@fideus-labs/ngff-zarr 0.19.0 → 0.22.0

package/esm/utils/structural_validation.js

@@ -53,6 +53,10 @@ export const SpecRule = {
     AxisOrientationConsistentType: "axis-orientation-consistent-type",
     /** If any spatial axis declares an orientation, all spatial axes do. */
     AxisOrientationCompleteness: "axis-orientation-completeness",
+    /** A v0.5 entry implies a Zarr v3 store: a leaked `zarr_format` must be 3. */
+    ZarrFormat: "zarr-format",
+    /** A v0.5 entry must not retain a group-level `ome`/`multiscales` wrapper. */
+    OmeNamespace: "ome-namespace",
     /** Each well's rowIndex/columnIndex agrees with the row/column in its path. */
     PlateRowIndexConsistency: "plate-row-index-consistency",
     /** Each well image references an acquisition when the plate declares many. */
@@ -530,6 +534,64 @@ function pyRepr(value) {
     const escaped = value.replaceAll("\\", "\\\\").replaceAll(quote, `\\${quote}`);
     return `${quote}${escaped}${quote}`;
 }
+/**
+ * Validate that a v0.5 multiscales entry implies a Zarr v3 store.
+ *
+ * OME-Zarr v0.5 metadata MUST be backed by a Zarr v3 store
+ * (`zarr_format === 3`). A v0.4 dataset is always Zarr v2 and carries no
+ * `zarr_format`, so this rule is inert below v0.5. The parsed {@link Metadata}
+ * does not surface the group's `zarr_format` byte -- its authoritative on-disk
+ * verification is a store-backed concern -- but a `zarr_format` mis-embedded
+ * *inside* the multiscale entry (captured in {@link Metadata.extra}) is
+ * reachable here: it belongs on the enclosing Zarr v3 group, never on the entry,
+ * and any value other than `3` is incompatible with v0.5.
+ *
+ * @param metadata - The parsed multiscales metadata to validate.
+ * @throws {ValidationError} With {@link SpecRule.ZarrFormat} when v0.5 metadata
+ * carries a `zarr_format` other than `3` in its `extra` passthrough; location
+ * `multiscales[0]`.
+ */
+export function validateZarrFormatForVersion(metadata) {
+    if (metadata.version !== "0.5") {
+        return;
+    }
+    const zarrFormat = metadata.extra?.zarr_format;
+    if (zarrFormat !== undefined && zarrFormat !== 3) {
+        throw new ValidationError(SpecRule.ZarrFormat, `OME-Zarr v0.5 requires a Zarr v3 store (zarr_format == 3), but ` +
+            `the entry declares zarr_format = ${String(zarrFormat)}.`, "multiscales[0]");
+    }
+}
+/**
+ * Validate that a v0.5 multiscales entry is not double-namespaced.
+ *
+ * At v0.5 the multiscales metadata lives under the top-level `ome` namespace key
+ * of the group's `zarr.json` attributes, with the spec `version` hoisted to
+ * `ome.version`. The reader unwraps that namespace into this {@link Metadata}, so
+ * the group-level wrapper keys -- `ome` itself and the `multiscales` array --
+ * must never reappear *inside* a multiscale entry. A surviving wrapper key
+ * (captured in {@link Metadata.extra}) means the document is double-namespaced,
+ * was not unwrapped, or is otherwise malformed with respect to the v0.5 `ome`
+ * namespacing. A v0.4 store keeps multiscales at the `.zattrs` top level with no
+ * `ome` wrapper, so this rule is inert below v0.5.
+ *
+ * @param metadata - The parsed multiscales metadata to validate.
+ * @throws {ValidationError} With {@link SpecRule.OmeNamespace} when v0.5 metadata
+ * retains a group-level `ome` or `multiscales` key in its `extra` passthrough;
+ * location `multiscales[0]`.
+ */
+export function validateOmeNamespace(metadata) {
+    if (metadata.version !== "0.5") {
+        return;
+    }
+    const extra = metadata.extra ?? {};
+    for (const wrapperKey of ["ome", "multiscales"]) {
+        if (wrapperKey in extra) {
+            throw new ValidationError(SpecRule.OmeNamespace, `v0.5 metadata entry retains the group-level '${wrapperKey}' ` +
+                `key; the 'ome' namespace wraps the group attributes, not each ` +
+                `multiscale entry.`, "multiscales[0]");
+        }
+    }
+}
 /**
  * Validate each plate well's recorded indices against its `path`.
  *
@@ -627,6 +689,11 @@ export function validateWellAcquisition(plate, well) {
  * 8. {@link validateDatasetOrder}
  * 9. {@link validateOmeroColorHex}
  * 10. {@link validateAxisOrientation}
+ * 11. {@link validateZarrFormatForVersion}
+ * 12. {@link validateOmeNamespace}
+ *
+ * Rules 11 and 12 are the OME-Zarr v0.5 namespacing checks; they fire only for
+ * v0.5 metadata and are inert (a no-op) for v0.4.
  *
  * Under {@link ValidationLevel.SchemaOnly} this function returns immediately
  * without running any structural rule -- shape/schema validation is the
@@ -664,6 +731,8 @@ export function validateStructural(metadata, options) {
     validateDatasetOrder(metadata);
     validateOmeroColorHex(metadata);
     validateAxisOrientation(metadata);
+    validateZarrFormatForVersion(metadata);
+    validateOmeNamespace(metadata);
 }
 /**
  * Run the structural HCS plate rules in canonical specification order.

package/esm/utils/structural_validation.js.map

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package/esm/utils/v06_metadata.d.ts

@@ -0,0 +1,44 @@
+/**
+ * RFC 5 / OME-Zarr v0.6 coordinate-transformation serialization helpers.
+ *
+ * The in-memory {@link MetadataInterface} model is version-agnostic: axes plus a
+ * per-dataset scale and translation. On the wire, v0.6 instead carries
+ * `coordinateSystems` and represents each dataset's mapping into the implicit
+ * "intrinsic" system as a `sequence` of scale + translation. These helpers
+ * convert between the two, mirroring `py/ngff_zarr/v06/zarr_metadata.py`.
+ */
+import type { MetadataInterface, Transform, V06Transform } from "../types/zarr_metadata.js";
+/**
+ * Build the on-disk v0.6 `multiscales[0]` entry from the version-agnostic
+ * in-memory metadata. `processedAxes` are the RFC-processed axes (orientation
+ * filtered per enabled RFCs); they back the intrinsic coordinate system so v0.6
+ * matches the v0.4/v0.5 writers.
+ */
+export declare function buildV06MultiscalesEntry(metadata: MetadataInterface, processedAxes: Array<Record<string, unknown>>): Record<string, unknown>;
+/** Serialize a single v0.6 transformation to its on-disk dictionary form. */
+export declare function serializeV06Transform(transform: V06Transform): Record<string, unknown>;
+/**
+ * Parse a list of (possibly nested) v0.6 transformation dictionaries into typed
+ * {@link V06Transform}s. `coordinateSystemNames` gates which `input`/`output`
+ * `name` references are retained, matching the Python `_parse_transforms`: a
+ * `name` is kept only when it identifies a known coordinate system, while a
+ * `path` (a dataset array reference) is always kept.
+ */
+export declare function parseV06Transforms(raw: Array<Record<string, unknown>>, coordinateSystemNames: string[]): V06Transform[];
+/**
+ * Extract the effective scale and translation from a dataset's v0.6
+ * transformations (unwrapping a `sequence`), defaulting to identity. Mirrors
+ * the convenience extraction in the Python `_from_zarr_attrs`.
+ */
+export declare function extractScaleTranslation(transforms: V06Transform[], dims: string[]): {
+    scale: number[];
+    translation: number[];
+};
+/**
+ * Reduce v0.6 top-level transformations to the simple scale/translation subset
+ * permitted by v0.4/v0.5, dropping richer transforms (rotation, affine,
+ * sequence) and the coordinate-system references they carry. Used when writing
+ * a value read at v0.6 back out at an older version.
+ */
+export declare function legacyTopLevelTransforms(transforms: V06Transform[] | undefined): Transform[] | undefined;
+//# sourceMappingURL=v06_metadata.d.ts.map

package/esm/utils/v06_metadata.d.ts.map

@@ -0,0 +1 @@
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package/esm/utils/v06_metadata.js

@@ -0,0 +1,293 @@
+// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
+// SPDX-License-Identifier: MIT
+import { INTRINSIC_COORDINATE_SYSTEM_NAME } from "../types/zarr_metadata.js";
+/**
+ * Build the on-disk v0.6 `multiscales[0]` entry from the version-agnostic
+ * in-memory metadata. `processedAxes` are the RFC-processed axes (orientation
+ * filtered per enabled RFCs); they back the intrinsic coordinate system so v0.6
+ * matches the v0.4/v0.5 writers.
+ */
+export function buildV06MultiscalesEntry(metadata, processedAxes) {
+    const coordinateSystems = metadata.coordinateSystems && metadata.coordinateSystems.length > 0
+        ? metadata.coordinateSystems
+        : [{ name: INTRINSIC_COORDINATE_SYSTEM_NAME, axes: metadata.axes }];
+    const intrinsicName = coordinateSystems[0].name;
+    // The first (intrinsic) coordinate system uses the RFC-processed axes; any
+    // additional systems (e.g. a user-supplied output space) are serialized
+    // verbatim.
+    const serializedCoordinateSystems = coordinateSystems.map((cs, index) => ({
+        name: cs.name,
+        axes: index === 0 ? processedAxes : cs.axes,
+    }));
+    const datasets = metadata.datasets.map((ds, index) => {
+        let scale;
+        let translation;
+        for (const transform of ds.coordinateTransformations) {
+            if (transform.type === "scale") {
+                scale = transform.scale;
+            }
+            else if (transform.type === "translation") {
+                translation = transform.translation;
+            }
+        }
+        const transformations = [];
+        if (scale !== undefined) {
+            transformations.push({ type: "scale", scale });
+        }
+        if (translation !== undefined) {
+            transformations.push({ type: "translation", translation });
+        }
+        return {
+            path: ds.path,
+            coordinateTransformations: [
+                {
+                    type: "sequence",
+                    name: `scale${index}_to_${intrinsicName}`,
+                    input: { path: ds.path },
+                    output: { name: intrinsicName },
+                    transformations,
+                },
+            ],
+        };
+    });
+    const entry = {
+        name: metadata.name,
+        coordinateSystems: serializedCoordinateSystems,
+        datasets,
+    };
+    if (metadata.coordinateTransformations &&
+        metadata.coordinateTransformations.length > 0) {
+        entry.coordinateTransformations = metadata.coordinateTransformations.map(serializeV06Transform);
+    }
+    if (metadata.type !== undefined) {
+        entry.type = metadata.type;
+    }
+    if (metadata.metadata !== undefined) {
+        entry.metadata = metadata.metadata;
+    }
+    return entry;
+}
+/** Serialize a single v0.6 transformation to its on-disk dictionary form. */
+export function serializeV06Transform(transform) {
+    const out = { type: transform.type };
+    if (transform.name !== undefined) {
+        out.name = transform.name;
+    }
+    if (transform.input !== undefined) {
+        const input = identifierToDict(transform.input);
+        if (input !== undefined) {
+            out.input = input;
+        }
+    }
+    if (transform.output !== undefined) {
+        const output = identifierToDict(transform.output);
+        if (output !== undefined) {
+            out.output = output;
+        }
+    }
+    switch (transform.type) {
+        case "identity":
+            break;
+        case "scale":
+            out.scale = transform.scale;
+            break;
+        case "translation":
+            out.translation = transform.translation;
+            break;
+        case "rotation":
+            out.rotation = transform.rotation;
+            if (transform.path !== undefined) {
+                out.path = transform.path;
+            }
+            break;
+        case "affine":
+            out.affine = transform.affine;
+            if (transform.path !== undefined) {
+                out.path = transform.path;
+            }
+            break;
+        case "sequence":
+            out.transformations = transform.transformations.map(serializeV06Transform);
+            break;
+    }
+    return out;
+}
+/**
+ * Parse a list of (possibly nested) v0.6 transformation dictionaries into typed
+ * {@link V06Transform}s. `coordinateSystemNames` gates which `input`/`output`
+ * `name` references are retained, matching the Python `_parse_transforms`: a
+ * `name` is kept only when it identifies a known coordinate system, while a
+ * `path` (a dataset array reference) is always kept.
+ */
+export function parseV06Transforms(raw, coordinateSystemNames) {
+    return raw.map((entry) => parseV06Transform(entry, coordinateSystemNames));
+}
+function parseV06Transform(entry, coordinateSystemNames) {
+    const type = String(entry.type);
+    let transform;
+    switch (type) {
+        case "identity":
+            transform = { type: "identity" };
+            break;
+        case "scale":
+            transform = { type: "scale", scale: asNumberArray(entry.scale, "scale") };
+            break;
+        case "translation":
+            transform = {
+                type: "translation",
+                translation: asNumberArray(entry.translation, "translation"),
+            };
+            break;
+        case "rotation":
+            transform = {
+                type: "rotation",
+                rotation: asNumberMatrix(entry.rotation, "rotation"),
+            };
+            if (typeof entry.path === "string") {
+                transform.path = entry.path;
+            }
+            break;
+        case "affine":
+            transform = {
+                type: "affine",
+                affine: asNumberMatrix(entry.affine, "affine"),
+            };
+            if (typeof entry.path === "string") {
+                transform.path = entry.path;
+            }
+            break;
+        case "sequence":
+            if (!Array.isArray(entry.transformations)) {
+                throw new Error("Invalid sequence transform: 'transformations' must be an array");
+            }
+            transform = {
+                type: "sequence",
+                transformations: parseV06Transforms(entry.transformations, coordinateSystemNames),
+            };
+            break;
+        default:
+            throw new Error(`Unsupported transform type: ${type}`);
+    }
+    const input = dictToIdentifier(entry.input, coordinateSystemNames);
+    if (input !== undefined) {
+        transform.input = input;
+    }
+    const output = dictToIdentifier(entry.output, coordinateSystemNames);
+    if (output !== undefined) {
+        transform.output = output;
+    }
+    if (typeof entry.name === "string") {
+        transform.name = entry.name;
+    }
+    return transform;
+}
+/**
+ * Extract the effective scale and translation from a dataset's v0.6
+ * transformations (unwrapping a `sequence`), defaulting to identity. Mirrors
+ * the convenience extraction in the Python `_from_zarr_attrs`.
+ */
+export function extractScaleTranslation(transforms, dims) {
+    let scale = dims.map(() => 1.0);
+    let translation = dims.map(() => 0.0);
+    for (const transform of transforms) {
+        if (transform.type === "sequence") {
+            for (const sub of transform.transformations) {
+                if (sub.type === "scale") {
+                    scale = sub.scale;
+                }
+                else if (sub.type === "identity") {
+                    // Within a sequence an identity resets only the scale, not the
+                    // translation, matching the Python reference `_from_zarr_attrs`. A
+                    // sibling translation composes with the identity (identity ∘
+                    // translation = translation), so it must be preserved. Spec-conformant
+                    // dataset sequences are `[scale, translation]` and never include an
+                    // identity, so this branch is defensive.
+                    scale = dims.map(() => 1.0);
+                }
+                else if (sub.type === "translation") {
+                    translation = sub.translation;
+                }
+            }
+        }
+        else if (transform.type === "scale") {
+            scale = transform.scale;
+        }
+        else if (transform.type === "translation") {
+            translation = transform.translation;
+        }
+        else if (transform.type === "identity") {
+            scale = dims.map(() => 1.0);
+            translation = dims.map(() => 0.0);
+        }
+    }
+    return { scale, translation };
+}
+/**
+ * Reduce v0.6 top-level transformations to the simple scale/translation subset
+ * permitted by v0.4/v0.5, dropping richer transforms (rotation, affine,
+ * sequence) and the coordinate-system references they carry. Used when writing
+ * a value read at v0.6 back out at an older version.
+ */
+export function legacyTopLevelTransforms(transforms) {
+    if (!transforms) {
+        return undefined;
+    }
+    const simple = [];
+    for (const transform of transforms) {
+        if (transform.type === "scale") {
+            simple.push({ type: "scale", scale: transform.scale });
+        }
+        else if (transform.type === "translation") {
+            simple.push({ type: "translation", translation: transform.translation });
+        }
+    }
+    return simple.length > 0 ? simple : undefined;
+}
+/**
+ * Validate that a parsed transform field is a flat array of numbers. The reader
+ * consumes untrusted on-disk metadata, so a malformed value (missing, a string,
+ * a nested array) is rejected with a clear message rather than passed through an
+ * unchecked `as number[]` cast that surfaces as a confusing error downstream.
+ */
+function asNumberArray(value, field) {
+    if (!Array.isArray(value) || !value.every((v) => typeof v === "number")) {
+        throw new Error(`Invalid ${field} transform: '${field}' must be an array of numbers`);
+    }
+    return value;
+}
+/** Validate that a parsed transform field is a 2D array of numbers. */
+function asNumberMatrix(value, field) {
+    if (!Array.isArray(value) ||
+        !value.every((row) => Array.isArray(row) && row.every((v) => typeof v === "number"))) {
+        throw new Error(`Invalid ${field} transform: '${field}' must be a 2D array of numbers`);
+    }
+    return value;
+}
+function identifierToDict(id) {
+    const out = {};
+    if (id.path !== undefined) {
+        out.path = id.path;
+    }
+    if (id.name !== undefined) {
+        out.name = id.name;
+    }
+    // An identifier carrying neither `path` nor `name` is meaningless and invalid
+    // per the v0.6 schema (input requires a path, output requires a name); omit
+    // it rather than emitting `input: {}` / `output: {}`.
+    return out.path !== undefined || out.name !== undefined ? out : undefined;
+}
+function dictToIdentifier(value, coordinateSystemNames) {
+    if (value === null || typeof value !== "object") {
+        return undefined;
+    }
+    const dict = value;
+    const id = {};
+    if (typeof dict.name === "string" && coordinateSystemNames.includes(dict.name)) {
+        id.name = dict.name;
+    }
+    if (typeof dict.path === "string") {
+        id.path = dict.path;
+    }
+    return id.name !== undefined || id.path !== undefined ? id : undefined;
+}
+//# sourceMappingURL=v06_metadata.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@fideus-labs/ngff-zarr",
-  "version": "0.19.0",
+  "version": "0.22.0",
   "description": "TypeScript implementation of ngff-zarr for reading and writing OME-Zarr files",
   "license": "MIT",
   "type": "module",