@fideus-labs/ngff-zarr 0.17.0 → 0.19.0

package/esm/utils/factory.js

@@ -3,7 +3,7 @@
 import * as zarr from "zarrita";
 import { defaultCodecs } from "../utils/codecs.js";
 import { NgffImage } from "../types/ngff_image.js";
-import { Multiscales } from "../types/multiscales.js";
+import { NgffMultiscales } from "../types/multiscales.js";
 // Create a zarr.Array for testing using an in-memory store
 async function createTestZarrArray(shape, dtype, chunks, name) {
     const store = new Map();
@@ -71,8 +71,8 @@ export function createMetadata(axes, datasets, name = "image", version = "0.4")
         version,
     };
 }
-export function createMultiscales(images, metadata, scaleFactors, method) {
-    return new Multiscales({
+export function createNgffMultiscales(images, metadata, scaleFactors, method) {
+    return new NgffMultiscales({
         images: [...images],
         metadata,
         scaleFactors: scaleFactors || undefined,
@@ -80,4 +80,6 @@ export function createMultiscales(images, metadata, scaleFactors, method) {
         chunks: undefined,
     });
 }
+// Backwards-compatible alias
+export const createMultiscales = createNgffMultiscales;
 //# sourceMappingURL=factory.js.map

package/esm/utils/factory.js.map

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

@@ -1 +1 @@
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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

package/esm/utils/rfc4_validation.js.map

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