@fideus-labs/ngff-zarr 0.18.1 → 0.19.0

package/esm/browser-mod.d.ts

@@ -25,6 +25,7 @@ export type { ChannelStatisticsAccumulator } from "./utils/compute_omero-shared.
 export { buildOmeroFromAccumulators, computeChannelStatistics, createAccumulator, extractChannel, finalizeStatistics, QUANTILE_SAMPLE_SIZE, updateAccumulator, validateQuantiles, } from "./utils/compute_omero-shared.js";
 export { createAxis, createDataset, createMetadata, createMultiscales, createNgffImage, createNgffMultiscales, } from "./utils/factory.js";
 export { getMethodMetadata } from "./utils/method_metadata.js";
+export { SpecRule, type ValidateOptions, validatePlate, validateStructural, validateWell, ValidationError, ValidationLevel, } from "./utils/structural_validation.js";
 export { isValidDimension, isValidUnit, validateMetadata, } from "./utils/validation.js";
 export { terminateWorkerPool, zarrGet, zarrSet } from "./utils/worker_pool.js";
 //# sourceMappingURL=browser-mod.d.ts.map

package/esm/browser-mod.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"browser-mod.d.ts","sourceRoot":"","sources":["../src/browser-mod.ts"],"names":[],"mappings":"AAQA,OAAO,EAAE,MAAM,EAAE,iBAAiB,EAAE,MAAM,aAAa,CAAC;AAIxD,OAAO,EACL,KAAK,UAAU,EACf,YAAY,EACZ,KAAK,mBAAmB,EACxB,WAAW,EACX,KAAK,kBAAkB,EACvB,KAAK,WAAW,GACjB,MAAM,gCAAgC,CAAC;AAExC,OAAO,EACL,mBAAmB,EACnB,KAAK,0BAA0B,GAChC,MAAM,iCAAiC,CAAC;AACzC,OAAO,EACL,uBAAuB,EACvB,mBAAmB,EACnB,KAAK,0BAA0B,GAChC,MAAM,iCAAiC,CAAC;AACzC,YAAY,EAAE,uBAAuB,EAAE,MAAM,kBAAkB,CAAC;AAEhE,OAAO,EACL,2BAA2B,EAC3B,cAAc,EACd,gBAAgB,EAChB,iBAAiB,EACjB,cAAc,GACf,MAAM,kBAAkB,CAAC;AAC1B,OAAO,EACL,SAAS,EACT,UAAU,EACV,KAAK,iBAAiB,EACtB,aAAa,EACb,KAAK,oBAAoB,EACzB,SAAS,EACT,KAAK,gBAAgB,EACrB,YAAY,EACZ,KAAK,mBAAmB,GACzB,MAAM,8BAA8B,CAAC;AAEtC,cAAc,qCAAqC,CAAC;AACpD,cAAc,sBAAsB,CAAC;AACrC,cAAc,0BAA0B,CAAC;AACzC,cAAc,yBAAyB,CAAC;AACxC,cAAc,oBAAoB,CAAC;AACnC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,oBAAoB,CAAC;AACnC,cAAc,wBAAwB,CAAC;AACvC,cAAc,uBAAuB,CAAC;AACtC,cAAc,kBAAkB,CAAC;AACjC,cAAc,0BAA0B,CAAC;AACzC,YAAY,EAAE,SAAS,EAAE,SAAS,EAAE,MAAM,mBAAmB,CAAC;AAC9D,OAAO,EACL,gBAAgB,EAChB,eAAe,EACf,aAAa,EACb,aAAa,GACd,MAAM,mBAAmB,CAAC;AAC3B,YAAY,EACV,kCAAkC,EAClC,mBAAmB,GACpB,MAAM,0BAA0B,CAAC;AAElC,OAAO,EACL,2BAA2B,EAC3B,yBAAyB,EACzB,gBAAgB,EAChB,cAAc,EACd,wBAAwB,GACzB,MAAM,0BAA0B,CAAC;AAClC,YAAY,EAAE,4BAA4B,EAAE,MAAM,iCAAiC,CAAC;AAEpF,OAAO,EACL,0BAA0B,EAC1B,wBAAwB,EACxB,iBAAiB,EACjB,cAAc,EACd,kBAAkB,EAClB,oBAAoB,EACpB,iBAAiB,EACjB,iBAAiB,GAClB,MAAM,iCAAiC,CAAC;AACzC,OAAO,EACL,UAAU,EACV,aAAa,EACb,cAAc,EACd,iBAAiB,EACjB,eAAe,EACf,qBAAqB,GACtB,MAAM,oBAAoB,CAAC;AAC5B,OAAO,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAC/D,OAAO,EACL,gBAAgB,EAChB,WAAW,EACX,gBAAgB,GACjB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EAAE,mBAAmB,EAAE,OAAO,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC"}
+{"version":3,"file":"browser-mod.d.ts","sourceRoot":"","sources":["../src/browser-mod.ts"],"names":[],"mappings":"AAQA,OAAO,EAAE,MAAM,EAAE,iBAAiB,EAAE,MAAM,aAAa,CAAC;AAIxD,OAAO,EACL,KAAK,UAAU,EACf,YAAY,EACZ,KAAK,mBAAmB,EACxB,WAAW,EACX,KAAK,kBAAkB,EACvB,KAAK,WAAW,GACjB,MAAM,gCAAgC,CAAC;AAExC,OAAO,EACL,mBAAmB,EACnB,KAAK,0BAA0B,GAChC,MAAM,iCAAiC,CAAC;AACzC,OAAO,EACL,uBAAuB,EACvB,mBAAmB,EACnB,KAAK,0BAA0B,GAChC,MAAM,iCAAiC,CAAC;AACzC,YAAY,EAAE,uBAAuB,EAAE,MAAM,kBAAkB,CAAC;AAEhE,OAAO,EACL,2BAA2B,EAC3B,cAAc,EACd,gBAAgB,EAChB,iBAAiB,EACjB,cAAc,GACf,MAAM,kBAAkB,CAAC;AAC1B,OAAO,EACL,SAAS,EACT,UAAU,EACV,KAAK,iBAAiB,EACtB,aAAa,EACb,KAAK,oBAAoB,EACzB,SAAS,EACT,KAAK,gBAAgB,EACrB,YAAY,EACZ,KAAK,mBAAmB,GACzB,MAAM,8BAA8B,CAAC;AAEtC,cAAc,qCAAqC,CAAC;AACpD,cAAc,sBAAsB,CAAC;AACrC,cAAc,0BAA0B,CAAC;AACzC,cAAc,yBAAyB,CAAC;AACxC,cAAc,oBAAoB,CAAC;AACnC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,oBAAoB,CAAC;AACnC,cAAc,wBAAwB,CAAC;AACvC,cAAc,uBAAuB,CAAC;AACtC,cAAc,kBAAkB,CAAC;AACjC,cAAc,0BAA0B,CAAC;AACzC,YAAY,EAAE,SAAS,EAAE,SAAS,EAAE,MAAM,mBAAmB,CAAC;AAC9D,OAAO,EACL,gBAAgB,EAChB,eAAe,EACf,aAAa,EACb,aAAa,GACd,MAAM,mBAAmB,CAAC;AAC3B,YAAY,EACV,kCAAkC,EAClC,mBAAmB,GACpB,MAAM,0BAA0B,CAAC;AAElC,OAAO,EACL,2BAA2B,EAC3B,yBAAyB,EACzB,gBAAgB,EAChB,cAAc,EACd,wBAAwB,GACzB,MAAM,0BAA0B,CAAC;AAClC,YAAY,EAAE,4BAA4B,EAAE,MAAM,iCAAiC,CAAC;AAEpF,OAAO,EACL,0BAA0B,EAC1B,wBAAwB,EACxB,iBAAiB,EACjB,cAAc,EACd,kBAAkB,EAClB,oBAAoB,EACpB,iBAAiB,EACjB,iBAAiB,GAClB,MAAM,iCAAiC,CAAC;AACzC,OAAO,EACL,UAAU,EACV,aAAa,EACb,cAAc,EACd,iBAAiB,EACjB,eAAe,EACf,qBAAqB,GACtB,MAAM,oBAAoB,CAAC;AAC5B,OAAO,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAC/D,OAAO,EACL,QAAQ,EACR,KAAK,eAAe,EACpB,aAAa,EACb,kBAAkB,EAClB,YAAY,EACZ,eAAe,EACf,eAAe,GAChB,MAAM,kCAAkC,CAAC;AAC1C,OAAO,EACL,gBAAgB,EAChB,WAAW,EACX,gBAAgB,GACjB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EAAE,mBAAmB,EAAE,OAAO,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC"}

package/esm/browser-mod.js

@@ -36,6 +36,7 @@ export { computeOmeroFromMultiscales, computeOmeroFromNgffImage, getDefaultColor
 export { buildOmeroFromAccumulators, computeChannelStatistics, createAccumulator, extractChannel, finalizeStatistics, QUANTILE_SAMPLE_SIZE, updateAccumulator, validateQuantiles, } from "./utils/compute_omero-shared.js";
 export { createAxis, createDataset, createMetadata, createMultiscales, createNgffImage, createNgffMultiscales, } from "./utils/factory.js";
 export { getMethodMetadata } from "./utils/method_metadata.js";
+export { SpecRule, validatePlate, validateStructural, validateWell, ValidationError, ValidationLevel, } from "./utils/structural_validation.js";
 export { isValidDimension, isValidUnit, validateMetadata, } from "./utils/validation.js";
 export { terminateWorkerPool, zarrGet, zarrSet } from "./utils/worker_pool.js";
 //# sourceMappingURL=browser-mod.js.map

package/esm/browser-mod.js.map

@@ -1 +1 @@
-{"version":3,"file":"browser-mod.js","sourceRoot":"","sources":["../src/browser-mod.ts"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,+BAA+B;AAC/B,oCAAoC;AACpC,wEAAwE;AACxE,EAAE;AACF,kFAAkF;AAClF,yEAAyE;AAEzE,OAAO,EAAE,MAAM,EAAE,iBAAiB,EAAE,MAAM,aAAa,CAAC;AACxD,iCAAiC;AACjC,0EAA0E;AAC1E,iFAAiF;AACjF,OAAO,EAEL,YAAY,EAEZ,WAAW,GAGZ,MAAM,gCAAgC,CAAC;AACxC,gCAAgC;AAChC,OAAO,EACL,mBAAmB,GAEpB,MAAM,iCAAiC,CAAC;AACzC,OAAO,EACL,uBAAuB,EACvB,mBAAmB,GAEpB,MAAM,iCAAiC,CAAC;AAEzC,gBAAgB;AAChB,OAAO,EACL,2BAA2B,EAC3B,cAAc,EACd,gBAAgB,EAChB,iBAAiB,EACjB,cAAc,GACf,MAAM,kBAAkB,CAAC;AAC1B,OAAO,EACL,SAAS,EACT,UAAU,EAEV,aAAa,EAEb,SAAS,EAET,YAAY,GAEb,MAAM,8BAA8B,CAAC;AACtC,wCAAwC;AACxC,cAAc,qCAAqC,CAAC;AACpD,cAAc,sBAAsB,CAAC;AACrC,cAAc,0BAA0B,CAAC;AACzC,cAAc,yBAAyB,CAAC;AACxC,cAAc,oBAAoB,CAAC;AACnC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,oBAAoB,CAAC;AACnC,cAAc,wBAAwB,CAAC;AACvC,cAAc,uBAAuB,CAAC;AACtC,cAAc,kBAAkB,CAAC;AACjC,cAAc,0BAA0B,CAAC;AAEzC,OAAO,EACL,gBAAgB,EAChB,eAAe,EACf,aAAa,EACb,aAAa,GACd,MAAM,mBAAmB,CAAC;AAK3B,oCAAoC;AACpC,OAAO,EACL,2BAA2B,EAC3B,yBAAyB,EACzB,gBAAgB,EAChB,cAAc,EACd,wBAAwB,GACzB,MAAM,0BAA0B,CAAC;AAElC,qEAAqE;AACrE,OAAO,EACL,0BAA0B,EAC1B,wBAAwB,EACxB,iBAAiB,EACjB,cAAc,EACd,kBAAkB,EAClB,oBAAoB,EACpB,iBAAiB,EACjB,iBAAiB,GAClB,MAAM,iCAAiC,CAAC;AACzC,OAAO,EACL,UAAU,EACV,aAAa,EACb,cAAc,EACd,iBAAiB,EACjB,eAAe,EACf,qBAAqB,GACtB,MAAM,oBAAoB,CAAC;AAC5B,OAAO,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAC/D,OAAO,EACL,gBAAgB,EAChB,WAAW,EACX,gBAAgB,GACjB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EAAE,mBAAmB,EAAE,OAAO,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC"}
+{"version":3,"file":"browser-mod.js","sourceRoot":"","sources":["../src/browser-mod.ts"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,+BAA+B;AAC/B,oCAAoC;AACpC,wEAAwE;AACxE,EAAE;AACF,kFAAkF;AAClF,yEAAyE;AAEzE,OAAO,EAAE,MAAM,EAAE,iBAAiB,EAAE,MAAM,aAAa,CAAC;AACxD,iCAAiC;AACjC,0EAA0E;AAC1E,iFAAiF;AACjF,OAAO,EAEL,YAAY,EAEZ,WAAW,GAGZ,MAAM,gCAAgC,CAAC;AACxC,gCAAgC;AAChC,OAAO,EACL,mBAAmB,GAEpB,MAAM,iCAAiC,CAAC;AACzC,OAAO,EACL,uBAAuB,EACvB,mBAAmB,GAEpB,MAAM,iCAAiC,CAAC;AAEzC,gBAAgB;AAChB,OAAO,EACL,2BAA2B,EAC3B,cAAc,EACd,gBAAgB,EAChB,iBAAiB,EACjB,cAAc,GACf,MAAM,kBAAkB,CAAC;AAC1B,OAAO,EACL,SAAS,EACT,UAAU,EAEV,aAAa,EAEb,SAAS,EAET,YAAY,GAEb,MAAM,8BAA8B,CAAC;AACtC,wCAAwC;AACxC,cAAc,qCAAqC,CAAC;AACpD,cAAc,sBAAsB,CAAC;AACrC,cAAc,0BAA0B,CAAC;AACzC,cAAc,yBAAyB,CAAC;AACxC,cAAc,oBAAoB,CAAC;AACnC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,oBAAoB,CAAC;AACnC,cAAc,wBAAwB,CAAC;AACvC,cAAc,uBAAuB,CAAC;AACtC,cAAc,kBAAkB,CAAC;AACjC,cAAc,0BAA0B,CAAC;AAEzC,OAAO,EACL,gBAAgB,EAChB,eAAe,EACf,aAAa,EACb,aAAa,GACd,MAAM,mBAAmB,CAAC;AAK3B,oCAAoC;AACpC,OAAO,EACL,2BAA2B,EAC3B,yBAAyB,EACzB,gBAAgB,EAChB,cAAc,EACd,wBAAwB,GACzB,MAAM,0BAA0B,CAAC;AAElC,qEAAqE;AACrE,OAAO,EACL,0BAA0B,EAC1B,wBAAwB,EACxB,iBAAiB,EACjB,cAAc,EACd,kBAAkB,EAClB,oBAAoB,EACpB,iBAAiB,EACjB,iBAAiB,GAClB,MAAM,iCAAiC,CAAC;AACzC,OAAO,EACL,UAAU,EACV,aAAa,EACb,cAAc,EACd,iBAAiB,EACjB,eAAe,EACf,qBAAqB,GACtB,MAAM,oBAAoB,CAAC;AAC5B,OAAO,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAC/D,OAAO,EACL,QAAQ,EAER,aAAa,EACb,kBAAkB,EAClB,YAAY,EACZ,eAAe,EACf,eAAe,GAChB,MAAM,kCAAkC,CAAC;AAC1C,OAAO,EACL,gBAAgB,EAChB,WAAW,EACX,gBAAgB,GACjB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EAAE,mBAAmB,EAAE,OAAO,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC"}

package/esm/io/hcs.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"hcs.d.ts","sourceRoot":"","sources":["../../src/io/hcs.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,QAAQ,EAAiB,MAAM,iBAAiB,CAAC;AAG/D,MAAM,WAAW,kBAAkB;IACjC,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,cAAc,CAAC,EAAE,MAAM,CAAC;CACzB;AAED,MAAM,WAAW,gBAAgB;IAE/B,gBAAgB,CAAC,EAAE,MAAM,CAAC;CAC3B;AAED;;GAEG;AACH,wBAAgB,WAAW,CACzB,KAAK,EAAE,MAAM,GAAG,MAAM,EACtB,OAAO,GAAE,kBAAuB,GAC/B,QAAQ,CAkCV;AAED;;GAEG;AACH,wBAAgB,SAAS,CACvB,KAAK,EAAE,QAAQ,EACf,KAAK,EAAE,MAAM,GAAG,MAAM,EACtB,QAAQ,GAAE,gBAAqB,GAC9B,IAAI,CAaN"}
+{"version":3,"file":"hcs.d.ts","sourceRoot":"","sources":["../../src/io/hcs.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,QAAQ,EAAiB,MAAM,iBAAiB,CAAC;AAO/D,MAAM,WAAW,kBAAkB;IACjC,QAAQ,CAAC,EAAE,OAAO,CAAC;IACnB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,cAAc,CAAC,EAAE,MAAM,CAAC;CACzB;AAED,MAAM,WAAW,gBAAgB;IAE/B,gBAAgB,CAAC,EAAE,MAAM,CAAC;CAC3B;AAED;;GAEG;AACH,wBAAgB,WAAW,CACzB,KAAK,EAAE,MAAM,GAAG,MAAM,EACtB,OAAO,GAAE,kBAAuB,GAC/B,QAAQ,CAyCV;AAED;;GAEG;AACH,wBAAgB,SAAS,CACvB,KAAK,EAAE,QAAQ,EACf,KAAK,EAAE,MAAM,GAAG,MAAM,EACtB,QAAQ,GAAE,gBAAqB,GAC9B,IAAI,CAaN"}

package/esm/io/hcs.js

@@ -1,12 +1,10 @@
 import { HCSPlate as HCSPlateClass } from "../types/hcs.js";
+import { validatePlate, ValidationLevel, } from "../utils/structural_validation.js";
 /**
  * Read an HCS plate from an OME-Zarr NGFF store.
  */
 export function fromHcsZarr(store, options = {}) {
     const { validate = false, wellCacheSize, imageCacheSize } = options;
-    if (validate) {
-        console.warn("HCS validation not yet implemented");
-    }
     if (typeof store !== "string") {
         throw new Error("Non-string store types not yet supported");
     }
@@ -26,11 +24,21 @@ export function fromHcsZarr(store, options = {}) {
         field_count: 2,
         name: "Test Plate",
     };
+    if (validate) {
+        // Strict structural validation of the parsed plate, layered after the
+        // schema pass (schema first, then structural -- mirrors the image reader).
+        // Per-well image rules run lazily in HCSPlate.getWell, where each well's
+        // own metadata is loaded. These plate/well rules are version-agnostic and
+        // the HCS reader handles only v0.4/v0.5 plates, so -- unlike the image
+        // reader's structural pass -- no >=0.4 version gate is required.
+        validatePlate(plateMetadata, { level: ValidationLevel.Strict });
+    }
     return new HCSPlateClass({
         store,
         metadata: plateMetadata,
         wellCacheSize,
         imageCacheSize,
+        validate,
     });
 }
 /**

package/esm/io/hcs.js.map

@@ -1 +1 @@
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+{"version":3,"file":"hcs.js","sourceRoot":"","sources":["../../src/io/hcs.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,QAAQ,IAAI,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAC5D,OAAO,EACL,aAAa,EACb,eAAe,GAChB,MAAM,mCAAmC,CAAC;AAa3C;;GAEG;AACH,MAAM,UAAU,WAAW,CACzB,KAAsB,EACtB,UAA8B,EAAE;IAEhC,MAAM,EAAE,QAAQ,GAAG,KAAK,EAAE,aAAa,EAAE,cAAc,EAAE,GAAG,OAAO,CAAC;IAEpE,IAAI,OAAO,KAAK,KAAK,QAAQ,EAAE,CAAC;QAC9B,MAAM,IAAI,KAAK,CAAC,0CAA0C,CAAC,CAAC;IAC9D,CAAC;IAED,wCAAwC;IACxC,iFAAiF;IACjF,MAAM,aAAa,GAAkB;QACnC,OAAO,EAAE,CAAC,EAAE,IAAI,EAAE,GAAG,EAAE,EAAE,EAAE,IAAI,EAAE,GAAG,EAAE,CAAC;QACvC,IAAI,EAAE,CAAC,EAAE,IAAI,EAAE,GAAG,EAAE,EAAE,EAAE,IAAI,EAAE,GAAG,EAAE,CAAC;QACpC,KAAK,EAAE;YACL,EAAE,IAAI,EAAE,KAAK,EAAE,QAAQ,EAAE,CAAC,EAAE,WAAW,EAAE,CAAC,EAAE;YAC5C,EAAE,IAAI,EAAE,KAAK,EAAE,QAAQ,EAAE,CAAC,EAAE,WAAW,EAAE,CAAC,EAAE;YAC5C,EAAE,IAAI,EAAE,KAAK,EAAE,QAAQ,EAAE,CAAC,EAAE,WAAW,EAAE,CAAC,EAAE;YAC5C,EAAE,IAAI,EAAE,KAAK,EAAE,QAAQ,EAAE,CAAC,EAAE,WAAW,EAAE,CAAC,EAAE;SAC7C;QACD,OAAO,EAAE,KAAK;QACd,YAAY,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,IAAI,EAAE,kBAAkB,EAAE,CAAC;QACnD,WAAW,EAAE,CAAC;QACd,IAAI,EAAE,YAAY;KACnB,CAAC;IAEF,IAAI,QAAQ,EAAE,CAAC;QACb,sEAAsE;QACtE,2EAA2E;QAC3E,yEAAyE;QACzE,0EAA0E;QAC1E,uEAAuE;QACvE,iEAAiE;QACjE,aAAa,CAAC,aAAa,EAAE,EAAE,KAAK,EAAE,eAAe,CAAC,MAAM,EAAE,CAAC,CAAC;IAClE,CAAC;IAED,OAAO,IAAI,aAAa,CAAC;QACvB,KAAK;QACL,QAAQ,EAAE,aAAa;QACvB,aAAa;QACb,cAAc;QACd,QAAQ;KACT,CAAC,CAAC;AACL,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,SAAS,CACvB,KAAe,EACf,KAAsB,EACtB,WAA6B,EAAE;IAE/B,IAAI,OAAO,KAAK,KAAK,QAAQ,EAAE,CAAC;QAC9B,MAAM,IAAI,KAAK,CAAC,0CAA0C,CAAC,CAAC;IAC9D,CAAC;IAED,8BAA8B;IAC9B,OAAO,CAAC,GAAG,CAAC,2CAA2C,KAAK,EAAE,CAAC,CAAC;IAChE,OAAO,CAAC,GAAG,CAAC,UAAU,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;IACpC,OAAO,CAAC,GAAG,CAAC,UAAU,KAAK,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC,CAAC;IAC5C,OAAO,CAAC,GAAG,CAAC,SAAS,KAAK,CAAC,IAAI,CAAC,MAAM,cAAc,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC,CAAC;IAC5E,IAAI,KAAK,CAAC,YAAY,EAAE,CAAC;QACvB,OAAO,CAAC,GAAG,CAAC,iBAAiB,KAAK,CAAC,YAAY,CAAC,MAAM,EAAE,CAAC,CAAC;IAC5D,CAAC;AACH,CAAC"}

package/esm/io/to_ngff_zarr-browser.d.ts

@@ -7,6 +7,8 @@ export interface ToOmeZarrOptions {
     overwrite?: boolean;
     version?: "0.4" | "0.5";
     chunksPerShard?: number | number[] | Record<string, number>;
+    /** List of RFC numbers to enable (e.g., [4] for RFC 4 anatomical orientation) */
+    enabledRfcs?: number[];
     /**
      * Custom codec pipeline for array compression. When omitted the default
      * ``blosc(zstd)`` pipeline from {@link defaultCodecs} is used. Use

package/esm/io/to_ngff_zarr-browser.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"to_ngff_zarr-browser.d.ts","sourceRoot":"","sources":["../../src/io/to_ngff_zarr-browser.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAEhC,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,yBAAyB,CAAC;AAE/D,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAC;AAGpD,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,6BAA6B,CAAC;AAI/D,OAAO,EAAE,SAAS,EAAE,MAAM,eAAe,CAAC;AAE1C,MAAM,WAAW,gBAAgB;IAC/B,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,OAAO,CAAC,EAAE,KAAK,GAAG,KAAK,CAAC;IACxB,cAAc,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAC5D;;;;OAIG;IACH,MAAM,CAAC,EAAE,SAAS,EAAE,CAAC;CACtB;AAED,wDAAwD;AACxD,MAAM,MAAM,iBAAiB,GAAG,gBAAgB,CAAC;AAEjD;;;GAGG;AACH,MAAM,WAAW,mBAAmB;IAClC,iFAAiF;IACjF,WAAW,CAAC,EAAE,MAAM,EAAE,GAAG,SAAS,CAAC;IACnC;;;;;;OAMG;IACH,UAAU,CAAC,EACP,CAAC,CAAC,eAAe,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,KAAK,IAAI,CAAC,GACxD,SAAS,CAAC;CACf;AAED,2DAA2D;AAC3D,MAAM,MAAM,oBAAoB,GAAG,mBAAmB,CAAC;AAEvD;;;;GAIG;AACH,wBAAsB,SAAS,CAC7B,KAAK,EAAE,MAAM,GAAG,WAAW,GAAG,IAAI,CAAC,UAAU,EAC7C,WAAW,EAAE,eAAe,EAC5B,OAAO,GAAE,gBAAqB,GAC7B,OAAO,CAAC,IAAI,CAAC,CA2Ff;AAED,iDAAiD;AACjD,eAAO,MAAM,UAAU,kBAAY,CAAC;AA2VpC;;;;;;;;;;;;;;;GAeG;AACH,wBAAsB,YAAY,CAChC,WAAW,EAAE,eAAe,EAC5B,QAAQ,GAAE,mBAAwB,GACjC,OAAO,CAAC,UAAU,CAAC,CAmBrB;AAED,oDAAoD;AACpD,eAAO,MAAM,aAAa,qBAAe,CAAC"}
+{"version":3,"file":"to_ngff_zarr-browser.d.ts","sourceRoot":"","sources":["../../src/io/to_ngff_zarr-browser.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAEhC,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,yBAAyB,CAAC;AAE/D,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAC;AAGpD,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,6BAA6B,CAAC;AAO/D,OAAO,EAAE,SAAS,EAAE,MAAM,eAAe,CAAC;AAE1C,MAAM,WAAW,gBAAgB;IAC/B,SAAS,CAAC,EAAE,OAAO,CAAC;IACpB,OAAO,CAAC,EAAE,KAAK,GAAG,KAAK,CAAC;IACxB,cAAc,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IAC5D,iFAAiF;IACjF,WAAW,CAAC,EAAE,MAAM,EAAE,CAAC;IACvB;;;;OAIG;IACH,MAAM,CAAC,EAAE,SAAS,EAAE,CAAC;CACtB;AAED,wDAAwD;AACxD,MAAM,MAAM,iBAAiB,GAAG,gBAAgB,CAAC;AAEjD;;;GAGG;AACH,MAAM,WAAW,mBAAmB;IAClC,iFAAiF;IACjF,WAAW,CAAC,EAAE,MAAM,EAAE,GAAG,SAAS,CAAC;IACnC;;;;;;OAMG;IACH,UAAU,CAAC,EACP,CAAC,CAAC,eAAe,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,KAAK,IAAI,CAAC,GACxD,SAAS,CAAC;CACf;AAED,2DAA2D;AAC3D,MAAM,MAAM,oBAAoB,GAAG,mBAAmB,CAAC;AAEvD;;;;GAIG;AACH,wBAAsB,SAAS,CAC7B,KAAK,EAAE,MAAM,GAAG,WAAW,GAAG,IAAI,CAAC,UAAU,EAC7C,WAAW,EAAE,eAAe,EAC5B,OAAO,GAAE,gBAAqB,GAC7B,OAAO,CAAC,IAAI,CAAC,CAkGf;AAED,iDAAiD;AACjD,eAAO,MAAM,UAAU,kBAAY,CAAC;AA2VpC;;;;;;;;;;;;;;;GAeG;AACH,wBAAsB,YAAY,CAChC,WAAW,EAAE,eAAe,EAC5B,QAAQ,GAAE,mBAAwB,GACjC,OAAO,CAAC,UAAU,CAAC,CAmBrB;AAED,oDAAoD;AACpD,eAAO,MAAM,aAAa,qBAAe,CAAC"}

package/esm/io/to_ngff_zarr-browser.js

@@ -6,7 +6,7 @@ import * as zarr from "zarrita";
 import { defaultCodecs } from "../utils/codecs.js";
 import { createWriteQueue, zarrGet, zarrSet } from "../utils/worker_pool.js";
 import { memoryStoreToZip } from "./rfc9_zip.js";
-import { writeNgffMultiscalesToMemoryStore } from "./to_ngff_zarr_ozx_common.js";
+import { processAxesForRfcs, writeNgffMultiscalesToMemoryStore, } from "./to_ngff_zarr_ozx_common.js";
 export { isOzxPath } from "./rfc9_zip.js";
 /**
  * Browser-compatible version of toOmeZarr.
@@ -16,6 +16,7 @@ export { isOzxPath } from "./rfc9_zip.js";
 export async function toOmeZarr(store, multiscales, options = {}) {
     const _overwrite = options.overwrite ?? true;
     const _version = options.version ?? "0.4";
+    const enabledRfcs = options.enabledRfcs;
     try {
         // Determine the appropriate store type based on the path
         let _resolvedStore;
@@ -34,11 +35,13 @@ export async function toOmeZarr(store, multiscales, options = {}) {
         }
         // Create root location and group with zarrita v0.5.2 API
         const root = zarr.root(_resolvedStore);
+        // Process axes - filter orientation based on enabledRfcs
+        const processedAxes = processAxesForRfcs(multiscales.metadata.axes, enabledRfcs);
         // Prepare multiscales metadata
         const multiscalesMetadata = {
             version: _version,
             name: multiscales.metadata.name,
-            axes: multiscales.metadata.axes,
+            axes: processedAxes,
             datasets: multiscales.metadata.datasets,
             ...(multiscales.metadata.coordinateTransformations && {
                 coordinateTransformations: multiscales.metadata.coordinateTransformations,

package/esm/io/to_ngff_zarr-browser.js.map

@@ -1 +1 @@
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package/esm/mod.d.ts

@@ -29,6 +29,7 @@ export { createAxis, createDataset, createMetadata, createMultiscales, createNgf
 export { fromZarrAttrsV04, fromZarrAttrsV05 } from "./utils/from_zarr_attrs.js";
 export { getMethodMetadata } from "./utils/method_metadata.js";
 export { detectVersion, extractMethodMetadata, parseOmero, } from "./utils/parse_metadata.js";
+export { SpecRule, type ValidateOptions, validatePlate, validateStructural, validateWell, ValidationError, ValidationLevel, } from "./utils/structural_validation.js";
 export { isValidDimension, isValidUnit, validateMetadata, } from "./utils/validation.js";
 export { terminateWorkerPool, zarrGet, zarrSet } from "./utils/worker_pool.js";
 //# sourceMappingURL=mod.d.ts.map

package/esm/mod.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"mod.d.ts","sourceRoot":"","sources":["../src/mod.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,MAAM,EAAE,iBAAiB,EAAE,MAAM,aAAa,CAAC;AACxD,cAAc,wBAAwB,CAAC;AACvC,cAAc,aAAa,CAAC;AAC5B,cAAc,iCAAiC,CAAC;AAChD,cAAc,iCAAiC,CAAC;AAChD,YAAY,EAAE,uBAAuB,EAAE,MAAM,kBAAkB,CAAC;AAEhE,OAAO,EACL,2BAA2B,EAC3B,cAAc,EACd,SAAS,EACT,gBAAgB,EAChB,iBAAiB,EACjB,gBAAgB,EAChB,cAAc,GACf,MAAM,kBAAkB,CAAC;AAC1B,cAAc,sBAAsB,CAAC;AACrC,cAAc,kCAAkC,CAAC;AACjD,cAAc,sBAAsB,CAAC;AACrC,cAAc,0BAA0B,CAAC;AACzC,cAAc,yBAAyB,CAAC;AACxC,cAAc,oBAAoB,CAAC;AACnC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,gBAAgB,CAAC;AAC/B,cAAc,oBAAoB,CAAC;AACnC,cAAc,wBAAwB,CAAC;AACvC,cAAc,uBAAuB,CAAC;AACtC,cAAc,iBAAiB,CAAC;AAChC,cAAc,+BAA+B,CAAC;AAC9C,cAAc,kBAAkB,CAAC;AACjC,cAAc,0BAA0B,CAAC;AACzC,YAAY,EAAE,SAAS,EAAE,SAAS,EAAE,MAAM,mBAAmB,CAAC;AAC9D,OAAO,EACL,gBAAgB,EAChB,eAAe,EACf,aAAa,EACb,aAAa,GACd,MAAM,mBAAmB,CAAC;AAC3B,YAAY,EACV,kCAAkC,EAClC,mBAAmB,GACpB,MAAM,0BAA0B,CAAC;AAClC,OAAO,EACL,2BAA2B,EAC3B,yBAAyB,EACzB,gBAAgB,EAChB,cAAc,EACd,wBAAwB,GACzB,MAAM,0BAA0B,CAAC;AAClC,OAAO,EACL,UAAU,EACV,aAAa,EACb,cAAc,EACd,iBAAiB,EACjB,eAAe,EACf,qBAAqB,GACtB,MAAM,oBAAoB,CAAC;AAC5B,OAAO,EAAE,gBAAgB,EAAE,gBAAgB,EAAE,MAAM,4BAA4B,CAAC;AAChF,OAAO,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAC/D,OAAO,EACL,aAAa,EACb,qBAAqB,EACrB,UAAU,GACX,MAAM,2BAA2B,CAAC;AACnC,OAAO,EACL,gBAAgB,EAChB,WAAW,EACX,gBAAgB,GACjB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EAAE,mBAAmB,EAAE,OAAO,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC"}
+{"version":3,"file":"mod.d.ts","sourceRoot":"","sources":["../src/mod.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,MAAM,EAAE,iBAAiB,EAAE,MAAM,aAAa,CAAC;AACxD,cAAc,wBAAwB,CAAC;AACvC,cAAc,aAAa,CAAC;AAC5B,cAAc,iCAAiC,CAAC;AAChD,cAAc,iCAAiC,CAAC;AAChD,YAAY,EAAE,uBAAuB,EAAE,MAAM,kBAAkB,CAAC;AAEhE,OAAO,EACL,2BAA2B,EAC3B,cAAc,EACd,SAAS,EACT,gBAAgB,EAChB,iBAAiB,EACjB,gBAAgB,EAChB,cAAc,GACf,MAAM,kBAAkB,CAAC;AAC1B,cAAc,sBAAsB,CAAC;AACrC,cAAc,kCAAkC,CAAC;AACjD,cAAc,sBAAsB,CAAC;AACrC,cAAc,0BAA0B,CAAC;AACzC,cAAc,yBAAyB,CAAC;AACxC,cAAc,oBAAoB,CAAC;AACnC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,gBAAgB,CAAC;AAC/B,cAAc,oBAAoB,CAAC;AACnC,cAAc,wBAAwB,CAAC;AACvC,cAAc,uBAAuB,CAAC;AACtC,cAAc,iBAAiB,CAAC;AAChC,cAAc,+BAA+B,CAAC;AAC9C,cAAc,kBAAkB,CAAC;AACjC,cAAc,0BAA0B,CAAC;AACzC,YAAY,EAAE,SAAS,EAAE,SAAS,EAAE,MAAM,mBAAmB,CAAC;AAC9D,OAAO,EACL,gBAAgB,EAChB,eAAe,EACf,aAAa,EACb,aAAa,GACd,MAAM,mBAAmB,CAAC;AAC3B,YAAY,EACV,kCAAkC,EAClC,mBAAmB,GACpB,MAAM,0BAA0B,CAAC;AAClC,OAAO,EACL,2BAA2B,EAC3B,yBAAyB,EACzB,gBAAgB,EAChB,cAAc,EACd,wBAAwB,GACzB,MAAM,0BAA0B,CAAC;AAClC,OAAO,EACL,UAAU,EACV,aAAa,EACb,cAAc,EACd,iBAAiB,EACjB,eAAe,EACf,qBAAqB,GACtB,MAAM,oBAAoB,CAAC;AAC5B,OAAO,EAAE,gBAAgB,EAAE,gBAAgB,EAAE,MAAM,4BAA4B,CAAC;AAChF,OAAO,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAC/D,OAAO,EACL,aAAa,EACb,qBAAqB,EACrB,UAAU,GACX,MAAM,2BAA2B,CAAC;AACnC,OAAO,EACL,QAAQ,EACR,KAAK,eAAe,EACpB,aAAa,EACb,kBAAkB,EAClB,YAAY,EACZ,eAAe,EACf,eAAe,GAChB,MAAM,kCAAkC,CAAC;AAC1C,OAAO,EACL,gBAAgB,EAChB,WAAW,EACX,gBAAgB,GACjB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EAAE,mBAAmB,EAAE,OAAO,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC"}

package/esm/mod.js

@@ -29,6 +29,7 @@ export { createAxis, createDataset, createMetadata, createMultiscales, createNgf
 export { fromZarrAttrsV04, fromZarrAttrsV05 } from "./utils/from_zarr_attrs.js";
 export { getMethodMetadata } from "./utils/method_metadata.js";
 export { detectVersion, extractMethodMetadata, parseOmero, } from "./utils/parse_metadata.js";
+export { SpecRule, validatePlate, validateStructural, validateWell, ValidationError, ValidationLevel, } from "./utils/structural_validation.js";
 export { isValidDimension, isValidUnit, validateMetadata, } from "./utils/validation.js";
 export { terminateWorkerPool, zarrGet, zarrSet } from "./utils/worker_pool.js";
 //# sourceMappingURL=mod.js.map

package/esm/mod.js.map

@@ -1 +1 @@
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+{"version":3,"file":"mod.js","sourceRoot":"","sources":["../src/mod.ts"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,+BAA+B;AAE/B,OAAO,EAAE,MAAM,EAAE,iBAAiB,EAAE,MAAM,aAAa,CAAC;AACxD,cAAc,wBAAwB,CAAC;AACvC,cAAc,aAAa,CAAC;AAC5B,cAAc,iCAAiC,CAAC;AAChD,cAAc,iCAAiC,CAAC;AAEhD,gBAAgB;AAChB,OAAO,EACL,2BAA2B,EAC3B,cAAc,EACd,SAAS,EACT,gBAAgB,EAChB,iBAAiB,EACjB,gBAAgB,EAChB,cAAc,GACf,MAAM,kBAAkB,CAAC;AAC1B,cAAc,sBAAsB,CAAC;AACrC,cAAc,kCAAkC,CAAC;AACjD,cAAc,sBAAsB,CAAC;AACrC,cAAc,0BAA0B,CAAC;AACzC,cAAc,yBAAyB,CAAC;AACxC,cAAc,oBAAoB,CAAC;AACnC,cAAc,4BAA4B,CAAC;AAC3C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,gBAAgB,CAAC;AAC/B,cAAc,oBAAoB,CAAC;AACnC,cAAc,wBAAwB,CAAC;AACvC,cAAc,uBAAuB,CAAC;AACtC,cAAc,iBAAiB,CAAC;AAChC,cAAc,+BAA+B,CAAC;AAC9C,cAAc,kBAAkB,CAAC;AACjC,cAAc,0BAA0B,CAAC;AAEzC,OAAO,EACL,gBAAgB,EAChB,eAAe,EACf,aAAa,EACb,aAAa,GACd,MAAM,mBAAmB,CAAC;AAK3B,OAAO,EACL,2BAA2B,EAC3B,yBAAyB,EACzB,gBAAgB,EAChB,cAAc,EACd,wBAAwB,GACzB,MAAM,0BAA0B,CAAC;AAClC,OAAO,EACL,UAAU,EACV,aAAa,EACb,cAAc,EACd,iBAAiB,EACjB,eAAe,EACf,qBAAqB,GACtB,MAAM,oBAAoB,CAAC;AAC5B,OAAO,EAAE,gBAAgB,EAAE,gBAAgB,EAAE,MAAM,4BAA4B,CAAC;AAChF,OAAO,EAAE,iBAAiB,EAAE,MAAM,4BAA4B,CAAC;AAC/D,OAAO,EACL,aAAa,EACb,qBAAqB,EACrB,UAAU,GACX,MAAM,2BAA2B,CAAC;AACnC,OAAO,EACL,QAAQ,EAER,aAAa,EACb,kBAAkB,EAClB,YAAY,EACZ,eAAe,EACf,eAAe,GAChB,MAAM,kCAAkC,CAAC;AAC1C,OAAO,EACL,gBAAgB,EAChB,WAAW,EACX,gBAAgB,GACjB,MAAM,uBAAuB,CAAC;AAC/B,OAAO,EAAE,mBAAmB,EAAE,OAAO,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC"}

package/esm/types/hcs.d.ts

@@ -30,6 +30,12 @@ export interface HCSPlateOptions {
     metadata: PlateMetadata;
     wellCacheSize?: number | undefined;
     imageCacheSize?: number | undefined;
+    /**
+     * When `true`, each well's structural rules run as it is first loaded via
+     * {@link HCSPlate.getWell}. Defaults to `false`, leaving the read path
+     * unvalidated. Set by `fromHcsZarr` when its own `validate` flag is enabled.
+     */
+    validate?: boolean | undefined;
 }
 export interface HCSWellOptions {
     store: string | object;
@@ -57,6 +63,7 @@ export declare class HCSPlate {
     readonly metadata: PlateMetadata;
     private readonly _wells;
     private readonly imageCacheSize;
+    private readonly _validate;
     constructor(options: HCSPlateOptions);
     get name(): string | undefined;
     get rows(): PlateRow[];

package/esm/types/hcs.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"hcs.d.ts","sourceRoot":"","sources":["../../src/types/hcs.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAC;AACxD,OAAO,KAAK,EACV,gBAAgB,EAChB,WAAW,EACX,QAAQ,EACR,SAAS,EACT,SAAS,EACV,MAAM,qBAAqB,CAAC;AAM7B,MAAM,WAAW,eAAe;IAC9B,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,qBAAa,QAAQ,CAAC,CAAC,EAAE,CAAC;IACxB,OAAO,CAAC,KAAK,CAAY;IACzB,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAS;gBAErB,OAAO,EAAE,eAAe;IAKpC,GAAG,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,GAAG,SAAS;IAU1B,GAAG,CAAC,GAAG,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,GAAG,IAAI;IAc3B,GAAG,CAAC,GAAG,EAAE,CAAC,GAAG,OAAO;IAIpB,KAAK,IAAI,IAAI;CAGd;AAED,MAAM,WAAW,aAAa;IAC5B,OAAO,EAAE,WAAW,EAAE,CAAC;IACvB,IAAI,EAAE,QAAQ,EAAE,CAAC;IACjB,KAAK,EAAE,SAAS,EAAE,CAAC;IACnB,OAAO,EAAE,MAAM,CAAC;IAChB,YAAY,CAAC,EAAE,gBAAgB,EAAE,GAAG,SAAS,CAAC;IAC9C,WAAW,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IACjC,IAAI,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;CAC3B;AAED,MAAM,WAAW,YAAY;IAC3B,MAAM,EAAE,SAAS,EAAE,CAAC;IACpB,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,MAAM,WAAW,eAAe;IAC9B,KAAK,EAAE,MAAM,GAAG,MAAM,CAAC;IACvB,QAAQ,EAAE,aAAa,CAAC;IACxB,aAAa,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IACnC,cAAc,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IACpC;;;;OAIG;IACH,QAAQ,CAAC,EAAE,OAAO,GAAG,SAAS,CAAC;CAChC;AAED,MAAM,WAAW,cAAc;IAC7B,KAAK,EAAE,MAAM,GAAG,MAAM,CAAC;IACvB,QAAQ,EAAE,MAAM,CAAC;IACjB,aAAa,EAAE,SAAS,CAAC;IACzB,iBAAiB,EAAE,YAAY,CAAC;IAChC,cAAc,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;CACrC;AAED,qBAAa,OAAO;IAClB,OAAO,CAAC,QAAQ,CAAC,KAAK,CAAkB;IACxC,SAAgB,IAAI,EAAE,MAAM,CAAC;IAC7B,SAAgB,aAAa,EAAE,SAAS,CAAC;IACzC,SAAgB,QAAQ,EAAE,YAAY,CAAC;IACvC,OAAO,CAAC,QAAQ,CAAC,OAAO,CAAoC;gBAEhD,OAAO,EAAE,cAAc;IAenC,IAAI,QAAQ,IAAI,MAAM,CAErB;IAED,IAAI,WAAW,IAAI,MAAM,CAExB;IAED,IAAI,MAAM,IAAI,SAAS,EAAE,CAExB;IAEK,QAAQ,CAAC,UAAU,GAAE,MAAU,GAAG,OAAO,CAAC,eAAe,GAAG,IAAI,CAAC;IAqCvE,qBAAqB,CACnB,aAAa,EAAE,MAAM,EACrB,UAAU,GAAE,MAAU,GACrB,OAAO,CAAC,eAAe,GAAG,IAAI,CAAC;IAiBlC,MAAM,CAAC,SAAS,CACd,KAAK,EAAE,MAAM,GAAG,MAAM,EACtB,QAAQ,EAAE,MAAM,EAChB,YAAY,EAAE,SAAS,EACvB,cAAc,CAAC,EAAE,MAAM,GAAG,SAAS,GAClC,OAAO;CAkBX;AAED,qBAAa,QAAQ;IACnB,OAAO,CAAC,QAAQ,CAAC,KAAK,CAAkB;IACxC,SAAgB,QAAQ,EAAE,aAAa,CAAC;IACxC,OAAO,CAAC,QAAQ,CAAC,MAAM,CAA4B;IACnD,OAAO,CAAC,QAAQ,CAAC,cAAc,CAAqB;IACpD,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAU;gBAExB,OAAO,EAAE,eAAe;IAoBpC,IAAI,IAAI,IAAI,MAAM,GAAG,SAAS,CAE7B;IAED,IAAI,IAAI,IAAI,QAAQ,EAAE,CAErB;IAED,IAAI,OAAO,IAAI,WAAW,EAAE,CAE3B;IAED,IAAI,KAAK,IAAI,SAAS,EAAE,CAEvB;IAED,IAAI,YAAY,IAAI,gBAAgB,EAAE,GAAG,SAAS,CAIjD;IAED,IAAI,UAAU,IAAI,MAAM,GAAG,SAAS,CAEnC;IAED,OAAO,CAAC,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,GAAG,OAAO,GAAG,IAAI;IA2C5D,gBAAgB,CAAC,QAAQ,EAAE,MAAM,EAAE,WAAW,EAAE,MAAM,GAAG,OAAO,GAAG,IAAI;CAcxE"}

package/esm/types/hcs.js

@@ -1,3 +1,4 @@
+import { validateWell, ValidationLevel, } from "../utils/structural_validation.js";
 export class LRUCache {
     cache;
     maxSize;
@@ -130,6 +131,7 @@ export class HCSPlate {
     metadata;
     _wells;
     imageCacheSize;
+    _validate;
     constructor(options) {
         this.store = options.store;
         this.metadata = {
@@ -144,6 +146,7 @@ export class HCSPlate {
             name: options.metadata.name,
         };
         this.imageCacheSize = options.imageCacheSize;
+        this._validate = options.validate ?? false;
         const wellCacheSize = options.wellCacheSize ?? 500;
         this._wells = new LRUCache({ maxSize: wellCacheSize });
     }
@@ -180,15 +183,25 @@ export class HCSPlate {
             return cached;
         }
         // Load the well
+        let well;
         try {
-            const well = HCSWell.fromStore(this.store, wellPath, wellMeta, this.imageCacheSize);
-            this._wells.set(wellPath, well);
-            return well;
+            well = HCSWell.fromStore(this.store, wellPath, wellMeta, this.imageCacheSize);
         }
         catch (error) {
             console.error(`Failed to load well at ${wellPath}:`, error);
             return null;
         }
+        if (this._validate) {
+            // Strict structural validation of the well's own metadata in the context
+            // of this plate, performed where each well is first loaded (mirrors the
+            // schema/structural split in fromHcsZarr). A ValidationError propagates
+            // to the caller rather than being swallowed as a load failure.
+            validateWell(this.metadata, well.metadata, {
+                level: ValidationLevel.Strict,
+            });
+        }
+        this._wells.set(wellPath, well);
+        return well;
     }
     getWellByIndices(rowIndex, columnIndex) {
         if (rowIndex < 0 ||

package/esm/types/hcs.js.map

@@ -1 +1 @@
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package/esm/utils/from_zarr_attrs.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"from_zarr_attrs.d.ts","sourceRoot":"","sources":["../../src/utils/from_zarr_attrs.ts"],"names":[],"mappings":"AAGA;;GAEG;AAEH,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAChC,OAAO,KAAK,EAGV,mBAAmB,EAMpB,MAAM,2BAA2B,CAAC;AAKnC,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AAsE3D;;;;GAIG;AACH,wBAAsB,gBAAgB,CACpC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAClC,KAAK,EAAE,WAAW,GAAG,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,QAAQ,EACpD,QAAQ,UAAQ,GACf,OAAO,CAAC,mBAAmB,CAAC,CA6R9B;AAED;;;;;;GAMG;AACH,wBAAsB,gBAAgB,CACpC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAClC,KAAK,EAAE,WAAW,GAAG,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,QAAQ,EACpD,QAAQ,UAAQ,GACf,OAAO,CAAC,mBAAmB,CAAC,CA6B9B"}
+{"version":3,"file":"from_zarr_attrs.d.ts","sourceRoot":"","sources":["../../src/utils/from_zarr_attrs.ts"],"names":[],"mappings":"AAGA;;GAEG;AAEH,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAChC,OAAO,KAAK,EAGV,mBAAmB,EAMpB,MAAM,2BAA2B,CAAC;AAKnC,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AAiG3D;;;;GAIG;AACH,wBAAsB,gBAAgB,CACpC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAClC,KAAK,EAAE,WAAW,GAAG,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,QAAQ,EACpD,QAAQ,UAAQ,GACf,OAAO,CAAC,mBAAmB,CAAC,CA+S9B;AAED;;;;;;GAMG;AACH,wBAAsB,gBAAgB,CACpC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAClC,KAAK,EAAE,WAAW,GAAG,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,QAAQ,EACpD,QAAQ,UAAQ,GACf,OAAO,CAAC,mBAAmB,CAAC,CA6B9B"}

package/esm/utils/from_zarr_attrs.js

@@ -8,6 +8,7 @@ import { SUPPORTED_DIMS } from "../types/zarr_metadata.js";
 import { NgffImage } from "../types/ngff_image.js";
 import { parseOmero } from "./parse_metadata.js";
 import { hasRfc4OrientationMetadata, validateRfc4Orientation, } from "./rfc4_validation.js";
+import { validateStructural, ValidationLevel, } from "./structural_validation.js";
 import { AnatomicalOrientationValues } from "../types/rfc4.js";
 /**
  * Map string orientation values to enum values
@@ -60,6 +61,28 @@ function extractOrientationsFromAxes(axesData) {
     }
     return hasOrientation ? orientations : undefined;
 }
+/**
+ * Return whether an OME-Zarr spec version string is `0.4` or newer.
+ *
+ * The dotted version is compared component-wise as integers, so multi-digit
+ * minor versions order correctly: `"0.10"` is newer than `"0.4"`, not older.
+ * A plain `Number.parseFloat("0.10")` would yield `0.1` and wrongly drop v0.10+
+ * metadata from structural validation. This mirrors the Python port's
+ * `packaging.version.parse(version) >= packaging.version.parse("0.4")` gate.
+ *
+ * Returns `false` for an unparsable version (leading component not a number),
+ * matching the prior `Number.isNaN` guard that skipped validation in that case.
+ */
+function isSpecVersionAtLeastV04(version) {
+    const [major, minor = 0] = version
+        .split(".")
+        .map((part) => Number.parseInt(part, 10));
+    if (Number.isNaN(major)) {
+        return false;
+    }
+    // A NaN minor (e.g. "0.x") fails `minor >= 4`, so it needs no separate guard.
+    return major > 0 || (major === 0 && minor >= 4);
+}
 /**
  * Parse Metadata and NgffImages from OME-Zarr v0.4 root attributes.
  *
@@ -143,6 +166,13 @@ export async function fromZarrAttrsV04(rootAttrs, store, validate = false) {
                     name: String(axisObj.name),
                     type: String(axisObj.type),
                     unit: axisObj.unit,
+                    // Preserve RFC 4 orientation on the parsed axis so the strict
+                    // structural pass below can run validateAxisOrientation; dropping it
+                    // here makes that rule a no-op. This mirrors the Python port, whose
+                    // _filter_axis_dict keeps the raw orientation field on each Axis.
+                    ...(axisObj.orientation !== undefined && axisObj.orientation !== null
+                        ? { orientation: axisObj.orientation }
+                        : {}),
                 };
             });
         }
@@ -288,6 +318,16 @@ export async function fromZarrAttrsV04(rootAttrs, store, validate = false) {
             }
             : {}),
     };
+    // Strict structural validation of the parsed metadata, layered after the
+    // schema pass and RFC 4 dict check above. The structural rules encode the
+    // v0.4+ metadata model (typed axes and per-dataset coordinate
+    // transformations); the legacy v0.1-0.3 layouts predate it, so the rules are
+    // scoped to v0.4 and newer.
+    if (validate) {
+        if (isSpecVersionAtLeastV04(metadata.version)) {
+            validateStructural(metadata, { level: ValidationLevel.Strict });
+        }
+    }
     return { metadata, images };
 }
 /**

package/esm/utils/from_zarr_attrs.js.map

@@ -1 +1 @@
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package/esm/utils/py_format.d.ts

@@ -0,0 +1,18 @@
+/**
+ * Python-style value formatting helpers shared across the validation modules.
+ *
+ * These keep `ValidationError` message bytes identical to the Python port,
+ * which the cross-language parity tests assert.
+ */
+/**
+ * Render a list of names as a Python-style list literal, e.g. `['z', 'y']`.
+ *
+ * Mirrors Python's `str(list_of_str)` / f-string rendering: bracketed,
+ * single-quoted elements, comma-space separated. Both the structural
+ * spatial-axis-order message and the RFC 4 axis-orientation-completeness
+ * message interpolate this verbatim, so the two ports stay byte-for-byte
+ * identical. Axis names reaching these rules are single-quote-free, so the
+ * plain single-quoted element form is exact.
+ */
+export declare function formatNameList(names: readonly string[]): string;
+//# sourceMappingURL=py_format.d.ts.map

package/esm/utils/py_format.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"py_format.d.ts","sourceRoot":"","sources":["../../src/utils/py_format.ts"],"names":[],"mappings":"AAEA;;;;;GAKG;AAEH;;;;;;;;;GASG;AACH,wBAAgB,cAAc,CAAC,KAAK,EAAE,SAAS,MAAM,EAAE,GAAG,MAAM,CAE/D"}

package/esm/utils/py_format.js

@@ -0,0 +1,22 @@
+// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
+// SPDX-License-Identifier: MIT
+/**
+ * Python-style value formatting helpers shared across the validation modules.
+ *
+ * These keep `ValidationError` message bytes identical to the Python port,
+ * which the cross-language parity tests assert.
+ */
+/**
+ * Render a list of names as a Python-style list literal, e.g. `['z', 'y']`.
+ *
+ * Mirrors Python's `str(list_of_str)` / f-string rendering: bracketed,
+ * single-quoted elements, comma-space separated. Both the structural
+ * spatial-axis-order message and the RFC 4 axis-orientation-completeness
+ * message interpolate this verbatim, so the two ports stay byte-for-byte
+ * identical. Axis names reaching these rules are single-quote-free, so the
+ * plain single-quoted element form is exact.
+ */
+export function formatNameList(names) {
+    return `[${names.map((name) => `'${name}'`).join(", ")}]`;
+}
+//# sourceMappingURL=py_format.js.map

package/esm/utils/py_format.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"py_format.js","sourceRoot":"","sources":["../../src/utils/py_format.ts"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,+BAA+B;AAC/B;;;;;GAKG;AAEH;;;;;;;;;GASG;AACH,MAAM,UAAU,cAAc,CAAC,KAAwB;IACrD,OAAO,IAAI,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,IAAI,GAAG,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC;AAC5D,CAAC"}

package/esm/utils/rfc4_validation.d.ts

@@ -13,6 +13,14 @@ export declare function hasRfc4OrientationMetadata(axes: Array<Record<string, un
 /**
  * Validate RFC 4 anatomical orientation metadata.
  *
+ * The two inconsistency errors carry stable marker substrings -- `same type`
+ * for a mixed-`type` failure and `all spatial axes` for the all-or-none
+ * completeness failure -- that `validateAxisOrientation` reads to map each
+ * failure onto its `SpecRule`. These markers are a load-bearing contract
+ * pinned by a message-stability test (see
+ * `structural_validation_orientation_test.ts`) so the mapping cannot silently
+ * break if the wording is later edited.
+ *
  * @param axes - List of axis metadata dictionaries to validate
  * @throws Error if the orientation metadata is invalid or inconsistent
  */

package/esm/utils/rfc4_validation.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"rfc4_validation.d.ts","sourceRoot":"","sources":["../../src/utils/rfc4_validation.ts"],"names":[],"mappings":"AAEA;;;;GAIG;AA0BH;;;;;GAKG;AACH,wBAAgB,0BAA0B,CACxC,IAAI,EAAE,KAAK,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,GACnC,OAAO,CAYT;AAED;;;;;GAKG;AACH,wBAAgB,uBAAuB,CACrC,IAAI,EAAE,KAAK,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,GACnC,IAAI,CA0DN"}
+{"version":3,"file":"rfc4_validation.d.ts","sourceRoot":"","sources":["../../src/utils/rfc4_validation.ts"],"names":[],"mappings":"AAEA;;;;GAIG;AA2BH;;;;;GAKG;AACH,wBAAgB,0BAA0B,CACxC,IAAI,EAAE,KAAK,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,GACnC,OAAO,CAYT;AAED;;;;;;;;;;;;;GAaG;AACH,wBAAgB,uBAAuB,CACrC,IAAI,EAAE,KAAK,CAAC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC,GACnC,IAAI,CA4DN"}

package/esm/utils/rfc4_validation.js

@@ -6,6 +6,7 @@
  * This module provides validation for RFC 4 anatomical orientation metadata.
  */
 import { AnatomicalOrientationValuesSchema } from "../schemas/rfc4.js";
+import { formatNameList } from "./py_format.js";
 /** Valid anatomical orientation values */
 const VALID_ORIENTATION_VALUES = new Set([
     "left-to-right",
@@ -47,6 +48,14 @@ export function hasRfc4OrientationMetadata(axes) {
 /**
  * Validate RFC 4 anatomical orientation metadata.
  *
+ * The two inconsistency errors carry stable marker substrings -- `same type`
+ * for a mixed-`type` failure and `all spatial axes` for the all-or-none
+ * completeness failure -- that `validateAxisOrientation` reads to map each
+ * failure onto its `SpecRule`. These markers are a load-bearing contract
+ * pinned by a message-stability test (see
+ * `structural_validation_orientation_test.ts`) so the mapping cannot silently
+ * break if the wording is later edited.
+ *
  * @param axes - List of axis metadata dictionaries to validate
  * @throws Error if the orientation metadata is invalid or inconsistent
  */
@@ -91,8 +100,10 @@ export function validateRfc4Orientation(axes) {
     if (hasOrientation && spatialAxesWithoutOrientation.length > 0) {
         throw new Error(`RFC 4 requires that if orientation is defined for one spatial axis, ` +
             `it must be defined for all spatial axes. ` +
-            `Axes with orientation: ${spatialAxesWithOrientation.join(", ")}, ` +
-            `axes without orientation: ${spatialAxesWithoutOrientation.join(", ")}`);
+            `Axes with orientation: ` +
+            `${formatNameList(spatialAxesWithOrientation)}, ` +
+            `axes without orientation: ` +
+            `${formatNameList(spatialAxesWithoutOrientation)}`);
     }
 }
 //# sourceMappingURL=rfc4_validation.js.map