region: z.string().describe("The name of a region to use to filter instances (i.e., rows) in the table").optional()
 });
-z.object({
+const obsSetsSpatialdataSchema = z.object({
   region: z.string().describe("The name of a region to use to filter instances (i.e., rows) in the table").optional(),
   tablePath: z.string().optional().describe("The path to a table which contains the index for the set values."),
   obsSets: annDataObsSets
@@ -9076,6 +9105,19 @@ z.object({
     z.array(annDataConvenienceObsEmbeddingItem)
   ])
 }).partial();
+z.object({
+  // TODO: should `image` be a special schema
+  // to allow specifying fileUid (like for embeddingType)?
+  image: imageSpatialdataSchema,
+  // TODO: should this be a special schema
+  // to allow specifying fileUid (like for embeddingType)?
+  labels: obsSegmentationsSpatialdataSchema,
+  obsFeatureMatrix: obsFeatureMatrixSpatialdataSchema,
+  obsSpots: obsSpotsSpatialdataSchema,
+  // TODO: obsPoints
+  // TODO: obsLocations
+  obsSets: obsSetsSpatialdataSchema
+}).partial();
 z.object({
   obsLabelsTypes: z.array(z.string()).optional(),
   embeddingTypes: z.array(z.string()).optional()
@@ -15921,11 +15963,12 @@ class VitessceConfigCoordinationScope {
    * Construct a new coordination scope instance.
    * @param {string} cType The coordination type for this coordination scope.
    * @param {string} cScope The name of the coordination scope.
+   * @param {[any]} cValue Optional. The coordination value of the coordination scope.
    */
-  constructor(cType, cScope) {
+  constructor(cType, cScope, cValue = null) {
     this.cType = cType;
     this.cScope = cScope;
-    this.cValue = null;
+    this.cValue = cValue;
   }
   /**
    * Set the coordination value of the coordination scope.
@@ -16032,6 +16075,7 @@ class VitessceConfig {
       layout: [],
       initStrategy: "auto"
     };
+    this.getNextScope = getNextScope;
   }
   /**
    * Add a new dataset to the config.
@@ -16045,7 +16089,7 @@ class VitessceConfig {
   addDataset(name = void 0, description = void 0, options = void 0) {
     const { uid } = options || {};
     const prevDatasetUids = this.config.datasets.map((d) => d.dataset.uid);
-    const nextUid = uid || getNextScope(prevDatasetUids);
+    const nextUid = uid || this.getNextScope(prevDatasetUids);
     const newDataset = new VitessceConfigDataset(nextUid, name, description);
     this.config.datasets.push(newDataset);
     const [newScope] = this.addCoordination(CoordinationType$1.DATASET);
@@ -16104,7 +16148,7 @@ class VitessceConfig {
     const result = [];
     cTypes.forEach((cType) => {
       const prevScopes = this.config.coordinationSpace[cType] ? Object.keys(this.config.coordinationSpace[cType]) : [];
-      const scope = new VitessceConfigCoordinationScope(cType, getNextScope(prevScopes));
+      const scope = new VitessceConfigCoordinationScope(cType, this.getNextScope(prevScopes));
       if (!this.config.coordinationSpace[scope.cType]) {
         this.config.coordinationSpace[scope.cType] = {};
       }
@@ -16122,8 +16166,8 @@ class VitessceConfig {
     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]) : [];
     const metaContainer = new VitessceConfigMetaCoordinationScope(
-      getNextScope(prevMetaScopes),
-      getNextScope(prevMetaByScopes)
+      this.getNextScope(prevMetaScopes),
+      this.getNextScope(prevMetaByScopes)
     );
     if (!this.config.coordinationSpace[CoordinationType$1.META_COORDINATION_SCOPES]) {
       this.config.coordinationSpace[CoordinationType$1.META_COORDINATION_SCOPES] = {};
@@ -16151,6 +16195,9 @@ class VitessceConfig {
   addCoordinationByObject(input) {
     const processLevel = (level) => {
       const result = {};
+      if (level === null) {
+        return result;
+      }
       Object.entries(level).forEach(([cType, nextLevelOrInitialValue]) => {
         if (nextLevelOrInitialValue instanceof CoordinationLevel) {
           const nextLevel = nextLevelOrInitialValue.value;
@@ -16225,10 +16272,18 @@ class VitessceConfig {
    * 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.
+   * @param {object|null} options
+   * @param {bool} options.meta Should meta-coordination be used? Optional.
+   * By default, true.
+   * @param {string|null} options.scopePrefix A prefix to add to all
+   * coordination scope names. Optional.
    * @returns {VitessceConfig} This, to allow chaining.
    */
-  linkViewsByObject(views, input, meta = true) {
+  linkViewsByObject(views, input, options = null) {
+    const { meta = true, scopePrefix = null } = options || {};
+    if (scopePrefix) {
+      this.getNextScope = createPrefixedGetNextScopeNumeric(scopePrefix);
+    }
     const scopes = this.addCoordinationByObject(input);
     if (meta) {
       const metaScope = this.addMetaCoordination();
@@ -16241,8 +16296,28 @@ class VitessceConfig {
         view.useCoordinationByObject(scopes);
       });
     }
+    if (scopePrefix) {
+      this.getNextScope = getNextScope;
+    }
     return this;
   }
+  /**
+   * Set the value for a coordination scope.
+   * If a coordination object for the coordination type does not yet exist
+   * in the coordination space, it will be created.
+   * @param {string} cType The coordination type.
+   * @param {string} cScope The coordination scope.
+   * @param {any} cValue The initial value for the coordination scope.
+   * @returns {VitessceConfigCoordinationScope} A coordination scope instance.
+   */
+  setCoordinationValue(cType, cScope, cValue) {
+    const scope = new VitessceConfigCoordinationScope(cType, cScope, cValue);
+    if (!this.config.coordinationSpace[scope.cType]) {
+      this.config.coordinationSpace[scope.cType] = {};
+    }
+    this.config.coordinationSpace[scope.cType][scope.cScope] = scope;
+    return scope;
+  }
   /**
    * Set the layout of views.
    * @param {VitessceConfigView|VitessceConfigViewHConcat|VitessceConfigViewVConcat} viewConcat A
@@ -16333,6 +16408,22 @@ class VitessceConfig {
     return vc;
   }
 }
+function getCoordinationSpaceAndScopes(partialCoordinationValues, scopePrefix) {
+  const vc = new VitessceConfig({ schemaVersion: "1.0.16", name: "__dummy__" });
+  vc.getNextScope = createPrefixedGetNextScopeNumeric(scopePrefix);
+  const dataset = vc.addDataset("__dummy__");
+  const v1 = vc.addView(dataset, "__dummy__");
+  vc.linkViewsByObject([v1], partialCoordinationValues, { meta: true });
+  const vcJson = vc.toJSON();
+  const { coordinationSpace } = vcJson;
+  const { coordinationScopes } = vcJson.layout[0];
+  const { coordinationScopesBy } = vcJson.layout[0];
+  return {
+    coordinationSpace,
+    coordinationScopes,
+    coordinationScopesBy
+  };
+}
 const SINGLE_CELL_WITH_HEATMAP_VIEWS = {
   obsSets: { x: 4, y: 0, w: 4, h: 4 },
   obsSetSizes: { x: 8, y: 0, w: 4, h: 4 },
@@ -16948,7 +17039,10 @@ export {
   HINT_TYPE_TO_FILE_TYPE_MAP,
   VitessceConfig,
   generateConfig,
+  getCoordinationSpaceAndScopes,
   getHintOptions,
+  getInitialCoordinationScopeName,
+  getInitialCoordinationScopePrefix,
   hconcat,
   vconcat
 };

package/dist-tsc/VitessceConfig.d.ts

@@ -13,6 +13,11 @@ export function hconcat(...views: (VitessceConfigView | VitessceConfigViewHConca
  */
 export function vconcat(...views: (VitessceConfigView | VitessceConfigViewHConcat | VitessceConfigViewVConcat)[]): VitessceConfigViewVConcat;
 export function CL(value: any): CoordinationLevel;
+export function getCoordinationSpaceAndScopes(partialCoordinationValues: any, scopePrefix: any): {
+    coordinationSpace: any;
+    coordinationScopes: any;
+    coordinationScopesBy: any;
+};
 /**
  * Class representing a file within a Vitessce config dataset.
  */
@@ -162,11 +167,12 @@ export class VitessceConfigCoordinationScope {
      * Construct a new coordination scope instance.
      * @param {string} cType The coordination type for this coordination scope.
      * @param {string} cScope The name of the coordination scope.
+     * @param {[any]} cValue Optional. The coordination value of the coordination scope.
      */
-    constructor(cType: string, cScope: string);
+    constructor(cType: string, cScope: string, cValue?: [any]);
     cType: string;
     cScope: string;
-    cValue: any;
+    cValue: [any];
     /**
      * Set the coordination value of the coordination scope.
      * @param {any} cValue The value to set.
@@ -237,6 +243,7 @@ export class VitessceConfig {
         layout: never[];
         initStrategy: string;
     };
+    getNextScope: any;
     /**
      * Add a new dataset to the config.
      * @param {string} name A name for the dataset. Optional.
@@ -315,10 +322,24 @@ export class VitessceConfig {
      * 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.
+     * @param {object|null} options
+     * @param {bool} options.meta Should meta-coordination be used? Optional.
+     * By default, true.
+     * @param {string|null} options.scopePrefix A prefix to add to all
+     * coordination scope names. Optional.
      * @returns {VitessceConfig} This, to allow chaining.
      */
-    linkViewsByObject(views: VitessceConfigView[], input: object, meta?: boolean): VitessceConfig;
+    linkViewsByObject(views: VitessceConfigView[], input: object, options?: object | null): VitessceConfig;
+    /**
+     * Set the value for a coordination scope.
+     * If a coordination object for the coordination type does not yet exist
+     * in the coordination space, it will be created.
+     * @param {string} cType The coordination type.
+     * @param {string} cScope The coordination scope.
+     * @param {any} cValue The initial value for the coordination scope.
+     * @returns {VitessceConfigCoordinationScope} A coordination scope instance.
+     */
+    setCoordinationValue(cType: string, cScope: string, cValue: any): VitessceConfigCoordinationScope;
     /**
      * Set the layout of views.
      * @param {VitessceConfigView|VitessceConfigViewHConcat|VitessceConfigViewVConcat} viewConcat A

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

@@ -1 +1 @@
-{"version":3,"file":"VitessceConfig.d.ts","sourceRoot":"","sources":["../src/VitessceConfig.js"],"names":[],"mappings":"AA0XA;;;;;GAKG;AACH,kCAJe,CAAC,kBAAkB,GAAC,yBAAyB,GAAC,yBAAyB,CAAC,KAE1E,yBAAyB,CAKrC;AAED;;;;;GAKG;AACH,kCAJe,CAAC,kBAAkB,GAAC,yBAAyB,GAAC,yBAAyB,CAAC,KAE1E,yBAAyB,CAKrC;AAsBD,kDAEC;AAlaD;;GAEG;AACH;IACE;;;;;;;;OAQG;IACH,iBAPW,MAAM,YAEN,MAAM,oCACN,MAAM,WAAO,IAAI,EAW3B;IANC;;;;;MAKC;IAGH;;OAEG;IACH,UAFa,MAAM,CAIlB;CACF;AAED;;GAEG;AACH;IACE;;;;;OAKG;IACH,iBAJW,MAAM,QACN,MAAM,eACN,MAAM,EAShB;IANC;;;;;MAKC;IAGH;;;;;;;;;;OAUG;IACH;QARoC,GAAG,EAA5B,MAAM,GAAC,SAAS;QACD,QAAQ,EAAvB,MAAM;QACmB,kBAAkB,EAA3C,MAAM,GAAC,SAAS;QACe,OAAO,EAAtC,MAAM,WAAO,SAAS;wBAGpB,qBAAqB,CA6BjC;IAED;;OAEG;IACH,UAFa,MAAM,CAOlB;CACF;AA0ID;;GAEG;AACH;IACE;;;;;;;;;OASG;IACH,uBARW,MAAM,sBACN,MAAM,KAEN,MAAM,KACN,MAAM,KACN,MAAM,KACN,MAAM,EAYhB;IATC;;;;;;;;MAQC;IAGH;;;;;OAKG;IACH,yBAJe,+BAA+B,KAEjC,kBAAkB,CAQ9B;IAED;;;;;OAKG;IACH,gCAJW,MAAM,GAEJ,kBAAkB,CAiB9B;IAED;;;;OAIG;IACH,+BAHW,mCAAmC,GACjC,kBAAkB,CAe9B;IAED;;;;;;;QAOI;IACJ,WANY,MAAM,KACN,MAAM,KACN,MAAM,KACN,MAAM,GACJ,kBAAkB,CAS/B;IAED;;;OAGG;IACH,sBAFa,kBAAkB,CAQ9B;IAED;;OAEG;IACH,UAFa,MAAM,CAIlB;CACF;AAED;;GAEG;AACH;IACE,wBAEC;IADC,WAAkB;CAErB;AAED;;GAEG;AACH;IACE,wBAEC;IADC,WAAkB;CAErB;AAgDD;;GAEG;AACH;IACE;;;;OAIG;IACH,mBAHW,MAAM,UACN,MAAM,EAMhB;IAHC,cAAkB;IAClB,eAAoB;IACpB,YAAkB;IAGpB;;;;OAIG;IACH,iBAHW,GAAG,GACD,+BAA+B,CAK3C;CACF;AAED;;;;GAIG;AACH;IACE;;;;OAIG;IACH,uBAHW,MAAM,eACN,MAAM,EAWhB;IARC,2CAGC;IACD,6CAGC;IAGH;;;;;OAKG;IACH,yBAJe,+BAA+B,KAEjC,mCAAmC,CAU/C;IAED;;;;;;OAMG;IACH,gCAJW,MAAM,GAEJ,kBAAkB,CAiB9B;CACF;AAED;;GAEG;AACH;IAoaE;;;;;;OAMG;IACH,wBAJW,MAAM,GACJ,cAAc,CAiC1B;IAxcD;;;;;;OAMG;IACH;QAJ0B,aAAa,EAA5B,MAAM;QACS,IAAI,EAAnB,MAAM;QACmB,WAAW,EAApC,MAAM,GAAC,SAAS;uBAmC1B;IATC;;;;;;;;MAQC;IAGH;;;;;;;;OAQG;IACH,kBAPW,MAAM,gBACN,MAAM;QAEU,GAAG,EAAnB,MAAM;QAEJ,qBAAqB,CAWjC;IAED;;;;;;;;;;;;;OAaG;IACH,iBAZW,qBAAqB,aAErB,MAAM;QAEU,CAAC,EAAjB,MAAM;QACU,CAAC,EAAjB,MAAM;QACU,CAAC,EAAjB,MAAM;QACU,CAAC,EAAjB,MAAM;QACU,OAAO,EAAvB,MAAM;QAEJ,kBAAkB,CAmC9B;IAED;;;;;OAKG;IACH,yBAHc,MAAM,KACP,+BAA+B,EAAE,CAmB7C;IAED;;;;OAIG;IACH,uBAFa,mCAAmC,CA4B/C;IAED;;;;;;;;;;;;OAYG;IACH,+BATW,MAAM,GAKJ,MAAM,CAoIlB;IAED;;;;;;;OAOG;IACH,iBANW,kBAAkB,EAAE,UACpB,MAAM,EAAE,YACR,GAAG,EAAE,GAEH,cAAc,CAe1B;IAED;;;;;;;;;;;OAWG;IACH,yBATW,kBAAkB,EAAE,SACpB,MAAM,SAKN,OAAO,GACL,cAAc,CAiB1B;IAED;;;;;OAKG;IACH,mBAJW,kBAAkB,GAAC,yBAAyB,GAAC,yBAAyB,GAEpE,cAAc,CA0B1B;IAED;;;OAGG;IACH,UAFa,MAAM,CAmBlB;CAwCF;AA7jBD;IACE,wBAGC;IAFC,WAAkB;IAClB,iBAAuB;IAGzB,qCAEC;IAED,iBAEC;IAED,oBAEC;CACF"}
+{"version":3,"file":"VitessceConfig.d.ts","sourceRoot":"","sources":["../src/VitessceConfig.js"],"names":[],"mappings":"AA0XA;;;;;GAKG;AACH,kCAJe,CAAC,kBAAkB,GAAC,yBAAyB,GAAC,yBAAyB,CAAC,KAE1E,yBAAyB,CAKrC;AAED;;;;;GAKG;AACH,kCAJe,CAAC,kBAAkB,GAAC,yBAAyB,GAAC,yBAAyB,CAAC,KAE1E,yBAAyB,CAKrC;AAsBD,kDAEC;AA8kBD;;;;EAiBC;AAjgCD;;GAEG;AACH;IACE;;;;;;;;OAQG;IACH,iBAPW,MAAM,YAEN,MAAM,oCACN,MAAM,WAAO,IAAI,EAW3B;IANC;;;;;MAKC;IAGH;;OAEG;IACH,UAFa,MAAM,CAIlB;CACF;AAED;;GAEG;AACH;IACE;;;;;OAKG;IACH,iBAJW,MAAM,QACN,MAAM,eACN,MAAM,EAShB;IANC;;;;;MAKC;IAGH;;;;;;;;;;OAUG;IACH;QARoC,GAAG,EAA5B,MAAM,GAAC,SAAS;QACD,QAAQ,EAAvB,MAAM;QACmB,kBAAkB,EAA3C,MAAM,GAAC,SAAS;QACe,OAAO,EAAtC,MAAM,WAAO,SAAS;wBAGpB,qBAAqB,CA6BjC;IAED;;OAEG;IACH,UAFa,MAAM,CAOlB;CACF;AA0ID;;GAEG;AACH;IACE;;;;;;;;;OASG;IACH,uBARW,MAAM,sBACN,MAAM,KAEN,MAAM,KACN,MAAM,KACN,MAAM,KACN,MAAM,EAYhB;IATC;;;;;;;;MAQC;IAGH;;;;;OAKG;IACH,yBAJe,+BAA+B,KAEjC,kBAAkB,CAQ9B;IAED;;;;;OAKG;IACH,gCAJW,MAAM,GAEJ,kBAAkB,CAiB9B;IAED;;;;OAIG;IACH,+BAHW,mCAAmC,GACjC,kBAAkB,CAe9B;IAED;;;;;;;QAOI;IACJ,WANY,MAAM,KACN,MAAM,KACN,MAAM,KACN,MAAM,GACJ,kBAAkB,CAS/B;IAED;;;OAGG;IACH,sBAFa,kBAAkB,CAQ9B;IAED;;OAEG;IACH,UAFa,MAAM,CAIlB;CACF;AAED;;GAEG;AACH;IACE,wBAEC;IADC,WAAkB;CAErB;AAED;;GAEG;AACH;IACE,wBAEC;IADC,WAAkB;CAErB;AAgDD;;GAEG;AACH;IACE;;;;;OAKG;IACH,mBAJW,MAAM,UACN,MAAM,WACN,CAAC,GAAG,CAAC,EAMf;IAHC,cAAkB;IAClB,eAAoB;IACpB,cAAoB;IAGtB;;;;OAIG;IACH,iBAHW,GAAG,GACD,+BAA+B,CAK3C;CACF;AAED;;;;GAIG;AACH;IACE;;;;OAIG;IACH,uBAHW,MAAM,eACN,MAAM,EAWhB;IARC,2CAGC;IACD,6CAGC;IAGH;;;;;OAKG;IACH,yBAJe,+BAA+B,KAEjC,mCAAmC,CAU/C;IAED;;;;;;OAMG;IACH,gCAJW,MAAM,GAEJ,kBAAkB,CAiB9B;CACF;AAED;;GAEG;AACH;IAscE;;;;;;OAMG;IACH,wBAJW,MAAM,GACJ,cAAc,CAiC1B;IA1eD;;;;;;OAMG;IACH;QAJ0B,aAAa,EAA5B,MAAM;QACS,IAAI,EAAnB,MAAM;QACmB,WAAW,EAApC,MAAM,GAAC,SAAS;uBAoC1B;IAVC;;;;;;;;MAQC;IACD,kBAAgC;IAGlC;;;;;;;;OAQG;IACH,kBAPW,MAAM,gBACN,MAAM;QAEU,GAAG,EAAnB,MAAM;QAEJ,qBAAqB,CAWjC;IAED;;;;;;;;;;;;;OAaG;IACH,iBAZW,qBAAqB,aAErB,MAAM;QAEU,CAAC,EAAjB,MAAM;QACU,CAAC,EAAjB,MAAM;QACU,CAAC,EAAjB,MAAM;QACU,CAAC,EAAjB,MAAM;QACU,OAAO,EAAvB,MAAM;QAEJ,kBAAkB,CAmC9B;IAED;;;;;OAKG;IACH,yBAHc,MAAM,KACP,+BAA+B,EAAE,CAmB7C;IAED;;;;OAIG;IACH,uBAFa,mCAAmC,CA4B/C;IAED;;;;;;;;;;;;OAYG;IACH,+BATW,MAAM,GAKJ,MAAM,CAuIlB;IAED;;;;;;;OAOG;IACH,iBANW,kBAAkB,EAAE,UACpB,MAAM,EAAE,YACR,GAAG,EAAE,GAEH,cAAc,CAe1B;IAED;;;;;;;;;;;;;;;OAeG;IACH,yBAbW,kBAAkB,EAAE,SACpB,MAAM,YAKN,MAAM,GAAC,IAAI,GAKT,cAAc,CAyB1B;IAED;;;;;;;;OAQG;IACH,4BALW,MAAM,UACN,MAAM,UACN,GAAG,GACD,+BAA+B,CAS3C;IAED;;;;;OAKG;IACH,mBAJW,kBAAkB,GAAC,yBAAyB,GAAC,yBAAyB,GAEpE,cAAc,CA0B1B;IAED;;;OAGG;IACH,UAFa,MAAM,CAmBlB;CAwCF;AAhmBD;IACE,wBAGC;IAFC,WAAkB;IAClB,iBAAuB;IAGzB,qCAEC;IAED,iBAEC;IAED,oBAEC;CACF"}

package/dist-tsc/VitessceConfig.js

@@ -1,6 +1,6 @@
 /* eslint-disable react-hooks/rules-of-hooks */
 import { CoordinationType } from '@vitessce/constants-internal';
-import { fromEntries, getNextScope } from '@vitessce/utils';
+import { fromEntries, getNextScope, createPrefixedGetNextScopeNumeric } from '@vitessce/utils';
 /**
  * Class representing a file within a Vitessce config dataset.
  */
@@ -393,11 +393,12 @@ export class VitessceConfigCoordinationScope {
      * Construct a new coordination scope instance.
      * @param {string} cType The coordination type for this coordination scope.
      * @param {string} cScope The name of the coordination scope.
+     * @param {[any]} cValue Optional. The coordination value of the coordination scope.
      */
-    constructor(cType, cScope) {
+    constructor(cType, cScope, cValue = null) {
         this.cType = cType;
         this.cScope = cScope;
-        this.cValue = null;
+        this.cValue = cValue;
     }
     /**
      * Set the coordination value of the coordination scope.
@@ -506,6 +507,7 @@ export class VitessceConfig {
             layout: [],
             initStrategy: 'auto',
         };
+        this.getNextScope = getNextScope;
     }
     /**
      * Add a new dataset to the config.
@@ -519,7 +521,7 @@ export class VitessceConfig {
     addDataset(name = undefined, description = undefined, options = undefined) {
         const { uid } = options || {};
         const prevDatasetUids = this.config.datasets.map(d => d.dataset.uid);
-        const nextUid = (uid || getNextScope(prevDatasetUids));
+        const nextUid = (uid || this.getNextScope(prevDatasetUids));
         const newDataset = new VitessceConfigDataset(nextUid, name, description);
         this.config.datasets.push(newDataset);
         const [newScope] = this.addCoordination(CoordinationType.DATASET);
@@ -580,7 +582,7 @@ export class VitessceConfig {
             const prevScopes = (this.config.coordinationSpace[cType]
                 ? Object.keys(this.config.coordinationSpace[cType])
                 : []);
-            const scope = new VitessceConfigCoordinationScope(cType, getNextScope(prevScopes));
+            const scope = new VitessceConfigCoordinationScope(cType, this.getNextScope(prevScopes));
             if (!this.config.coordinationSpace[scope.cType]) {
                 this.config.coordinationSpace[scope.cType] = {};
             }
@@ -601,7 +603,7 @@ export class VitessceConfig {
         const prevMetaByScopes = (this.config.coordinationSpace[CoordinationType.META_COORDINATION_SCOPES_BY]
             ? Object.keys(this.config.coordinationSpace[CoordinationType.META_COORDINATION_SCOPES_BY])
             : []);
-        const metaContainer = new VitessceConfigMetaCoordinationScope(getNextScope(prevMetaScopes), getNextScope(prevMetaByScopes));
+        const metaContainer = new VitessceConfigMetaCoordinationScope(this.getNextScope(prevMetaScopes), this.getNextScope(prevMetaByScopes));
         if (!this.config.coordinationSpace[CoordinationType.META_COORDINATION_SCOPES]) {
             this.config.coordinationSpace[CoordinationType.META_COORDINATION_SCOPES] = {};
         }
@@ -707,6 +709,9 @@ export class VitessceConfig {
         */
         const processLevel = (level) => {
             const result = {};
+            if (level === null) {
+                return result;
+            }
             Object.entries(level).forEach(([cType, nextLevelOrInitialValue]) => {
                 // Check if value of object is instanceof CoordinationLevel
                 // (otherwise assume it is the coordination value).
@@ -791,10 +796,18 @@ export class VitessceConfig {
      * 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.
+     * @param {object|null} options
+     * @param {bool} options.meta Should meta-coordination be used? Optional.
+     * By default, true.
+     * @param {string|null} options.scopePrefix A prefix to add to all
+     * coordination scope names. Optional.
      * @returns {VitessceConfig} This, to allow chaining.
      */
-    linkViewsByObject(views, input, meta = true) {
+    linkViewsByObject(views, input, options = null) {
+        const { meta = true, scopePrefix = null } = options || {};
+        if (scopePrefix) {
+            this.getNextScope = createPrefixedGetNextScopeNumeric(scopePrefix);
+        }
         const scopes = this.addCoordinationByObject(input);
         if (meta) {
             const metaScope = this.addMetaCoordination();
@@ -808,8 +821,28 @@ export class VitessceConfig {
                 view.useCoordinationByObject(scopes);
             });
         }
+        if (scopePrefix) {
+            this.getNextScope = getNextScope;
+        }
         return this;
     }
+    /**
+     * Set the value for a coordination scope.
+     * If a coordination object for the coordination type does not yet exist
+     * in the coordination space, it will be created.
+     * @param {string} cType The coordination type.
+     * @param {string} cScope The coordination scope.
+     * @param {any} cValue The initial value for the coordination scope.
+     * @returns {VitessceConfigCoordinationScope} A coordination scope instance.
+     */
+    setCoordinationValue(cType, cScope, cValue) {
+        const scope = new VitessceConfigCoordinationScope(cType, cScope, cValue);
+        if (!this.config.coordinationSpace[scope.cType]) {
+            this.config.coordinationSpace[scope.cType] = {};
+        }
+        this.config.coordinationSpace[scope.cType][scope.cScope] = scope;
+        return scope;
+    }
     /**
      * Set the layout of views.
      * @param {VitessceConfigView|VitessceConfigViewHConcat|VitessceConfigViewVConcat} viewConcat A
@@ -898,3 +931,21 @@ export class VitessceConfig {
         return vc;
     }
 }
+// For usage during auto-initialization.
+export function getCoordinationSpaceAndScopes(partialCoordinationValues, scopePrefix) {
+    const vc = new VitessceConfig({ schemaVersion: '1.0.16', name: '__dummy__' });
+    vc.getNextScope = createPrefixedGetNextScopeNumeric(scopePrefix);
+    const dataset = vc.addDataset('__dummy__');
+    const v1 = vc.addView(dataset, '__dummy__');
+    vc.linkViewsByObject([v1], partialCoordinationValues, { meta: true });
+    const vcJson = vc.toJSON();
+    // TODO: remove the "dataset" coordination type from these objects.
+    const { coordinationSpace } = vcJson;
+    const { coordinationScopes } = vcJson.layout[0];
+    const { coordinationScopesBy } = vcJson.layout[0];
+    return {
+        coordinationSpace,
+        coordinationScopes,
+        coordinationScopesBy,
+    };
+}

package/dist-tsc/VitessceConfig.test.js

@@ -701,6 +701,111 @@ describe('src/api/VitessceConfig.js', () => {
                 initStrategy: 'auto',
             });
         });
+        it('can use _meta_ complex coordination with a scope prefix via the linkViewsByObject convenience function', () => {
+            const config = new VitessceConfig({
+                schemaVersion: '1.0.16',
+                name: 'My config',
+            });
+            const dataset = config.addDataset('My dataset');
+            const spatialView = config.addView(dataset, 'spatial');
+            const lcView = config.addView(dataset, 'layerController');
+            config.linkViewsByObject([spatialView, lcView], {
+                spatialImageLayer: CL([
+                    {
+                        spatialLayerOpacity: 1,
+                        spatialImageChannel: CL([
+                            {
+                                spatialTargetC: 0,
+                                spatialChannelColor: [255, 0, 0],
+                            },
+                            {
+                                spatialTargetC: 1,
+                                spatialChannelColor: [0, 255, 0],
+                            },
+                        ]),
+                    },
+                ]),
+            }, { scopePrefix: 'SOME_PREFIX_' });
+            const configJSON = config.toJSON();
+            expect(configJSON).toEqual({
+                version: '1.0.16',
+                name: 'My config',
+                datasets: [
+                    { uid: 'A', name: 'My dataset', files: [] },
+                ],
+                coordinationSpace: {
+                    dataset: { A: 'A' },
+                    spatialImageLayer: { SOME_PREFIX_0: '__dummy__' },
+                    spatialLayerOpacity: { SOME_PREFIX_0: 1 },
+                    spatialImageChannel: {
+                        SOME_PREFIX_0: '__dummy__',
+                        SOME_PREFIX_1: '__dummy__',
+                    },
+                    spatialTargetC: {
+                        SOME_PREFIX_0: 0,
+                        SOME_PREFIX_1: 1,
+                    },
+                    spatialChannelColor: {
+                        SOME_PREFIX_0: [255, 0, 0],
+                        SOME_PREFIX_1: [0, 255, 0],
+                    },
+                    metaCoordinationScopes: {
+                        SOME_PREFIX_0: {
+                            spatialImageLayer: ['SOME_PREFIX_0'],
+                        },
+                    },
+                    metaCoordinationScopesBy: {
+                        SOME_PREFIX_0: {
+                            spatialImageLayer: {
+                                spatialLayerOpacity: {
+                                    SOME_PREFIX_0: 'SOME_PREFIX_0',
+                                },
+                                spatialImageChannel: {
+                                    SOME_PREFIX_0: ['SOME_PREFIX_0', 'SOME_PREFIX_1'],
+                                },
+                            },
+                            spatialImageChannel: {
+                                spatialTargetC: {
+                                    SOME_PREFIX_0: 'SOME_PREFIX_0',
+                                    SOME_PREFIX_1: 'SOME_PREFIX_1',
+                                },
+                                spatialChannelColor: {
+                                    SOME_PREFIX_0: 'SOME_PREFIX_0',
+                                    SOME_PREFIX_1: 'SOME_PREFIX_1',
+                                },
+                            },
+                        },
+                    },
+                },
+                layout: [
+                    {
+                        component: 'spatial',
+                        coordinationScopes: {
+                            dataset: 'A',
+                            metaCoordinationScopes: ['SOME_PREFIX_0'],
+                            metaCoordinationScopesBy: ['SOME_PREFIX_0'],
+                        },
+                        x: 0,
+                        y: 0,
+                        w: 1,
+                        h: 1,
+                    },
+                    {
+                        component: 'layerController',
+                        coordinationScopes: {
+                            dataset: 'A',
+                            metaCoordinationScopes: ['SOME_PREFIX_0'],
+                            metaCoordinationScopesBy: ['SOME_PREFIX_0'],
+                        },
+                        x: 0,
+                        y: 0,
+                        w: 1,
+                        h: 1,
+                    },
+                ],
+                initStrategy: 'auto',
+            });
+        });
         it('can add a coordination scope using the link views convenience function', () => {
             const config = new VitessceConfig({
                 schemaVersion: '1.0.4',

package/dist-tsc/index.d.ts

@@ -1,4 +1,4 @@
-export { VitessceConfig, vconcat, hconcat, CL as CoordinationLevel } from "./VitessceConfig.js";
+export { VitessceConfig, vconcat, hconcat, CL as CoordinationLevel, getCoordinationSpaceAndScopes } from "./VitessceConfig.js";
 export { generateConfig, getHintOptions } from "./VitessceAutoConfig.js";
 export { HINTS_CONFIG, HINT_TYPE_TO_FILE_TYPE_MAP } from "./constants.js";
 //# sourceMappingURL=index.d.ts.map

package/dist-tsc/index.js

@@ -1,3 +1,4 @@
-export { VitessceConfig, vconcat, hconcat, CL as CoordinationLevel } from './VitessceConfig.js';
+export { VitessceConfig, vconcat, hconcat, CL as CoordinationLevel, getCoordinationSpaceAndScopes } from './VitessceConfig.js';
 export { generateConfig, getHintOptions } from './VitessceAutoConfig.js';
 export { HINTS_CONFIG, HINT_TYPE_TO_FILE_TYPE_MAP } from './constants.js';
+export { getInitialCoordinationScopePrefix, getInitialCoordinationScopeName, } from '@vitessce/utils';

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/config",
-  "version": "3.3.1",
+  "version": "3.3.3",
   "author": "Gehlenborg Lab",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -16,8 +16,8 @@
     "dist-tsc"
   ],
   "dependencies": {
-    "@vitessce/constants-internal": "3.3.1",
-    "@vitessce/utils": "3.3.1"
+    "@vitessce/constants-internal": "3.3.3",
+    "@vitessce/utils": "3.3.3"
   },
   "scripts": {
     "bundle": "pnpm exec vite build -c ../../scripts/vite.config.js",

package/src/VitessceConfig.js

@@ -1,6 +1,6 @@
 /* eslint-disable react-hooks/rules-of-hooks */
 import { CoordinationType } from '@vitessce/constants-internal';
-import { fromEntries, getNextScope } from '@vitessce/utils';
+import { fromEntries, getNextScope, createPrefixedGetNextScopeNumeric } from '@vitessce/utils';
 
 /**
  * Class representing a file within a Vitessce config dataset.
@@ -430,11 +430,12 @@ export class VitessceConfigCoordinationScope {
    * Construct a new coordination scope instance.
    * @param {string} cType The coordination type for this coordination scope.
    * @param {string} cScope The name of the coordination scope.
+   * @param {[any]} cValue Optional. The coordination value of the coordination scope.
    */
-  constructor(cType, cScope) {
+  constructor(cType, cScope, cValue = null) {
     this.cType = cType;
     this.cScope = cScope;
-    this.cValue = null;
+    this.cValue = cValue;
   }
 
   /**
@@ -555,6 +556,7 @@ export class VitessceConfig {
       layout: [],
       initStrategy: 'auto',
     };
+    this.getNextScope = getNextScope;
   }
 
   /**
@@ -569,7 +571,7 @@ export class VitessceConfig {
   addDataset(name = undefined, description = undefined, options = undefined) {
     const { uid } = options || {};
     const prevDatasetUids = this.config.datasets.map(d => d.dataset.uid);
-    const nextUid = (uid || getNextScope(prevDatasetUids));
+    const nextUid = (uid || this.getNextScope(prevDatasetUids));
     const newDataset = new VitessceConfigDataset(nextUid, name, description);
     this.config.datasets.push(newDataset);
     const [newScope] = this.addCoordination(CoordinationType.DATASET);
@@ -641,7 +643,7 @@ export class VitessceConfig {
           ? Object.keys(this.config.coordinationSpace[cType])
           : []
       );
-      const scope = new VitessceConfigCoordinationScope(cType, getNextScope(prevScopes));
+      const scope = new VitessceConfigCoordinationScope(cType, this.getNextScope(prevScopes));
       if (!this.config.coordinationSpace[scope.cType]) {
         this.config.coordinationSpace[scope.cType] = {};
       }
@@ -668,8 +670,8 @@ export class VitessceConfig {
         : []
     );
     const metaContainer = new VitessceConfigMetaCoordinationScope(
-      getNextScope(prevMetaScopes),
-      getNextScope(prevMetaByScopes),
+      this.getNextScope(prevMetaScopes),
+      this.getNextScope(prevMetaByScopes),
     );
     if (!this.config.coordinationSpace[CoordinationType.META_COORDINATION_SCOPES]) {
       this.config.coordinationSpace[CoordinationType.META_COORDINATION_SCOPES] = {};
@@ -777,6 +779,9 @@ export class VitessceConfig {
     */
     const processLevel = (level) => {
       const result = {};
+      if (level === null) {
+        return result;
+      }
       Object.entries(level).forEach(([cType, nextLevelOrInitialValue]) => {
         // Check if value of object is instanceof CoordinationLevel
         // (otherwise assume it is the coordination value).
@@ -859,10 +864,19 @@ export class VitessceConfig {
    * 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.
+   * @param {object|null} options
+   * @param {bool} options.meta Should meta-coordination be used? Optional.
+   * By default, true.
+   * @param {string|null} options.scopePrefix A prefix to add to all
+   * coordination scope names. Optional.
    * @returns {VitessceConfig} This, to allow chaining.
    */
-  linkViewsByObject(views, input, meta = true) {
+  linkViewsByObject(views, input, options = null) {
+    const { meta = true, scopePrefix = null } = options || {};
+
+    if (scopePrefix) {
+      this.getNextScope = createPrefixedGetNextScopeNumeric(scopePrefix);
+    }
     const scopes = this.addCoordinationByObject(input);
     if (meta) {
       const metaScope = this.addMetaCoordination();
@@ -876,9 +890,30 @@ export class VitessceConfig {
         view.useCoordinationByObject(scopes);
       });
     }
+    if (scopePrefix) {
+      this.getNextScope = getNextScope;
+    }
     return this;
   }
 
+  /**
+   * Set the value for a coordination scope.
+   * If a coordination object for the coordination type does not yet exist
+   * in the coordination space, it will be created.
+   * @param {string} cType The coordination type.
+   * @param {string} cScope The coordination scope.
+   * @param {any} cValue The initial value for the coordination scope.
+   * @returns {VitessceConfigCoordinationScope} A coordination scope instance.
+   */
+  setCoordinationValue(cType, cScope, cValue) {
+    const scope = new VitessceConfigCoordinationScope(cType, cScope, cValue);
+    if (!this.config.coordinationSpace[scope.cType]) {
+      this.config.coordinationSpace[scope.cType] = {};
+    }
+    this.config.coordinationSpace[scope.cType][scope.cScope] = scope;
+    return scope;
+  }
+
   /**
    * Set the layout of views.
    * @param {VitessceConfigView|VitessceConfigViewHConcat|VitessceConfigViewVConcat} viewConcat A
@@ -973,3 +1008,23 @@ export class VitessceConfig {
     return vc;
   }
 }
+
+// For usage during auto-initialization.
+export function getCoordinationSpaceAndScopes(partialCoordinationValues, scopePrefix) {
+  const vc = new VitessceConfig({ schemaVersion: '1.0.16', name: '__dummy__' });
+  vc.getNextScope = createPrefixedGetNextScopeNumeric(scopePrefix);
+  const dataset = vc.addDataset('__dummy__');
+  const v1 = vc.addView(dataset, '__dummy__');
+  vc.linkViewsByObject([v1], partialCoordinationValues, { meta: true });
+  const vcJson = vc.toJSON();
+  // TODO: remove the "dataset" coordination type from these objects.
+  const { coordinationSpace } = vcJson;
+  const { coordinationScopes } = vcJson.layout[0];
+  const { coordinationScopesBy } = vcJson.layout[0];
+
+  return {
+    coordinationSpace,
+    coordinationScopes,
+    coordinationScopesBy,
+  };
+}

package/src/VitessceConfig.test.js

@@ -744,6 +744,116 @@ describe('src/api/VitessceConfig.js', () => {
       });
     });
 
+    it('can use _meta_ complex coordination with a scope prefix via the linkViewsByObject convenience function', () => {
+      const config = new VitessceConfig({
+        schemaVersion: '1.0.16',
+        name: 'My config',
+      });
+      const dataset = config.addDataset('My dataset');
+
+      const spatialView = config.addView(dataset, 'spatial');
+      const lcView = config.addView(dataset, 'layerController');
+
+      config.linkViewsByObject([spatialView, lcView], {
+        spatialImageLayer: CL([
+          {
+            spatialLayerOpacity: 1,
+            spatialImageChannel: CL([
+              {
+                spatialTargetC: 0,
+                spatialChannelColor: [255, 0, 0],
+              },
+              {
+                spatialTargetC: 1,
+                spatialChannelColor: [0, 255, 0],
+              },
+            ]),
+          },
+        ]),
+      }, { scopePrefix: 'SOME_PREFIX_' });
+
+      const configJSON = config.toJSON();
+
+      expect(configJSON).toEqual({
+        version: '1.0.16',
+        name: 'My config',
+        datasets: [
+          { uid: 'A', name: 'My dataset', files: [] },
+        ],
+        coordinationSpace: {
+          dataset: { A: 'A' },
+          spatialImageLayer: { SOME_PREFIX_0: '__dummy__' },
+          spatialLayerOpacity: { SOME_PREFIX_0: 1 },
+          spatialImageChannel: {
+            SOME_PREFIX_0: '__dummy__',
+            SOME_PREFIX_1: '__dummy__',
+          },
+          spatialTargetC: {
+            SOME_PREFIX_0: 0,
+            SOME_PREFIX_1: 1,
+          },
+          spatialChannelColor: {
+            SOME_PREFIX_0: [255, 0, 0],
+            SOME_PREFIX_1: [0, 255, 0],
+          },
+          metaCoordinationScopes: {
+            SOME_PREFIX_0: {
+              spatialImageLayer: ['SOME_PREFIX_0'],
+            },
+          },
+          metaCoordinationScopesBy: {
+            SOME_PREFIX_0: {
+              spatialImageLayer: {
+                spatialLayerOpacity: {
+                  SOME_PREFIX_0: 'SOME_PREFIX_0',
+                },
+                spatialImageChannel: {
+                  SOME_PREFIX_0: ['SOME_PREFIX_0', 'SOME_PREFIX_1'],
+                },
+              },
+              spatialImageChannel: {
+                spatialTargetC: {
+                  SOME_PREFIX_0: 'SOME_PREFIX_0',
+                  SOME_PREFIX_1: 'SOME_PREFIX_1',
+                },
+                spatialChannelColor: {
+                  SOME_PREFIX_0: 'SOME_PREFIX_0',
+                  SOME_PREFIX_1: 'SOME_PREFIX_1',
+                },
+              },
+            },
+          },
+        },
+        layout: [
+          {
+            component: 'spatial',
+            coordinationScopes: {
+              dataset: 'A',
+              metaCoordinationScopes: ['SOME_PREFIX_0'],
+              metaCoordinationScopesBy: ['SOME_PREFIX_0'],
+            },
+            x: 0,
+            y: 0,
+            w: 1,
+            h: 1,
+          },
+          {
+            component: 'layerController',
+            coordinationScopes: {
+              dataset: 'A',
+              metaCoordinationScopes: ['SOME_PREFIX_0'],
+              metaCoordinationScopesBy: ['SOME_PREFIX_0'],
+            },
+            x: 0,
+            y: 0,
+            w: 1,
+            h: 1,
+          },
+        ],
+        initStrategy: 'auto',
+      });
+    });
+
     it('can add a coordination scope using the link views convenience function', () => {
       const config = new VitessceConfig({
         schemaVersion: '1.0.4',

package/src/index.js

@@ -1,3 +1,7 @@
-export { VitessceConfig, vconcat, hconcat, CL as CoordinationLevel } from './VitessceConfig.js';
+export { VitessceConfig, vconcat, hconcat, CL as CoordinationLevel, getCoordinationSpaceAndScopes } from './VitessceConfig.js';
 export { generateConfig, getHintOptions } from './VitessceAutoConfig.js';
 export { HINTS_CONFIG, HINT_TYPE_TO_FILE_TYPE_MAP } from './constants.js';
+export {
+  getInitialCoordinationScopePrefix,
+  getInitialCoordinationScopeName,
+} from '@vitessce/utils';