@fideus-labs/ngff-zarr 0.15.1 → 0.16.0

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

@@ -1 +1 @@
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+{"version":3,"file":"ngff_image_to_itk_image.d.ts","sourceRoot":"","sources":["../../src/io/ngff_image_to_itk_image.ts"],"names":[],"mappings":"AAEA;;GAEG;AAEH,OAAO,KAAK,EACV,UAAU,EACV,KAAK,EAEL,QAAQ,EAGT,MAAM,UAAU,CAAC;AAClB,OAAO,KAAK,IAAI,MAAM,SAAS,CAAC;AAEhC,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AAInD,MAAM,WAAW,0BAA0B;IACzC;;;OAGG;IACH,MAAM,CAAC,EAAE,MAAM,CAAC;IAEhB;;;OAGG;IACH,MAAM,CAAC,EAAE,MAAM,CAAC;CACjB;AAED;;GAEG;AACH,wBAAgB,uBAAuB,CACrC,QAAQ,EAAE,IAAI,CAAC,QAAQ,GAErB,CAAC,OAAO,QAAQ,CAAC,CAAC,MAAM,OAAO,QAAQ,CAAC,GACxC,CAAC,OAAO,UAAU,CAAC,CAAC,MAAM,OAAO,UAAU,CAAC,CAyB/C;AAoCD;;;;;;;;;;GAUG;AACH,wBAAsB,mBAAmB,CACvC,SAAS,EAAE,SAAS,EACpB,OAAO,GAAE,0BAA+B,GACvC,OAAO,CAAC,KAAK,CAAC,CAuOhB"}

package/esm/io/ngff_image_to_itk_image.js

@@ -6,6 +6,7 @@
 import * as zarr from "zarrita";
 import { defaultCodecs } from "../utils/codecs.js";
 import { NgffImage } from "../types/ngff_image.js";
+import { anatomicalOrientationToItkDirection } from "../types/rfc4.js";
 import { zarrGet, zarrSet } from "../utils/worker_pool.js";
 /**
  * Convert the data type from zarr DataType to ITK-Wasm component type
@@ -202,10 +203,41 @@ export async function ngffImageToItkImage(ngffImage, options = {}) {
     // Read all data from zarr array
     const selection = new Array(data.shape.length).fill(null);
     const dataChunk = await zarrGet(data, selection);
-    // Create direction matrix (identity for now)
+    // Build direction matrix from anatomical orientations when available.
+    // sortedItkDims is in ITK physical-space order [x, y, z (, t)].
+    // Column j of the direction matrix corresponds to sortedItkDims[j].
     const direction = new Float64Array(dimension * dimension);
     for (let i = 0; i < dimension; i++) {
-        direction[i * dimension + i] = 1.0;
+        direction[i * dimension + i] = 1.0; // Start with identity
+    }
+    const orientations = workingImage.axesOrientations;
+    if (orientations) {
+        // Only spatial dims (not "t") contribute to the direction matrix.
+        const spatialItkDims = sortedItkDims.filter((d) => d !== "t");
+        const nSpatial = spatialItkDims.length;
+        const columns = [];
+        let useOrientations = true;
+        for (const dim of spatialItkDims) {
+            const ori = orientations[dim];
+            if (ori === undefined) {
+                useOrientations = false;
+                break;
+            }
+            const col = anatomicalOrientationToItkDirection(ori.value);
+            if (col === undefined) {
+                // Non-LPS orientation: fall back to identity
+                useOrientations = false;
+                break;
+            }
+            columns.push(col);
+        }
+        if (useOrientations && columns.length > 0) {
+            for (let colIdx = 0; colIdx < nSpatial; colIdx++) {
+                for (let row = 0; row < nSpatial; row++) {
+                    direction[row * dimension + colIdx] = columns[colIdx][row];
+                }
+            }
+        }
     }
     // Create ITK-Wasm Image
     const itkImage = {

package/esm/io/ngff_image_to_itk_image.js.map

@@ -1 +1 @@
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package/esm/types/rfc4.d.ts

@@ -98,6 +98,24 @@ export declare function itkLpsToAnatomicalOrientation(axisName: string): Anatomi
  * @throws Error if directionColumn has fewer than 2 elements
  */
 export declare function itkDirectionToAnatomicalOrientation(directionColumn: readonly number[]): AnatomicalOrientation;
+/**
+ * Convert an anatomical orientation to an ITK direction cosine vector.
+ *
+ * This is the reverse of {@link itkDirectionToAnatomicalOrientation}.
+ * Given an anatomical orientation value, it returns the unit direction
+ * column vector in ITK LPS physical space.
+ *
+ * Only the six LPS-compatible orientations are supported.  For any other
+ * orientation (e.g. dorsal, palmar, rostral, etc.) the function returns
+ * `undefined`, signalling that the caller should fall back to an identity
+ * direction matrix.
+ *
+ * @param orientation - The anatomical orientation value.
+ * @returns A 3-element unit direction column vector `[lps_x, lps_y, lps_z]`,
+ *   or `undefined` if the orientation is not one of the six LPS-compatible
+ *   values.
+ */
+export declare function anatomicalOrientationToItkDirection(orientation: AnatomicalOrientationValues): number[] | undefined;
 /**
  * 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

@@ -185,6 +185,39 @@ export function itkDirectionToAnatomicalOrientation(directionColumn) {
     const value = directionColumn[dominantAxis] >= 0 ? pair[0] : pair[1];
     return createAnatomicalOrientation(value);
 }
+/**
+ * Convert an anatomical orientation to an ITK direction cosine vector.
+ *
+ * This is the reverse of {@link itkDirectionToAnatomicalOrientation}.
+ * Given an anatomical orientation value, it returns the unit direction
+ * column vector in ITK LPS physical space.
+ *
+ * Only the six LPS-compatible orientations are supported.  For any other
+ * orientation (e.g. dorsal, palmar, rostral, etc.) the function returns
+ * `undefined`, signalling that the caller should fall back to an identity
+ * direction matrix.
+ *
+ * @param orientation - The anatomical orientation value.
+ * @returns A 3-element unit direction column vector `[lps_x, lps_y, lps_z]`,
+ *   or `undefined` if the orientation is not one of the six LPS-compatible
+ *   values.
+ */
+export function anatomicalOrientationToItkDirection(orientation) {
+    for (let axisIndex = 0; axisIndex < LPS_ORIENTATION_PAIRS.length; axisIndex++) {
+        const [pos, neg] = LPS_ORIENTATION_PAIRS[axisIndex];
+        if (orientation === pos) {
+            const col = [0, 0, 0];
+            col[axisIndex] = 1;
+            return col;
+        }
+        if (orientation === neg) {
+            const col = [0, 0, 0];
+            col[axisIndex] = -1;
+            return col;
+        }
+    }
+    return undefined;
+}
 /**
  * Check if RFC 4 is enabled in the list of enabled RFCs.
  */

package/esm/types/rfc4.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@fideus-labs/ngff-zarr",
-  "version": "0.15.1",
+  "version": "0.16.0",
   "description": "TypeScript implementation of ngff-zarr for reading and writing OME-Zarr files",
   "license": "MIT",
   "type": "module",