@fideus-labs/ngff-zarr 0.11.0 → 0.12.0

package/esm/browser-mod.d.ts

@@ -16,6 +16,8 @@ export * from "./types/multiscales.js";
 export * from "./types/ngff_image.js";
 export * from "./types/units.js";
 export * from "./types/zarr_metadata.js";
+export type { ZarrCodec } from "./utils/codecs.js";
+export { bytesOnlyCodecs, defaultCodecs } from "./utils/codecs.js";
 export type { ComputeOmeroFromMultiscalesOptions, ComputeOmeroOptions, } from "./utils/compute_omero.js";
 export { computeOmeroFromMultiscales, computeOmeroFromNgffImage, getDefaultColors, GLASBEY_COLORS, terminateOmeroWorkerPool, } from "./utils/compute_omero.js";
 export type { ChannelStatisticsAccumulator } from "./utils/compute_omero-shared.js";

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

@@ -1 +1 @@
-{"version":3,"file":"browser-mod.d.ts","sourceRoot":"","sources":["../src/browser-mod.ts"],"names":[],"mappings":"AAWA,OAAO,EACL,KAAK,UAAU,EACf,YAAY,EACZ,KAAK,mBAAmB,EACxB,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,GAC1B,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,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,GAChB,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":"AAWA,OAAO,EACL,KAAK,UAAU,EACf,YAAY,EACZ,KAAK,mBAAmB,EACxB,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,GAC1B,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,MAAM,mBAAmB,CAAC;AACnD,OAAO,EAAE,eAAe,EAAE,aAAa,EAAE,MAAM,mBAAmB,CAAC;AACnE,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,GAChB,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"}

package/esm/browser-mod.js

@@ -28,6 +28,7 @@ export * from "./types/multiscales.js";
 export * from "./types/ngff_image.js";
 export * from "./types/units.js";
 export * from "./types/zarr_metadata.js";
+export { bytesOnlyCodecs, defaultCodecs } from "./utils/codecs.js";
 // OMERO computation with WorkerPool
 export { computeOmeroFromMultiscales, computeOmeroFromNgffImage, getDefaultColors, GLASBEY_COLORS, terminateOmeroWorkerPool, } from "./utils/compute_omero.js";
 // Shared OMERO computation functions for benchmarking and direct use

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,iCAAiC;AACjC,0EAA0E;AAC1E,iFAAiF;AACjF,OAAO,EAEL,YAAY,GAGb,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,GAEd,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;AAKzC,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,GAChB,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,iCAAiC;AACjC,0EAA0E;AAC1E,iFAAiF;AACjF,OAAO,EAEL,YAAY,GAGb,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,GAEd,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,EAAE,eAAe,EAAE,aAAa,EAAE,MAAM,mBAAmB,CAAC;AAKnE,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,GAChB,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"}

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

@@ -1 +1 @@
-{"version":3,"file":"itk_image_to_ngff_image.d.ts","sourceRoot":"","sources":["../../src/io/itk_image_to_ngff_image.ts"],"names":[],"mappings":"AAEA;;GAEG;AAEH,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,UAAU,CAAC;AAKtC,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAMnD,MAAM,WAAW,0BAA0B;IACzC;;;OAGG;IACH,wBAAwB,CAAC,EAAE,OAAO,CAAC;IAEnC;;;OAGG;IACH,IAAI,CAAC,EAAE,MAAM,CAAC;IAEd;;;;;OAKG;IACH,MAAM,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;CAC5B;AAED;;;;;;;;;;GAUG;AACH,wBAAsB,mBAAmB,CACvC,QAAQ,EAAE,KAAK,EACf,OAAO,GAAE,0BAA+B,GACvC,OAAO,CAAC,SAAS,CAAC,CAoIpB"}
+{"version":3,"file":"itk_image_to_ngff_image.d.ts","sourceRoot":"","sources":["../../src/io/itk_image_to_ngff_image.ts"],"names":[],"mappings":"AAEA;;GAEG;AAEH,OAAO,KAAK,EAAE,KAAK,EAAE,MAAM,UAAU,CAAC;AAKtC,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AASnD,MAAM,WAAW,0BAA0B;IACzC;;;OAGG;IACH,wBAAwB,CAAC,EAAE,OAAO,CAAC;IAEnC;;;OAGG;IACH,IAAI,CAAC,EAAE,MAAM,CAAC;IAEd;;;;;OAKG;IACH,MAAM,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,CAAC;CAC5B;AA2BD;;;;;;;;;;GAUG;AACH,wBAAsB,mBAAmB,CACvC,QAAQ,EAAE,KAAK,EACf,OAAO,GAAE,0BAA+B,GACvC,OAAO,CAAC,SAAS,CAAC,CA0KpB"}

package/esm/io/itk_image_to_ngff_image.js

@@ -7,9 +7,30 @@ import * as zarr from "zarrita";
 // Import the get_strides function from zarrita utilities
 import { _zarrita_internal_get_strides as getStrides } from "zarrita";
 import { NgffImage } from "../types/ngff_image.js";
-import { itkLpsToAnatomicalOrientation } from "../types/rfc4.js";
+import { itkDirectionToAnatomicalOrientation, itkLpsToAnatomicalOrientation, } from "../types/rfc4.js";
 import { defaultCodecs } from "../utils/codecs.js";
 import { zarrSet } from "../utils/worker_pool.js";
+/**
+ * Check whether an ITK direction matrix is the identity matrix.
+ *
+ * When the direction is identity, the image axes align directly with
+ * the physical LPS axes and the simple LPS lookup is sufficient.
+ *
+ * @param direction - Flat (row-major) direction matrix from ITK-Wasm
+ * @param n - Number of spatial dimensions (2 or 3)
+ * @returns `true` if every element matches the identity matrix
+ */
+function isIdentityDirection(direction, n) {
+    for (let row = 0; row < n; row++) {
+        for (let col = 0; col < n; col++) {
+            const expected = row === col ? 1 : 0;
+            if (Number(direction[row * n + col]) !== expected) {
+                return false;
+            }
+        }
+    }
+    return true;
+}
 /**
  * Convert an ITK-Wasm Image to an NgffImage, preserving spatial metadata.
  *
@@ -116,14 +137,50 @@ export async function itkImageToNgffImage(itkImage, options = {}) {
     };
     // Write all data to the zarr array using worker-accelerated set function
     // This handles chunking and encoding automatically
-    await zarrSet(zarrArray, selection, dataChunk); // Add anatomical orientation if requested
+    await zarrSet(zarrArray, selection, dataChunk);
+    // Add anatomical orientation if requested
     let axesOrientations;
     if (addAnatomicalOrientation) {
         axesOrientations = {};
-        for (const dim of spatialDims) {
-            const orientation = itkLpsToAnatomicalOrientation(dim);
-            if (orientation !== undefined) {
-                axesOrientations[dim] = orientation;
+        const direction = itkImage.direction;
+        const nSpatial = spatialDims.length;
+        // Check whether the direction matrix is available and has a
+        // non-identity rotation (permutation or oblique).
+        const hasDirection = direction !== undefined && direction.length > 0;
+        const hasNonIdentityDirection = hasDirection &&
+            !isIdentityDirection(direction, nSpatial);
+        if (hasNonIdentityDirection) {
+            // Use the direction cosine matrix to determine each axis'
+            // anatomical orientation. The direction matrix is stored
+            // row-major as a flat array: direction[row * nSpatial + col].
+            //
+            // spatialDims is in array order (e.g. ["z", "y", "x"]) and
+            // maps to reversed ITK axis indices:
+            //   spatialDims[0] = "z" → ITK axis 2 → direction column 2
+            //   spatialDims[1] = "y" → ITK axis 1 → direction column 1
+            //   spatialDims[2] = "x" → ITK axis 0 → direction column 0
+            //
+            // Column j of the direction matrix contains the LPS-space
+            // direction cosine for ITK axis j.
+            for (let i = 0; i < nSpatial; i++) {
+                const dim = spatialDims[i];
+                // Reverse index: spatialDims[0] → last ITK axis, etc.
+                const itkAxisIndex = nSpatial - 1 - i;
+                // Extract direction column, handling both 2D and 3D cases
+                const col = [];
+                for (let row = 0; row < nSpatial; row++) {
+                    col.push(Number(direction[row * nSpatial + itkAxisIndex]));
+                }
+                axesOrientations[dim] = itkDirectionToAnatomicalOrientation(col);
+            }
+        }
+        else {
+            // Identity direction or no direction: fall back to LPS labels
+            for (const dim of spatialDims) {
+                const orientation = itkLpsToAnatomicalOrientation(dim);
+                if (orientation !== undefined) {
+                    axesOrientations[dim] = orientation;
+                }
             }
         }
     }

package/esm/io/itk_image_to_ngff_image.js.map

@@ -1 +1 @@
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package/esm/methods/itkwasm-browser.d.ts

@@ -1,6 +1,7 @@
 import { NgffImage } from "../types/ngff_image.js";
+import type { ZarrCodec } from "../utils/codecs.js";
 /**
  * Main downsampling function for ITK-Wasm (browser version)
  */
-export declare function downsampleItkWasm(ngffImage: NgffImage, scaleFactors: (Record<string, number> | number)[], smoothing: "gaussian" | "bin_shrink" | "label_image", chunks?: number | number[] | Record<string, number>): Promise<NgffImage[]>;
+export declare function downsampleItkWasm(ngffImage: NgffImage, scaleFactors: (Record<string, number> | number)[], smoothing: "gaussian" | "bin_shrink" | "label_image", chunks?: number | number[] | Record<string, number>, codecs?: ZarrCodec[]): Promise<NgffImage[]>;
 //# sourceMappingURL=itkwasm-browser.d.ts.map

package/esm/methods/itkwasm-browser.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"itkwasm-browser.d.ts","sourceRoot":"","sources":["../../src/methods/itkwasm-browser.ts"],"names":[],"mappings":"AAgBA,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AA86BnD;;GAEG;AACH,wBAAsB,iBAAiB,CACrC,SAAS,EAAE,SAAS,EACpB,YAAY,EAAE,CAAC,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,MAAM,CAAC,EAAE,EACjD,SAAS,EAAE,UAAU,GAAG,YAAY,GAAG,aAAa,EACpD,MAAM,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAClD,OAAO,CAAC,SAAS,EAAE,CAAC,CAyHtB"}
+{"version":3,"file":"itkwasm-browser.d.ts","sourceRoot":"","sources":["../../src/methods/itkwasm-browser.ts"],"names":[],"mappings":"AAeA,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAC;AA47BpD;;GAEG;AACH,wBAAsB,iBAAiB,CACrC,SAAS,EAAE,SAAS,EACpB,YAAY,EAAE,CAAC,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,MAAM,CAAC,EAAE,EACjD,SAAS,EAAE,UAAU,GAAG,YAAY,GAAG,aAAa,EACpD,MAAM,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,EACnD,MAAM,CAAC,EAAE,SAAS,EAAE,GACnB,OAAO,CAAC,SAAS,EAAE,CAAC,CA4HtB"}

package/esm/methods/itkwasm-browser.js

@@ -6,9 +6,9 @@
  */
 import { downsample, downsampleBinShrink, downsampleLabelImage, } from "@itk-wasm/downsample";
 import * as zarr from "zarrita";
-import { zarrGet, zarrSet } from "../utils/worker_pool.js";
-import { defaultCodecs } from "../utils/codecs.js";
 import { NgffImage } from "../types/ngff_image.js";
+import { defaultCodecs } from "../utils/codecs.js";
+import { zarrGet, zarrSet } from "../utils/worker_pool.js";
 import { dimScaleFactors, itkImageToZarr, MAX_VECTOR_COMPONENTS, nextScaleMetadata, SPATIAL_DIMS, updatePreviousDimFactors, zarrToItkImage, } from "./itkwasm-shared.js";
 /**
  * Compute chunk shape from configurable chunks option
@@ -36,7 +36,7 @@ function computeChunkShape(shape, chunks, dims, defaultChunk = 256) {
 /**
  * Perform Gaussian downsampling using ITK-Wasm (browser version)
  */
-async function downsampleGaussian(image, dimFactors, spatialDims, chunks) {
+async function downsampleGaussian(image, dimFactors, spatialDims, chunks, codecs) {
     // Handle time dimension by processing each time slice independently
     if (image.dims.includes("t")) {
         const tDimIndex = image.dims.indexOf("t");
@@ -62,7 +62,7 @@ async function downsampleGaussian(image, dimFactors, spatialDims, chunks) {
                 chunk_shape: sliceChunkShape,
                 data_type: image.data.dtype,
                 fill_value: 0,
-                codecs: defaultCodecs(image.data.dtype),
+                codecs: codecs ?? defaultCodecs(image.data.dtype),
             });
             const fullSelection = new Array(sliceShape.length).fill(null);
             await zarrSet(sliceArray, fullSelection, sliceData);
@@ -79,7 +79,7 @@ async function downsampleGaussian(image, dimFactors, spatialDims, chunks) {
                 computedCallbacks: image.computedCallbacks,
             });
             // Recursively downsample this slice (without 't', so no infinite loop)
-            const downsampledSlice = await downsampleGaussian(sliceImage, dimFactors, spatialDims, sliceChunks);
+            const downsampledSlice = await downsampleGaussian(sliceImage, dimFactors, spatialDims, sliceChunks, codecs);
             downsampledSlices.push(downsampledSlice.data);
         }
         // Combine downsampled slices back into a single array with 't' dimension
@@ -101,7 +101,7 @@ async function downsampleGaussian(image, dimFactors, spatialDims, chunks) {
             chunk_shape: computeChunkShape(combinedShape, chunks, image.dims),
             data_type: image.data.dtype,
             fill_value: 0,
-            codecs: defaultCodecs(image.data.dtype),
+            codecs: codecs ?? defaultCodecs(image.data.dtype),
         });
         // Copy each downsampled slice into the combined array
         for (let t = 0; t < tSize; t++) {
@@ -154,7 +154,7 @@ async function downsampleGaussian(image, dimFactors, spatialDims, chunks) {
                 chunk_shape: sliceChunkShape,
                 data_type: image.data.dtype,
                 fill_value: 0,
-                codecs: defaultCodecs(image.data.dtype),
+                codecs: codecs ?? defaultCodecs(image.data.dtype),
             });
             const fullSelection = new Array(sliceShape.length).fill(null);
             await zarrSet(sliceArray, fullSelection, sliceData);
@@ -171,7 +171,7 @@ async function downsampleGaussian(image, dimFactors, spatialDims, chunks) {
                 computedCallbacks: image.computedCallbacks,
             });
             // Recursively downsample this slice (without 'c', so no infinite loop)
-            const downsampledSlice = await downsampleGaussian(sliceImage, dimFactors, spatialDims, sliceChunks);
+            const downsampledSlice = await downsampleGaussian(sliceImage, dimFactors, spatialDims, sliceChunks, codecs);
             downsampledSlices.push(downsampledSlice.data);
         }
         // Combine downsampled slices back into a single array with 'c' dimension
@@ -193,7 +193,7 @@ async function downsampleGaussian(image, dimFactors, spatialDims, chunks) {
             chunk_shape: computeChunkShape(combinedShape, chunks, image.dims),
             data_type: image.data.dtype,
             fill_value: 0,
-            codecs: defaultCodecs(image.data.dtype),
+            codecs: codecs ?? defaultCodecs(image.data.dtype),
         });
         // Copy each downsampled slice into the combined array
         for (let c = 0; c < cSize; c++) {
@@ -238,7 +238,7 @@ async function downsampleGaussian(image, dimFactors, spatialDims, chunks) {
     // downsampled.size is in ITK order [x, y, z], reverse to get array order [z, y, x]
     const reversedShape = [...downsampled.size].reverse();
     const chunkShape = computeChunkShape(reversedShape, chunks, image.dims);
-    const array = await itkImageToZarr(downsampled, store, "image", chunkShape, image.dims);
+    const array = await itkImageToZarr(downsampled, store, "image", chunkShape, image.dims, codecs);
     return new NgffImage({
         data: array,
         dims: image.dims,
@@ -252,7 +252,7 @@ async function downsampleGaussian(image, dimFactors, spatialDims, chunks) {
 /**
  * Perform bin shrink downsampling using ITK-Wasm (browser version)
  */
-async function downsampleBinShrinkImpl(image, dimFactors, spatialDims, chunks) {
+async function downsampleBinShrinkImpl(image, dimFactors, spatialDims, chunks, codecs) {
     // Handle time dimension by processing each time slice independently
     if (image.dims.includes("t")) {
         const tDimIndex = image.dims.indexOf("t");
@@ -278,7 +278,7 @@ async function downsampleBinShrinkImpl(image, dimFactors, spatialDims, chunks) {
                 chunk_shape: sliceChunkShape,
                 data_type: image.data.dtype,
                 fill_value: 0,
-                codecs: defaultCodecs(image.data.dtype),
+                codecs: codecs ?? defaultCodecs(image.data.dtype),
             });
             const fullSelection = new Array(sliceShape.length).fill(null);
             await zarrSet(sliceArray, fullSelection, sliceData);
@@ -295,7 +295,7 @@ async function downsampleBinShrinkImpl(image, dimFactors, spatialDims, chunks) {
                 computedCallbacks: image.computedCallbacks,
             });
             // Recursively downsample this slice
-            const downsampledSlice = await downsampleBinShrinkImpl(sliceImage, dimFactors, spatialDims, sliceChunks);
+            const downsampledSlice = await downsampleBinShrinkImpl(sliceImage, dimFactors, spatialDims, sliceChunks, codecs);
             downsampledSlices.push(downsampledSlice.data);
         }
         // Combine downsampled slices back into a single array with 't' dimension
@@ -317,7 +317,7 @@ async function downsampleBinShrinkImpl(image, dimFactors, spatialDims, chunks) {
             chunk_shape: computeChunkShape(combinedShape, chunks, image.dims),
             data_type: image.data.dtype,
             fill_value: 0,
-            codecs: defaultCodecs(image.data.dtype),
+            codecs: codecs ?? defaultCodecs(image.data.dtype),
         });
         // Copy each downsampled slice into the combined array
         for (let t = 0; t < tSize; t++) {
@@ -370,7 +370,7 @@ async function downsampleBinShrinkImpl(image, dimFactors, spatialDims, chunks) {
                 chunk_shape: sliceChunkShape,
                 data_type: image.data.dtype,
                 fill_value: 0,
-                codecs: defaultCodecs(image.data.dtype),
+                codecs: codecs ?? defaultCodecs(image.data.dtype),
             });
             const fullSelection = new Array(sliceShape.length).fill(null);
             await zarrSet(sliceArray, fullSelection, sliceData);
@@ -387,7 +387,7 @@ async function downsampleBinShrinkImpl(image, dimFactors, spatialDims, chunks) {
                 computedCallbacks: image.computedCallbacks,
             });
             // Recursively downsample this slice (without 'c', so no infinite loop)
-            const downsampledSlice = await downsampleBinShrinkImpl(sliceImage, dimFactors, spatialDims, sliceChunks);
+            const downsampledSlice = await downsampleBinShrinkImpl(sliceImage, dimFactors, spatialDims, sliceChunks, codecs);
             downsampledSlices.push(downsampledSlice.data);
         }
         // Combine downsampled slices back into a single array with 'c' dimension
@@ -409,7 +409,7 @@ async function downsampleBinShrinkImpl(image, dimFactors, spatialDims, chunks) {
             chunk_shape: computeChunkShape(combinedShape, chunks, image.dims),
             data_type: image.data.dtype,
             fill_value: 0,
-            codecs: defaultCodecs(image.data.dtype),
+            codecs: codecs ?? defaultCodecs(image.data.dtype),
         });
         // Copy each downsampled slice into the combined array
         for (let c = 0; c < cSize; c++) {
@@ -451,7 +451,7 @@ async function downsampleBinShrinkImpl(image, dimFactors, spatialDims, chunks) {
     // downsampled.size is in ITK order [x, y, z], reverse to get array order [z, y, x]
     const reversedShape = [...downsampled.size].reverse();
     const chunkShape = computeChunkShape(reversedShape, chunks, image.dims);
-    const array = await itkImageToZarr(downsampled, store, "image", chunkShape, image.dims);
+    const array = await itkImageToZarr(downsampled, store, "image", chunkShape, image.dims, codecs);
     return new NgffImage({
         data: array,
         dims: image.dims,
@@ -465,7 +465,7 @@ async function downsampleBinShrinkImpl(image, dimFactors, spatialDims, chunks) {
 /**
  * Perform label image downsampling using ITK-Wasm (browser version)
  */
-async function downsampleLabelImageImpl(image, dimFactors, spatialDims, chunks) {
+async function downsampleLabelImageImpl(image, dimFactors, spatialDims, chunks, codecs) {
     // Handle time dimension by processing each time slice independently
     if (image.dims.includes("t")) {
         const tDimIndex = image.dims.indexOf("t");
@@ -491,7 +491,7 @@ async function downsampleLabelImageImpl(image, dimFactors, spatialDims, chunks)
                 chunk_shape: sliceChunkShape,
                 data_type: image.data.dtype,
                 fill_value: 0,
-                codecs: defaultCodecs(image.data.dtype),
+                codecs: codecs ?? defaultCodecs(image.data.dtype),
             });
             const fullSelection = new Array(sliceShape.length).fill(null);
             await zarrSet(sliceArray, fullSelection, sliceData);
@@ -508,7 +508,7 @@ async function downsampleLabelImageImpl(image, dimFactors, spatialDims, chunks)
                 computedCallbacks: image.computedCallbacks,
             });
             // Recursively downsample this slice
-            const downsampledSlice = await downsampleLabelImageImpl(sliceImage, dimFactors, spatialDims, sliceChunks);
+            const downsampledSlice = await downsampleLabelImageImpl(sliceImage, dimFactors, spatialDims, sliceChunks, codecs);
             downsampledSlices.push(downsampledSlice.data);
         }
         // Combine downsampled slices back into a single array with 't' dimension
@@ -530,7 +530,7 @@ async function downsampleLabelImageImpl(image, dimFactors, spatialDims, chunks)
             chunk_shape: computeChunkShape(combinedShape, chunks, image.dims),
             data_type: image.data.dtype,
             fill_value: 0,
-            codecs: defaultCodecs(image.data.dtype),
+            codecs: codecs ?? defaultCodecs(image.data.dtype),
         });
         // Copy each downsampled slice into the combined array
         for (let t = 0; t < tSize; t++) {
@@ -583,7 +583,7 @@ async function downsampleLabelImageImpl(image, dimFactors, spatialDims, chunks)
                 chunk_shape: sliceChunkShape,
                 data_type: image.data.dtype,
                 fill_value: 0,
-                codecs: defaultCodecs(image.data.dtype),
+                codecs: codecs ?? defaultCodecs(image.data.dtype),
             });
             const fullSelection = new Array(sliceShape.length).fill(null);
             await zarrSet(sliceArray, fullSelection, sliceData);
@@ -600,7 +600,7 @@ async function downsampleLabelImageImpl(image, dimFactors, spatialDims, chunks)
                 computedCallbacks: image.computedCallbacks,
             });
             // Recursively downsample this slice (without 'c', so no infinite loop)
-            const downsampledSlice = await downsampleLabelImageImpl(sliceImage, dimFactors, spatialDims, sliceChunks);
+            const downsampledSlice = await downsampleLabelImageImpl(sliceImage, dimFactors, spatialDims, sliceChunks, codecs);
             downsampledSlices.push(downsampledSlice.data);
         }
         // Combine downsampled slices back into a single array with 'c' dimension
@@ -622,7 +622,7 @@ async function downsampleLabelImageImpl(image, dimFactors, spatialDims, chunks)
             chunk_shape: computeChunkShape(combinedShape, chunks, image.dims),
             data_type: image.data.dtype,
             fill_value: 0,
-            codecs: defaultCodecs(image.data.dtype),
+            codecs: codecs ?? defaultCodecs(image.data.dtype),
         });
         // Copy each downsampled slice into the combined array
         for (let c = 0; c < cSize; c++) {
@@ -670,7 +670,7 @@ async function downsampleLabelImageImpl(image, dimFactors, spatialDims, chunks)
     // downsampled.size is in ITK order [x, y, z], reverse to get array order [z, y, x]
     const reversedShape = [...downsampled.size].reverse();
     const chunkShape = computeChunkShape(reversedShape, chunks, image.dims);
-    const array = await itkImageToZarr(downsampled, store, "image", chunkShape, image.dims);
+    const array = await itkImageToZarr(downsampled, store, "image", chunkShape, image.dims, codecs);
     return new NgffImage({
         data: array,
         dims: image.dims,
@@ -684,7 +684,7 @@ async function downsampleLabelImageImpl(image, dimFactors, spatialDims, chunks)
 /**
  * Main downsampling function for ITK-Wasm (browser version)
  */
-export async function downsampleItkWasm(ngffImage, scaleFactors, smoothing, chunks) {
+export async function downsampleItkWasm(ngffImage, scaleFactors, smoothing, chunks, codecs) {
     const multiscales = [ngffImage];
     const dims = ngffImage.dims;
     const spatialDims = dims.filter((dim) => SPATIAL_DIMS.includes(dim));
@@ -748,13 +748,13 @@ export async function downsampleItkWasm(ngffImage, scaleFactors, smoothing, chun
         }
         let downsampled;
         if (smoothing === "gaussian") {
-            downsampled = await downsampleGaussian(sourceImage, sourceDimFactors, spatialDims, chunks);
+            downsampled = await downsampleGaussian(sourceImage, sourceDimFactors, spatialDims, chunks, codecs);
         }
         else if (smoothing === "bin_shrink") {
-            downsampled = await downsampleBinShrinkImpl(sourceImage, sourceDimFactors, spatialDims, chunks);
+            downsampled = await downsampleBinShrinkImpl(sourceImage, sourceDimFactors, spatialDims, chunks, codecs);
         }
         else if (smoothing === "label_image") {
-            downsampled = await downsampleLabelImageImpl(sourceImage, sourceDimFactors, spatialDims, chunks);
+            downsampled = await downsampleLabelImageImpl(sourceImage, sourceDimFactors, spatialDims, chunks, codecs);
         }
         else {
             throw new Error(`Unknown smoothing method: ${smoothing}`);

package/esm/methods/itkwasm-browser.js.map

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package/esm/methods/itkwasm-node.d.ts

@@ -1,6 +1,7 @@
 import { NgffImage } from "../types/ngff_image.js";
+import type { ZarrCodec } from "../utils/codecs.js";
 /**
  * Main downsampling function for ITK-Wasm (Node version)
  */
-export declare function downsampleItkWasm(ngffImage: NgffImage, scaleFactors: (Record<string, number> | number)[], smoothing: "gaussian" | "bin_shrink" | "label_image", chunks?: number | number[] | Record<string, number>): Promise<NgffImage[]>;
+export declare function downsampleItkWasm(ngffImage: NgffImage, scaleFactors: (Record<string, number> | number)[], smoothing: "gaussian" | "bin_shrink" | "label_image", chunks?: number | number[] | Record<string, number>, codecs?: ZarrCodec[]): Promise<NgffImage[]>;
 //# sourceMappingURL=itkwasm-node.d.ts.map

package/esm/methods/itkwasm-node.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"itkwasm-node.d.ts","sourceRoot":"","sources":["../../src/methods/itkwasm-node.ts"],"names":[],"mappings":"AAoBA,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,KAAK,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAC;AA47BpD;;GAEG;AACH,wBAAsB,iBAAiB,CACrC,SAAS,EAAE,SAAS,EACpB,YAAY,EAAE,CAAC,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,MAAM,CAAC,EAAE,EACjD,SAAS,EAAE,UAAU,GAAG,YAAY,GAAG,aAAa,EACpD,MAAM,CAAC,EAAE,MAAM,GAAG,MAAM,EAAE,GAAG,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,EACnD,MAAM,CAAC,EAAE,SAAS,EAAE,GACnB,OAAO,CAAC,SAAS,EAAE,CAAC,CA4HtB"}