@fideus-labs/ngff-zarr 0.18.1 → 0.20.0

package/esm/types/zarr_metadata.d.ts

@@ -65,6 +65,14 @@ export interface MetadataInterface {
     version: string;
     type?: string;
     metadata?: MethodMetadata;
+    /**
+     * Unrecognized keys that leaked into the `multiscales[]` entry (a malformed
+     * or double-namespaced v0.5 document). Captured verbatim so the v0.5
+     * namespacing rules (`zarr-format`, `ome-namespace`) can flag them; mirrors
+     * the Rust port's `#[serde(flatten)]` `extra` passthrough. It is a read-side
+     * validation aid only and is never serialized back to the store.
+     */
+    extra?: Record<string, unknown>;
 }
 /**
  * Result from parsing zarr attributes

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

@@ -1 +1 @@
-{"version":3,"file":"zarr_metadata.d.ts","sourceRoot":"","sources":["../../src/types/zarr_metadata.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,QAAQ,EAAE,aAAa,EAAE,KAAK,EAAE,MAAM,YAAY,CAAC;AACjE,OAAO,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AACtD,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAC;AACjD,OAAO,KAAK,EAAE,qBAAqB,EAAE,MAAM,WAAW,CAAC;AAEvD;;;GAGG;AACH,MAAM,WAAW,eAAe;IAC9B,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,CAAC;CACf;AAED,MAAM,WAAW,IAAI;IACnB,IAAI,EAAE,aAAa,CAAC;IACpB,IAAI,EAAE,QAAQ,CAAC;IACf,IAAI,EAAE,KAAK,GAAG,SAAS,CAAC;IACxB,WAAW,CAAC,EAAE,eAAe,GAAG,qBAAqB,GAAG,SAAS,CAAC;CACnE;AAED,MAAM,WAAW,QAAQ;IACvB,IAAI,EAAE,UAAU,CAAC;CAClB;AAED,MAAM,WAAW,KAAK;IACpB,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,IAAI,EAAE,OAAO,CAAC;CACf;AAED,MAAM,WAAW,WAAW;IAC1B,WAAW,EAAE,MAAM,EAAE,CAAC;IACtB,IAAI,EAAE,aAAa,CAAC;CACrB;AAED,MAAM,MAAM,SAAS,GAAG,KAAK,GAAG,WAAW,CAAC;AAE5C,MAAM,WAAW,OAAO;IACtB,IAAI,EAAE,MAAM,CAAC;IACb,yBAAyB,EAAE,SAAS,EAAE,CAAC;CACxC;AAED,MAAM,WAAW,WAAW;IAC1B,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,GAAG,CAAC,EAAE,MAAM,CAAC;CACd;AAED,MAAM,WAAW,YAAY;IAC3B,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,WAAW,CAAC;IACpB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAED,MAAM,WAAW,KAAK;IACpB,QAAQ,EAAE,YAAY,EAAE,CAAC;IACzB,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAED,MAAM,WAAW,cAAc;IAC7B,WAAW,EAAE,MAAM,CAAC;IACpB,MAAM,EAAE,MAAM,CAAC;IACf,OAAO,EAAE,MAAM,CAAC;CACjB;AAED;;GAEG;AACH,MAAM,WAAW,iBAAiB;IAChC,IAAI,EAAE,IAAI,EAAE,CAAC;IACb,QAAQ,EAAE,OAAO,EAAE,CAAC;IACpB,yBAAyB,EAAE,SAAS,EAAE,GAAG,SAAS,CAAC;IACnD,KAAK,EAAE,KAAK,GAAG,SAAS,CAAC;IACzB,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,QAAQ,CAAC,EAAE,cAAc,CAAC;CAC3B;AAED;;GAEG;AACH,MAAM,WAAW,mBAAmB;IAClC,QAAQ,EAAE,iBAAiB,CAAC;IAC5B,MAAM,EAAE,SAAS,EAAE,CAAC;CACrB;AAGD,MAAM,MAAM,QAAQ,GAAG,iBAAiB,CAAC;AAEzC;;GAEG;AACH,MAAM,WAAW,mBAAmB;IAClC,QAAQ,EAAE,iBAAiB,CAAC;IAC5B,MAAM,EAAE,SAAS,EAAE,CAAC;CACrB;AAED;;GAEG;AACH,eAAO,MAAM,cAAc,EAAE,SAAS,aAAa,EAMzC,CAAC;AAEX;;GAEG;AACH,wBAAgB,yBAAyB,CACvC,QAAQ,EAAE,iBAAiB,EAC3B,aAAa,EAAE,MAAM,GAAG,WAAW,GAClC,iBAAiB,CAoBnB;AAED;;GAEG;AACH,wBAAgB,iBAAiB,CAAC,QAAQ,EAAE,iBAAiB,GAAG,MAAM,EAAE,CAEvE;AAED,wBAAgB,aAAa,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI,CAIjD;AAED,wBAAgB,WAAW,CAAC,KAAK,EAAE,MAAM,EAAE,GAAG,KAAK,CAElD;AAED,wBAAgB,iBAAiB,CAAC,WAAW,EAAE,MAAM,EAAE,GAAG,WAAW,CAEpE;AAED,wBAAgB,cAAc,IAAI,QAAQ,CAEzC"}
+{"version":3,"file":"zarr_metadata.d.ts","sourceRoot":"","sources":["../../src/types/zarr_metadata.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,QAAQ,EAAE,aAAa,EAAE,KAAK,EAAE,MAAM,YAAY,CAAC;AACjE,OAAO,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AACtD,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAC;AACjD,OAAO,KAAK,EAAE,qBAAqB,EAAE,MAAM,WAAW,CAAC;AAEvD;;;GAGG;AACH,MAAM,WAAW,eAAe;IAC9B,IAAI,EAAE,MAAM,CAAC;IACb,KAAK,EAAE,MAAM,CAAC;CACf;AAED,MAAM,WAAW,IAAI;IACnB,IAAI,EAAE,aAAa,CAAC;IACpB,IAAI,EAAE,QAAQ,CAAC;IACf,IAAI,EAAE,KAAK,GAAG,SAAS,CAAC;IACxB,WAAW,CAAC,EAAE,eAAe,GAAG,qBAAqB,GAAG,SAAS,CAAC;CACnE;AAED,MAAM,WAAW,QAAQ;IACvB,IAAI,EAAE,UAAU,CAAC;CAClB;AAED,MAAM,WAAW,KAAK;IACpB,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,IAAI,EAAE,OAAO,CAAC;CACf;AAED,MAAM,WAAW,WAAW;IAC1B,WAAW,EAAE,MAAM,EAAE,CAAC;IACtB,IAAI,EAAE,aAAa,CAAC;CACrB;AAED,MAAM,MAAM,SAAS,GAAG,KAAK,GAAG,WAAW,CAAC;AAE5C,MAAM,WAAW,OAAO;IACtB,IAAI,EAAE,MAAM,CAAC;IACb,yBAAyB,EAAE,SAAS,EAAE,CAAC;CACxC;AAED,MAAM,WAAW,WAAW;IAC1B,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,GAAG,CAAC,EAAE,MAAM,CAAC;IACb,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,GAAG,CAAC,EAAE,MAAM,CAAC;CACd;AAED,MAAM,WAAW,YAAY;IAC3B,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,WAAW,CAAC;IACpB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAED,MAAM,WAAW,KAAK;IACpB,QAAQ,EAAE,YAAY,EAAE,CAAC;IACzB,OAAO,CAAC,EAAE,MAAM,CAAC;CAClB;AAED,MAAM,WAAW,cAAc;IAC7B,WAAW,EAAE,MAAM,CAAC;IACpB,MAAM,EAAE,MAAM,CAAC;IACf,OAAO,EAAE,MAAM,CAAC;CACjB;AAED;;GAEG;AACH,MAAM,WAAW,iBAAiB;IAChC,IAAI,EAAE,IAAI,EAAE,CAAC;IACb,QAAQ,EAAE,OAAO,EAAE,CAAC;IACpB,yBAAyB,EAAE,SAAS,EAAE,GAAG,SAAS,CAAC;IACnD,KAAK,EAAE,KAAK,GAAG,SAAS,CAAC;IACzB,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,MAAM,CAAC;IACd,QAAQ,CAAC,EAAE,cAAc,CAAC;IAC1B;;;;;;OAMG;IACH,KAAK,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;CACjC;AAED;;GAEG;AACH,MAAM,WAAW,mBAAmB;IAClC,QAAQ,EAAE,iBAAiB,CAAC;IAC5B,MAAM,EAAE,SAAS,EAAE,CAAC;CACrB;AAGD,MAAM,MAAM,QAAQ,GAAG,iBAAiB,CAAC;AAEzC;;GAEG;AACH,MAAM,WAAW,mBAAmB;IAClC,QAAQ,EAAE,iBAAiB,CAAC;IAC5B,MAAM,EAAE,SAAS,EAAE,CAAC;CACrB;AAED;;GAEG;AACH,eAAO,MAAM,cAAc,EAAE,SAAS,aAAa,EAMzC,CAAC;AAEX;;GAEG;AACH,wBAAgB,yBAAyB,CACvC,QAAQ,EAAE,iBAAiB,EAC3B,aAAa,EAAE,MAAM,GAAG,WAAW,GAClC,iBAAiB,CAoBnB;AAED;;GAEG;AACH,wBAAgB,iBAAiB,CAAC,QAAQ,EAAE,iBAAiB,GAAG,MAAM,EAAE,CAEvE;AAED,wBAAgB,aAAa,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI,CAIjD;AAED,wBAAgB,WAAW,CAAC,KAAK,EAAE,MAAM,EAAE,GAAG,KAAK,CAElD;AAED,wBAAgB,iBAAiB,CAAC,WAAW,EAAE,MAAM,EAAE,GAAG,WAAW,CAEpE;AAED,wBAAgB,cAAc,IAAI,QAAQ,CAEzC"}

package/esm/types/zarr_metadata.js.map

@@ -1 +1 @@
-{"version":3,"file":"zarr_metadata.js","sourceRoot":"","sources":["../../src/types/zarr_metadata.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AAmGtD;;GAEG;AACH,MAAM,CAAC,MAAM,cAAc,GAA6B;IACtD,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;CACK,CAAC;AAEX;;GAEG;AACH,MAAM,UAAU,yBAAyB,CACvC,QAA2B,EAC3B,aAAmC;IAEnC,MAAM,OAAO,GAAG,OAAO,aAAa,KAAK,QAAQ;QAC/C,CAAC,CAAE,aAA6B;QAChC,CAAC,CAAC,aAAa,CAAC;IAElB,IAAI,OAAO,KAAK,WAAW,CAAC,GAAG,EAAE,CAAC;QAChC,OAAO;YACL,GAAG,QAAQ;YACX,OAAO,EAAE,KAAK;SACf,CAAC;IACJ,CAAC;SAAM,IAAI,OAAO,KAAK,WAAW,CAAC,GAAG,EAAE,CAAC;QACvC,OAAO;YACL,GAAG,QAAQ;YACX,OAAO,EAAE,KAAK;SACf,CAAC;IACJ,CAAC;SAAM,CAAC;QACN,MAAM,IAAI,KAAK,CACb,mCAAmC,QAAQ,CAAC,OAAO,OAAO,OAAO,EAAE,CACpE,CAAC;IACJ,CAAC;AACH,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,iBAAiB,CAAC,QAA2B;IAC3D,OAAO,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC;AAC5C,CAAC;AAED,MAAM,UAAU,aAAa,CAAC,KAAa;IACzC,IAAI,CAAC,kBAAkB,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;QACpC,MAAM,IAAI,KAAK,CAAC,kBAAkB,KAAK,0BAA0B,CAAC,CAAC;IACrE,CAAC;AACH,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,KAAe;IACzC,OAAO,EAAE,KAAK,EAAE,CAAC,GAAG,KAAK,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,CAAC;AAC9C,CAAC;AAED,MAAM,UAAU,iBAAiB,CAAC,WAAqB;IACrD,OAAO,EAAE,WAAW,EAAE,CAAC,GAAG,WAAW,CAAC,EAAE,IAAI,EAAE,aAAa,EAAE,CAAC;AAChE,CAAC;AAED,MAAM,UAAU,cAAc;IAC5B,OAAO,EAAE,IAAI,EAAE,UAAU,EAAE,CAAC;AAC9B,CAAC"}
+{"version":3,"file":"zarr_metadata.js","sourceRoot":"","sources":["../../src/types/zarr_metadata.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AA2GtD;;GAEG;AACH,MAAM,CAAC,MAAM,cAAc,GAA6B;IACtD,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;IACH,GAAG;CACK,CAAC;AAEX;;GAEG;AACH,MAAM,UAAU,yBAAyB,CACvC,QAA2B,EAC3B,aAAmC;IAEnC,MAAM,OAAO,GAAG,OAAO,aAAa,KAAK,QAAQ;QAC/C,CAAC,CAAE,aAA6B;QAChC,CAAC,CAAC,aAAa,CAAC;IAElB,IAAI,OAAO,KAAK,WAAW,CAAC,GAAG,EAAE,CAAC;QAChC,OAAO;YACL,GAAG,QAAQ;YACX,OAAO,EAAE,KAAK;SACf,CAAC;IACJ,CAAC;SAAM,IAAI,OAAO,KAAK,WAAW,CAAC,GAAG,EAAE,CAAC;QACvC,OAAO;YACL,GAAG,QAAQ;YACX,OAAO,EAAE,KAAK;SACf,CAAC;IACJ,CAAC;SAAM,CAAC;QACN,MAAM,IAAI,KAAK,CACb,mCAAmC,QAAQ,CAAC,OAAO,OAAO,OAAO,EAAE,CACpE,CAAC;IACJ,CAAC;AACH,CAAC;AAED;;GAEG;AACH,MAAM,UAAU,iBAAiB,CAAC,QAA2B;IAC3D,OAAO,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,IAAI,CAAC,CAAC;AAC5C,CAAC;AAED,MAAM,UAAU,aAAa,CAAC,KAAa;IACzC,IAAI,CAAC,kBAAkB,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;QACpC,MAAM,IAAI,KAAK,CAAC,kBAAkB,KAAK,0BAA0B,CAAC,CAAC;IACrE,CAAC;AACH,CAAC;AAED,MAAM,UAAU,WAAW,CAAC,KAAe;IACzC,OAAO,EAAE,KAAK,EAAE,CAAC,GAAG,KAAK,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,CAAC;AAC9C,CAAC;AAED,MAAM,UAAU,iBAAiB,CAAC,WAAqB;IACrD,OAAO,EAAE,WAAW,EAAE,CAAC,GAAG,WAAW,CAAC,EAAE,IAAI,EAAE,aAAa,EAAE,CAAC;AAChE,CAAC;AAED,MAAM,UAAU,cAAc;IAC5B,OAAO,EAAE,IAAI,EAAE,UAAU,EAAE,CAAC;AAC9B,CAAC"}

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;AA4H3D;;;;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,CAkU9B;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,CAuC9B"}

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
@@ -31,6 +32,12 @@ const ORIENTATION_VALUE_MAP = {
     "caudal-to-cranial": AnatomicalOrientationValues.CaudalToCranial,
     "proximal-to-distal": AnatomicalOrientationValues.ProximalToDistal,
     "distal-to-proximal": AnatomicalOrientationValues.DistalToProximal,
+    "superficial-to-deep": AnatomicalOrientationValues.SuperficialToDeep,
+    "deep-to-superficial": AnatomicalOrientationValues.DeepToSuperficial,
+    "apical-to-basal": AnatomicalOrientationValues.ApicalToBasal,
+    "basal-to-apical": AnatomicalOrientationValues.BasalToApical,
+    "apex-to-base": AnatomicalOrientationValues.ApexToBase,
+    "base-to-apex": AnatomicalOrientationValues.BaseToApex,
 };
 /**
  * Extract anatomical orientations from axes metadata.
@@ -60,6 +67,48 @@ 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);
+}
+/**
+ * Recognized keys of a single `multiscales[]` entry. Any other key present in an
+ * entry is a leak -- a group-level `ome` / `multiscales` wrapper, a
+ * `zarr_format` byte that belongs on the enclosing Zarr v3 group, and so on --
+ * and is routed to `Metadata.extra` for the v0.5 namespacing rules to inspect.
+ * `omero` is absent on purpose: it is a sibling of `multiscales`, parsed
+ * separately, never a field of the entry. `@type` *is* recognized: the Python
+ * writer stamps the JSON-LD `@type` (`"ngff:Image"`) onto every entry, so it is
+ * a legitimate library-written key, not a leak.
+ */
+const MULTISCALE_ENTRY_FIELDS = new Set([
+    "@type",
+    "version",
+    "name",
+    "axes",
+    "datasets",
+    "coordinateTransformations",
+    "type",
+    "metadata",
+]);
 /**
  * Parse Metadata and NgffImages from OME-Zarr v0.4 root attributes.
  *
@@ -143,6 +192,13 @@ 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 }
+                        : {}),
                 };
             });
         }
@@ -268,13 +324,31 @@ export async function fromZarrAttrsV04(rootAttrs, store, validate = false) {
         });
         images.push(ngffImage);
     }
+    // Keys that a malformed or double-namespaced document leaked into the
+    // multiscale entry -- e.g. a group-level `ome` / `multiscales` wrapper, or a
+    // `zarr_format` byte that belongs on the enclosing Zarr v3 group, never on the
+    // entry. Captured verbatim so the v0.5 namespacing rules can flag them.
+    const extra = {};
+    for (const [key, value] of Object.entries(multiscalesMetadata)) {
+        if (!MULTISCALE_ENTRY_FIELDS.has(key)) {
+            extra[key] = value;
+        }
+    }
     // Build the metadata object - use spread to only include optional properties if defined
     const metadata = {
         axes,
         datasets,
         name: multiscalesMetadata.name ?? "image",
-        version: multiscalesMetadata.version ?? "0.4",
+        // OME-Zarr v0.5 hoists the spec `version` to the group-level `ome`
+        // namespace; v0.4 carries it on each multiscale entry. Prefer the
+        // group-level value (which fromZarrAttrsV05 forwards as a top-level
+        // `version`) so the structural pass sees the true spec version -- which the
+        // v0.5 namespacing rules gate on. v0.4 has no top-level version, so this
+        // falls back to the entry's.
+        version: rootAttrs.version ??
+            multiscalesMetadata.version ?? "0.4",
         omero,
+        extra,
         coordinateTransformations: multiscalesMetadata.coordinateTransformations ??
             undefined,
         ...(multiscalesMetadata.type !== undefined &&
@@ -288,6 +362,16 @@ 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 };
 }
 /**
@@ -302,15 +386,25 @@ export async function fromZarrAttrsV05(rootAttrs, store, validate = false) {
     const omeData = rootAttrs.ome;
     let v04Attrs;
     if (omeData && "multiscales" in omeData) {
-        // Standard v0.5 format with "ome" wrapper
+        // Standard v0.5 format with "ome" wrapper. Forward the hoisted
+        // `ome.version` as a top-level `version` so fromZarrAttrsV04 records the
+        // true spec version (v0.5), which the v0.5 namespacing rules gate on. This
+        // entry point definitionally handles v0.5, so default to "0.5" when
+        // `ome.version` is absent -- otherwise a malformed v0.5 store missing its
+        // version would fall back to "0.4" and skip the v0.5 namespacing rules
+        // during the structural pass (which runs before the version is corrected
+        // below).
         v04Attrs = {
+            version: omeData.version ?? "0.5",
             multiscales: omeData.multiscales,
             omero: omeData.omero ?? rootAttrs.omero,
         };
     }
     else if ("multiscales" in rootAttrs) {
-        // Compatibility mode: multiscales at root level (as written by toNgffZarr)
+        // Compatibility mode: multiscales at root level (as written by toNgffZarr).
+        // Same v0.5 floor as the wrapped branch above.
         v04Attrs = {
+            version: rootAttrs.version ?? "0.5",
             multiscales: rootAttrs.multiscales,
             omero: rootAttrs.omero,
         };

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;AAiCH;;;;;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",
@@ -26,6 +27,12 @@ const VALID_ORIENTATION_VALUES = new Set([
     "caudal-to-cranial",
     "proximal-to-distal",
     "distal-to-proximal",
+    "superficial-to-deep",
+    "deep-to-superficial",
+    "apical-to-basal",
+    "basal-to-apical",
+    "apex-to-base",
+    "base-to-apex",
 ]);
 /**
  * Check if the axes contain RFC 4 anatomical orientation metadata.
@@ -47,6 +54,14 @@ 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 +106,10 @@ 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

package/esm/utils/rfc4_validation.js.map

@@ -1 +1 @@
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