@fideus-labs/ngff-zarr 0.11.0 → 0.12.0

package/esm/mod.js

@@ -1,32 +1,33 @@
 // SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
 // SPDX-License-Identifier: MIT
-export * from "./types/units.js";
-export * from "./types/methods.js";
+export * from "./io/from_ngff_zarr.js";
+export * from "./io/hcs.js";
+export * from "./io/itk_image_to_ngff_image.js";
+export * from "./io/ngff_image_to_itk_image.js";
+// RFC-9 exports
+export { getZipFileCompressionMethod, getZipFileList, isOzxPath, memoryStoreToZip, orderFilesForRfc9, readOzxJsonFirst, readOzxVersion, } from "./io/rfc9_zip.js";
+export * from "./io/to_ngff_zarr.js";
+export * from "./process/to_multiscales-node.js";
+export * from "./schemas/methods.js";
+export * from "./schemas/multiscales.js";
+export * from "./schemas/ngff_image.js";
+export * from "./schemas/units.js";
+export * from "./schemas/zarr_metadata.js";
 export * from "./types/array_interface.js";
-export * from "./types/zarr_metadata.js";
-export * from "./types/ngff_image.js";
+export * from "./types/hcs.js";
+export * from "./types/methods.js";
 export * from "./types/multiscales.js";
+export * from "./types/ngff_image.js";
 export * from "./types/rfc4.js";
-export * from "./types/hcs.js";
 export * from "./types/supported_versions.js";
-export * from "./schemas/units.js";
-export * from "./schemas/methods.js";
-export * from "./schemas/zarr_metadata.js";
-export * from "./schemas/ngff_image.js";
-export * from "./schemas/multiscales.js";
-export { isValidDimension, isValidUnit, validateMetadata, } from "./utils/validation.js";
+export * from "./types/units.js";
+export * from "./types/zarr_metadata.js";
+export { bytesOnlyCodecs, defaultCodecs } from "./utils/codecs.js";
+export { computeOmeroFromMultiscales, computeOmeroFromNgffImage, getDefaultColors, GLASBEY_COLORS, terminateOmeroWorkerPool, } from "./utils/compute_omero.js";
 export { createAxis, createDataset, createMetadata, createMultiscales, createNgffImage, } from "./utils/factory.js";
+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 { computeOmeroFromMultiscales, computeOmeroFromNgffImage, getDefaultColors, GLASBEY_COLORS, terminateOmeroWorkerPool, } from "./utils/compute_omero.js";
-export { fromZarrAttrsV04, fromZarrAttrsV05 } from "./utils/from_zarr_attrs.js";
+export { isValidDimension, isValidUnit, validateMetadata, } from "./utils/validation.js";
 export { terminateWorkerPool, zarrGet, zarrSet } from "./utils/worker_pool.js";
-export * from "./io/from_ngff_zarr.js";
-export * from "./io/to_ngff_zarr.js";
-export * from "./process/to_multiscales-node.js";
-export * from "./io/itk_image_to_ngff_image.js";
-export * from "./io/ngff_image_to_itk_image.js";
-export * from "./io/hcs.js";
-// RFC-9 exports
-export { getZipFileCompressionMethod, getZipFileList, isOzxPath, memoryStoreToZip, orderFilesForRfc9, readOzxJsonFirst, readOzxVersion, } from "./io/rfc9_zip.js";
 //# sourceMappingURL=mod.js.map

package/esm/mod.js.map

@@ -1 +1 @@
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package/esm/process/to_multiscales-shared.d.ts

@@ -3,18 +3,31 @@
  * This module contains types and helper functions used by both
  * browser and Node versions of toMultiscales.
  */
-import { NgffImage } from "../types/ngff_image.js";
-import { Multiscales } from "../types/multiscales.js";
 import { Methods } from "../types/methods.js";
+import type { Multiscales } from "../types/multiscales.js";
+import type { NgffImage } from "../types/ngff_image.js";
+import type { ZarrCodec } from "../utils/codecs.js";
+export type { ZarrCodec };
 export interface ToMultiscalesOptions {
     scaleFactors?: (Record<string, number> | number)[];
     method?: Methods;
     chunks?: number | number[] | Record<string, number>;
+    /**
+     * Codec pipeline for intermediate zarr arrays created during
+     * downsampling.  When omitted the default blosc+zstd pipeline is
+     * used ({@link defaultCodecs}).
+     *
+     * Pass {@link bytesOnlyCodecs | `bytesOnlyCodecs()`} to skip
+     * compression entirely — useful when the multiscale result will be
+     * immediately re-encoded into another format (e.g. OME-TIFF) and
+     * the compress/decompress round-trip would be wasted work.
+     */
+    codecs?: ZarrCodec[];
 }
 /**
  * Downsampling function type for ITK-Wasm implementations
  */
-export type DownsampleFunction = (image: NgffImage, scaleFactors: (Record<string, number> | number)[], smoothing: "gaussian" | "bin_shrink" | "label_image", chunks?: number | number[] | Record<string, number>) => Promise<NgffImage[]>;
+export type DownsampleFunction = (image: NgffImage, scaleFactors: (Record<string, number> | number)[], smoothing: "gaussian" | "bin_shrink" | "label_image", chunks?: number | number[] | Record<string, number>, codecs?: ZarrCodec[]) => Promise<NgffImage[]>;
 /**
  * Generate multiple resolution scales for an NgffImage
  * This is the core implementation used by both browser and Node versions.

package/esm/process/to_multiscales-shared.d.ts.map

@@ -1 +1 @@
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package/esm/process/to_multiscales-shared.js

@@ -1,5 +1,10 @@
 // SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
 // SPDX-License-Identifier: MIT
+/**
+ * Shared utilities for to_multiscales implementations
+ * This module contains types and helper functions used by both
+ * browser and Node versions of toMultiscales.
+ */
 import { Methods } from "../types/methods.js";
 import { createAxis, createDataset, createMetadata, createMultiscales, } from "../utils/factory.js";
 import { getMethodMetadata } from "../utils/method_metadata.js";
@@ -13,7 +18,7 @@ import { getMethodMetadata } from "../utils/method_metadata.js";
  * @returns Multiscales object
  */
 export async function toMultiscalesCore(image, options, downsampleItkWasm) {
-    const { scaleFactors = [2, 4], method = Methods.ITKWASM_GAUSSIAN, chunks: _chunks, } = options;
+    const { scaleFactors = [2, 4], method = Methods.ITKWASM_GAUSSIAN, chunks: _chunks, codecs, } = options;
     let images;
     // Check if we should perform actual downsampling
     if (method === Methods.ITKWASM_GAUSSIAN ||
@@ -25,7 +30,7 @@ export async function toMultiscalesCore(image, options, downsampleItkWasm) {
             : method === Methods.ITKWASM_BIN_SHRINK
                 ? "bin_shrink"
                 : "label_image";
-        images = await downsampleItkWasm(image, scaleFactors, smoothing, _chunks);
+        images = await downsampleItkWasm(image, scaleFactors, smoothing, _chunks, codecs);
     }
     else {
         // Fallback: create only the base image (no actual downsampling)

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package/esm/types/rfc4.d.ts

@@ -72,6 +72,32 @@ export declare const RAS: Record<string, AnatomicalOrientation>;
  * @returns The corresponding anatomical orientation, or undefined for non-spatial axes
  */
 export declare function itkLpsToAnatomicalOrientation(axisName: string): AnatomicalOrientation | undefined;
+/**
+ * Determine the anatomical orientation of a single image axis from its
+ * direction cosine vector in ITK LPS physical space.
+ *
+ * The direction vector is a column of the ITK direction matrix. Its
+ * dominant component (largest absolute value) determines which physical
+ * axis (L/R, A/P, or S/I) this image axis aligns with, and the sign
+ * of that component determines the direction.
+ *
+ * In LPS physical space:
+ * - Component 0: L/R axis (positive = Right→Left, negative = Left→Right)
+ * - Component 1: A/P axis (positive = Anterior→Posterior, negative = Posterior→Anterior)
+ * - Component 2: I/S axis (positive = Inferior→Superior, negative = Superior→Inferior)
+ *
+ * For 2D images, the direction column will have only 2 components, with the
+ * third component implicitly zero.
+ *
+ * @param directionColumn - Direction cosine vector for the image axis.
+ *   Can be 2-element (for 2D images) or 3-element (for 3D images).
+ *   `[lps_x, lps_y]` or `[lps_x, lps_y, lps_z]`
+ *   Must have at least 2 elements.
+ * @returns The anatomical orientation corresponding to the dominant
+ *   direction of this axis
+ * @throws Error if directionColumn has fewer than 2 elements
+ */
+export declare function itkDirectionToAnatomicalOrientation(directionColumn: readonly number[]): AnatomicalOrientation;
 /**
  * Check if RFC 4 is enabled in the list of enabled RFCs.
  */

package/esm/types/rfc4.d.ts.map

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package/esm/types/rfc4.js

@@ -101,6 +101,90 @@ export const RAS = {
 export function itkLpsToAnatomicalOrientation(axisName) {
     return LPS[axisName];
 }
+/**
+ * Maximum number of spatial dimensions (for ITK LPS coordinate system).
+ * LPS has 3 axes: Left/Right (X), Anterior/Posterior (Y),
+ * Inferior/Superior (Z).
+ */
+const MAX_SPATIAL_DIMENSIONS = 3;
+/**
+ * LPS orientation pairs: positive and negative orientations for each
+ * physical axis in the LPS coordinate system.
+ *
+ * Each row is `[positiveComponentOrientation, negativeComponentOrientation]`,
+ * where "positive component" (positive direction cosine value) indicates
+ * the direction along that axis, and "negative component" (negative
+ * direction cosine value) indicates the opposite direction.
+ *
+ * - Row 0 (L/R): positive component → RightToLeft
+ *   (positive direction points Left) / negative component → LeftToRight
+ *   (negative direction points Right)
+ * - Row 1 (A/P): positive component → AnteriorToPosterior
+ *   (positive direction points Posterior) / negative component →
+ *   PosteriorToAnterior (negative direction points Anterior)
+ * - Row 2 (I/S): positive component → InferiorToSuperior
+ *   (positive direction points Superior) / negative component →
+ *   SuperiorToInferior (negative direction points Inferior)
+ */
+const LPS_ORIENTATION_PAIRS = [
+    [
+        AnatomicalOrientationValues.RightToLeft,
+        AnatomicalOrientationValues.LeftToRight,
+    ],
+    [
+        AnatomicalOrientationValues.AnteriorToPosterior,
+        AnatomicalOrientationValues.PosteriorToAnterior,
+    ],
+    [
+        AnatomicalOrientationValues.InferiorToSuperior,
+        AnatomicalOrientationValues.SuperiorToInferior,
+    ],
+];
+/**
+ * Determine the anatomical orientation of a single image axis from its
+ * direction cosine vector in ITK LPS physical space.
+ *
+ * The direction vector is a column of the ITK direction matrix. Its
+ * dominant component (largest absolute value) determines which physical
+ * axis (L/R, A/P, or S/I) this image axis aligns with, and the sign
+ * of that component determines the direction.
+ *
+ * In LPS physical space:
+ * - Component 0: L/R axis (positive = Right→Left, negative = Left→Right)
+ * - Component 1: A/P axis (positive = Anterior→Posterior, negative = Posterior→Anterior)
+ * - Component 2: I/S axis (positive = Inferior→Superior, negative = Superior→Inferior)
+ *
+ * For 2D images, the direction column will have only 2 components, with the
+ * third component implicitly zero.
+ *
+ * @param directionColumn - Direction cosine vector for the image axis.
+ *   Can be 2-element (for 2D images) or 3-element (for 3D images).
+ *   `[lps_x, lps_y]` or `[lps_x, lps_y, lps_z]`
+ *   Must have at least 2 elements.
+ * @returns The anatomical orientation corresponding to the dominant
+ *   direction of this axis
+ * @throws Error if directionColumn has fewer than 2 elements
+ */
+export function itkDirectionToAnatomicalOrientation(directionColumn) {
+    if (directionColumn.length < 2) {
+        throw new Error(`Direction column must have at least 2 elements for 2D/3D images, got ${directionColumn.length}`);
+    }
+    // Find the dominant physical axis (largest absolute component)
+    let dominantAxis = 0;
+    let maxAbs = Math.abs(directionColumn[0]);
+    const n = Math.min(directionColumn.length, MAX_SPATIAL_DIMENSIONS);
+    for (let i = 1; i < n; i++) {
+        const absVal = Math.abs(directionColumn[i]);
+        if (absVal > maxAbs) {
+            maxAbs = absVal;
+            dominantAxis = i;
+        }
+    }
+    // Positive component → positive LPS direction, negative → opposite
+    const pair = LPS_ORIENTATION_PAIRS[dominantAxis];
+    const value = directionColumn[dominantAxis] >= 0 ? pair[0] : pair[1];
+    return createAnatomicalOrientation(value);
+}
 /**
  * Check if RFC 4 is enabled in the list of enabled RFCs.
  */

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package/esm/utils/codecs.d.ts

@@ -1,3 +1,13 @@
+/**
+ * Codec descriptor used in zarr v3 array metadata.
+ *
+ * @see {@link defaultCodecs} for the standard blosc+zstd pipeline.
+ * @see {@link bytesOnlyCodecs} for an uncompressed pipeline.
+ */
+export type ZarrCodec = {
+    name: string;
+    configuration: Record<string, unknown>;
+};
 /**
  * Return the byte size for a zarr v3 data type string.
  *
@@ -43,4 +53,14 @@ export declare function defaultCodecs(dataType: string): ({
         endian?: undefined;
     };
 })[];
+/**
+ * Build an uncompressed zarr v3 codec pipeline.
+ *
+ * Returns only the required `bytes` array-to-bytes codec (little-endian)
+ * with no bytes-to-bytes compression. This is useful when zarr arrays
+ * are ephemeral (e.g., in-memory multiscale pyramids that will be
+ * immediately re-encoded into another format like OME-TIFF) and the
+ * blosc compress/decompress round-trip would be wasted work.
+ */
+export declare function bytesOnlyCodecs(): ZarrCodec[];
 //# sourceMappingURL=codecs.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"codecs.d.ts","sourceRoot":"","sources":["../../src/utils/codecs.ts"],"names":[],"mappings":"AAGA;;;;;;;GAOG;AACH,wBAAgB,gBAAgB,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAgBtD;AAED;;;;;;;;;;;;;;GAcG;AACH,wBAAgB,aAAa,CAAC,QAAQ,EAAE,MAAM;;;;;;;;;;;;;;;;;;;;KAc7C"}
+{"version":3,"file":"codecs.d.ts","sourceRoot":"","sources":["../../src/utils/codecs.ts"],"names":[],"mappings":"AAGA;;;;;GAKG;AACH,MAAM,MAAM,SAAS,GAAG;IACtB,IAAI,EAAE,MAAM,CAAC;IACb,aAAa,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;CACxC,CAAC;AAEF;;;;;;;GAOG;AACH,wBAAgB,gBAAgB,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAgBtD;AAED;;;;;;;;;;;;;;GAcG;AACH,wBAAgB,aAAa,CAAC,QAAQ,EAAE,MAAM;;;;;;;;;;;;;;;;;;;;KAc7C;AAED;;;;;;;;GAQG;AACH,wBAAgB,eAAe,IAAI,SAAS,EAAE,CAE7C"}

package/esm/utils/codecs.js

@@ -55,4 +55,16 @@ export function defaultCodecs(dataType) {
         },
     ];
 }
+/**
+ * Build an uncompressed zarr v3 codec pipeline.
+ *
+ * Returns only the required `bytes` array-to-bytes codec (little-endian)
+ * with no bytes-to-bytes compression. This is useful when zarr arrays
+ * are ephemeral (e.g., in-memory multiscale pyramids that will be
+ * immediately re-encoded into another format like OME-TIFF) and the
+ * blosc compress/decompress round-trip would be wasted work.
+ */
+export function bytesOnlyCodecs() {
+    return [{ name: "bytes", configuration: { endian: "little" } }];
+}
 //# sourceMappingURL=codecs.js.map

package/esm/utils/codecs.js.map

@@ -1 +1 @@
-{"version":3,"file":"codecs.js","sourceRoot":"","sources":["../../src/utils/codecs.ts"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,+BAA+B;AAE/B;;;;;;;GAOG;AACH,MAAM,UAAU,gBAAgB,CAAC,KAAa;IAC5C,MAAM,KAAK,GAA2B;QACpC,IAAI,EAAE,CAAC;QACP,IAAI,EAAE,CAAC;QACP,KAAK,EAAE,CAAC;QACR,KAAK,EAAE,CAAC;QACR,MAAM,EAAE,CAAC;QACT,OAAO,EAAE,CAAC;QACV,KAAK,EAAE,CAAC;QACR,MAAM,EAAE,CAAC;QACT,OAAO,EAAE,CAAC;QACV,KAAK,EAAE,CAAC;QACR,MAAM,EAAE,CAAC;QACT,OAAO,EAAE,CAAC;KACX,CAAC;IACF,OAAO,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;AAC3B,CAAC;AAED;;;;;;;;;;;;;;GAcG;AACH,MAAM,UAAU,aAAa,CAAC,QAAgB;IAC5C,OAAO;QACL,EAAE,IAAI,EAAE,OAAO,EAAE,aAAa,EAAE,EAAE,MAAM,EAAE,QAAQ,EAAE,EAAE;QACtD;YACE,IAAI,EAAE,OAAO;YACb,aAAa,EAAE;gBACb,KAAK,EAAE,MAAM;gBACb,MAAM,EAAE,CAAC;gBACT,OAAO,EAAE,SAAS;gBAClB,QAAQ,EAAE,gBAAgB,CAAC,QAAQ,CAAC;gBACpC,SAAS,EAAE,CAAC;aACb;SACF;KACF,CAAC;AACJ,CAAC"}
+{"version":3,"file":"codecs.js","sourceRoot":"","sources":["../../src/utils/codecs.ts"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,+BAA+B;AAa/B;;;;;;;GAOG;AACH,MAAM,UAAU,gBAAgB,CAAC,KAAa;IAC5C,MAAM,KAAK,GAA2B;QACpC,IAAI,EAAE,CAAC;QACP,IAAI,EAAE,CAAC;QACP,KAAK,EAAE,CAAC;QACR,KAAK,EAAE,CAAC;QACR,MAAM,EAAE,CAAC;QACT,OAAO,EAAE,CAAC;QACV,KAAK,EAAE,CAAC;QACR,MAAM,EAAE,CAAC;QACT,OAAO,EAAE,CAAC;QACV,KAAK,EAAE,CAAC;QACR,MAAM,EAAE,CAAC;QACT,OAAO,EAAE,CAAC;KACX,CAAC;IACF,OAAO,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;AAC3B,CAAC;AAED;;;;;;;;;;;;;;GAcG;AACH,MAAM,UAAU,aAAa,CAAC,QAAgB;IAC5C,OAAO;QACL,EAAE,IAAI,EAAE,OAAO,EAAE,aAAa,EAAE,EAAE,MAAM,EAAE,QAAQ,EAAE,EAAE;QACtD;YACE,IAAI,EAAE,OAAO;YACb,aAAa,EAAE;gBACb,KAAK,EAAE,MAAM;gBACb,MAAM,EAAE,CAAC;gBACT,OAAO,EAAE,SAAS;gBAClB,QAAQ,EAAE,gBAAgB,CAAC,QAAQ,CAAC;gBACpC,SAAS,EAAE,CAAC;aACb;SACF;KACF,CAAC;AACJ,CAAC;AAED;;;;;;;;GAQG;AACH,MAAM,UAAU,eAAe;IAC7B,OAAO,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,aAAa,EAAE,EAAE,MAAM,EAAE,QAAQ,EAAE,EAAE,CAAC,CAAC;AAClE,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@fideus-labs/ngff-zarr",
-  "version": "0.11.0",
+  "version": "0.12.0",
   "description": "TypeScript implementation of ngff-zarr for reading and writing OME-Zarr files",
   "license": "MIT",
   "type": "module",