@fideus-labs/fidnii 0.4.0 → 0.6.0

package/dist/fromTiff.js.map

@@ -1 +1 @@
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+{"version":3,"file":"fromTiff.js","sourceRoot":"","sources":["../src/fromTiff.ts"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,+BAA+B;AAY/B,OAAO,EAAE,SAAS,EAAE,MAAM,mBAAmB,CAAA;AAG7C,OAAO,EAAE,YAAY,EAAE,MAAM,gCAAgC,CAAA;AAgC7D;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA6BG;AACH,MAAM,CAAC,KAAK,UAAU,QAAQ,CAC5B,MAA+C,EAC/C,UAA2B,EAAE;IAE7B,0EAA0E;IAC1E,MAAM,QAAQ,GAAiC,OAAO,CAAC,IAAI;QACzD,CAAC,CAAC,EAAE,GAAG,OAAO,CAAC,IAAI,EAAE,IAAI,EAAE,OAAO,CAAC,IAAI,EAAE;QACzC,CAAC,CAAC,OAAO,CAAC,IAAI,CAAA;IAEhB,IAAI,KAAgB,CAAA;IACpB,IAAI,MAAM,YAAY,SAAS,EAAE,CAAC;QAChC,mEAAmE;QACnE,0EAA0E;QAC1E,KAAK,GAAG,MAAM,CAAA;IAChB,CAAC;SAAM,IAAI,OAAO,MAAM,KAAK,QAAQ,EAAE,CAAC;QACtC,KAAK,GAAG,MAAM,SAAS,CAAC,OAAO,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IACnD,CAAC;SAAM,IAAI,MAAM,YAAY,IAAI,EAAE,CAAC;QAClC,KAAK,GAAG,MAAM,SAAS,CAAC,QAAQ,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IACpD,CAAC;SAAM,IAAI,MAAM,YAAY,WAAW,EAAE,CAAC;QACzC,KAAK,GAAG,MAAM,SAAS,CAAC,eAAe,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IAC3D,CAAC;SAAM,CAAC;QACN,MAAM,IAAI,KAAK,CACb,wDAAwD;YACtD,2BAA2B,CAC9B,CAAA;IACH,CAAC;IAED,iEAAiE;IACjE,kEAAkE;IAClE,mEAAmE;IACnE,iEAAiE;IACjE,EAAE;IACF,oDAAoD;IACpD,OAAO,YAAY,CAAC,KAA4B,EAAE;QAChD,OAAO,EAAE,KAAK;QACd,GAAG,OAAO,CAAC,QAAQ;KACpB,CAAC,CAAA;AACJ,CAAC"}

package/dist/index.d.ts

@@ -30,7 +30,7 @@
  * // await image.populateVolume();
  * ```
  */
-export type { TiffStoreOptions } from "@fideus-labs/fiff";
+export type { DeflatePool, TiffStoreOptions } from "@fideus-labs/fiff";
 export { TiffStore } from "@fideus-labs/fiff";
 export { Methods } from "@fideus-labs/ngff-zarr";
 export { terminateOmeroWorkerPool, terminateWorkerPool, } from "@fideus-labs/ngff-zarr/browser";
@@ -46,9 +46,11 @@ export { OMEZarrNVImage } from "./OMEZarrNVImage.js";
 export { buildSelection, RegionCoalescer } from "./RegionCoalescer.js";
 export type { OrthogonalAxis } from "./ResolutionSelector.js";
 export { alignRegionToChunks, calculateUpsampleFactor, getChunkShape, getFullVolumeDimensions, getMiddleResolutionIndex, getVolumeShape, select2DResolution, selectResolution, } from "./ResolutionSelector.js";
-export type { AttachedNiivueState, ChannelInfo, ChunkAlignedRegion, ChunkCache, ClipPlane, ClipPlanes, OMEZarrNVImageOptions, PixelRegion, RegionFetchResult, ResolutionSelection, SlabBufferState, SlabSliceType, TypedArray, VolumeBounds, ZarrDtype, } from "./types.js";
+export type { AttachedNiivueState, CachedTimeFrame, ChannelInfo, ChunkAlignedRegion, ChunkCache, ClipPlane, ClipPlanes, OMEZarrNVImageOptions, PixelRegion, RegionFetchResult, ResolutionSelection, SlabBufferState, SlabSliceType, TimeAxisInfo, TimeUnit, TypedArray, VolumeBounds, ZarrDtype, } from "./types.js";
 export { getBytesPerPixel, getChannelInfo, getNiftiDataType, getRGBNiftiDataType, getTypedArrayConstructor, isRGBImage, NiftiDataType, needsRGBNormalization, parseZarritaDtype, SLICE_TYPE, } from "./types.js";
 export { affineToNiftiSrows, calculateWorldBounds, createAffineFromNgffImage, createAffineFromOMEZarr, getPixelDimensions, updateAffineForRegion, } from "./utils/affine.js";
 export { ceilPixelCoord, clampPixelCoord, floorPixelCoord, normalizedToWorld, pixelToWorld, pixelToWorldAffine, roundPixelCoord, worldToNormalized, worldToPixel, worldToPixelAffine, } from "./utils/coordinates.js";
+export type { OrientationMapping, OrientationSigns, } from "./utils/orientation.js";
+export { applyOrientationToAffine, getOrientationInfo, getOrientationMapping, getOrientationSigns, } from "./utils/orientation.js";
 export { boundsApproxEqual, computeViewportBounds2D, computeViewportBounds3D, intersectBounds, } from "./ViewportBounds.js";
 //# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAGA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+BG;AAEH,YAAY,EAAE,WAAW,EAAE,gBAAgB,EAAE,MAAM,mBAAmB,CAAA;AACtE,OAAO,EAAE,SAAS,EAAE,MAAM,mBAAmB,CAAA;AAE7C,OAAO,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAA;AAEhD,OAAO,EACL,wBAAwB,EACxB,mBAAmB,GACpB,MAAM,gCAAgC,CAAA;AAGvC,OAAO,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAA;AAElD,OAAO,EACL,aAAa,EACb,wBAAwB,EACxB,oBAAoB,EACpB,uBAAuB,EACvB,kBAAkB,EAClB,uBAAuB,EACvB,iBAAiB,EACjB,0BAA0B,EAC1B,eAAe,EACf,uBAAuB,EACvB,8BAA8B,EAC9B,kBAAkB,EAClB,eAAe,EACf,eAAe,EACf,wBAAwB,EACxB,oBAAoB,EACpB,kBAAkB,GACnB,MAAM,iBAAiB,CAAA;AACxB,YAAY,EACV,2BAA2B,EAC3B,kCAAkC,EAClC,sBAAsB,EACtB,eAAe,GAChB,MAAM,aAAa,CAAA;AAEpB,OAAO,EAAE,mBAAmB,EAAE,MAAM,aAAa,CAAA;AACjD,YAAY,EAAE,eAAe,EAAE,MAAM,eAAe,CAAA;AAEpD,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAExC,YAAY,EAAE,aAAa,EAAE,MAAM,gBAAgB,CAAA;AACnD,OAAO,EAAE,oBAAoB,EAAE,gBAAgB,EAAE,MAAM,gBAAgB,CAAA;AAEvE,OAAO,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAA;AAEpD,OAAO,EAAE,cAAc,EAAE,eAAe,EAAE,MAAM,sBAAsB,CAAA;AACtE,YAAY,EAAE,cAAc,EAAE,MAAM,yBAAyB,CAAA;AAE7D,OAAO,EACL,mBAAmB,EACnB,uBAAuB,EACvB,aAAa,EACb,uBAAuB,EACvB,wBAAwB,EACxB,cAAc,EACd,kBAAkB,EAClB,gBAAgB,GACjB,MAAM,yBAAyB,CAAA;AAEhC,YAAY,EACV,mBAAmB,EACnB,eAAe,EACf,WAAW,EACX,kBAAkB,EAClB,UAAU,EACV,SAAS,EACT,UAAU,EACV,qBAAqB,EACrB,WAAW,EACX,iBAAiB,EACjB,mBAAmB,EACnB,eAAe,EACf,aAAa,EACb,YAAY,EACZ,QAAQ,EACR,UAAU,EACV,YAAY,EACZ,SAAS,GACV,MAAM,YAAY,CAAA;AAGnB,OAAO,EACL,gBAAgB,EAChB,cAAc,EACd,gBAAgB,EAChB,mBAAmB,EACnB,wBAAwB,EACxB,UAAU,EACV,aAAa,EACb,qBAAqB,EACrB,iBAAiB,EACjB,UAAU,GACX,MAAM,YAAY,CAAA;AAEnB,OAAO,EACL,kBAAkB,EAClB,oBAAoB,EACpB,yBAAyB,EACzB,uBAAuB,EACvB,kBAAkB,EAClB,qBAAqB,GACtB,MAAM,mBAAmB,CAAA;AAE1B,OAAO,EACL,cAAc,EACd,eAAe,EACf,eAAe,EACf,iBAAiB,EACjB,YAAY,EACZ,kBAAkB,EAClB,eAAe,EACf,iBAAiB,EACjB,YAAY,EACZ,kBAAkB,GACnB,MAAM,wBAAwB,CAAA;AAE/B,YAAY,EACV,kBAAkB,EAClB,gBAAgB,GACjB,MAAM,wBAAwB,CAAA;AAC/B,OAAO,EACL,wBAAwB,EACxB,kBAAkB,EAClB,qBAAqB,EACrB,mBAAmB,GACpB,MAAM,wBAAwB,CAAA;AAE/B,OAAO,EACL,iBAAiB,EACjB,uBAAuB,EACvB,uBAAuB,EACvB,eAAe,GAChB,MAAM,qBAAqB,CAAA"}

package/dist/index.js

@@ -27,6 +27,7 @@ export { getBytesPerPixel, getChannelInfo, getNiftiDataType, getRGBNiftiDataType
 export { affineToNiftiSrows, calculateWorldBounds, createAffineFromNgffImage, createAffineFromOMEZarr, getPixelDimensions, updateAffineForRegion, } from "./utils/affine.js";
 // Coordinate utilities
 export { ceilPixelCoord, clampPixelCoord, floorPixelCoord, normalizedToWorld, pixelToWorld, pixelToWorldAffine, roundPixelCoord, worldToNormalized, worldToPixel, worldToPixelAffine, } from "./utils/coordinates.js";
+export { applyOrientationToAffine, getOrientationInfo, getOrientationMapping, getOrientationSigns, } from "./utils/orientation.js";
 // Viewport bounds utilities
 export { boundsApproxEqual, computeViewportBounds2D, computeViewportBounds3D, intersectBounds, } from "./ViewportBounds.js";
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,wDAAwD;AACxD,+BAA+B;AAoC/B,OAAO,EAAE,SAAS,EAAE,MAAM,mBAAmB,CAAA;AAC7C,sFAAsF;AACtF,OAAO,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAA;AAChD,qDAAqD;AACrD,OAAO,EACL,wBAAwB,EACxB,mBAAmB,GACpB,MAAM,gCAAgC,CAAA;AAEvC,iBAAiB;AACjB,OAAO,EAAE,aAAa,EAAE,MAAM,oBAAoB,CAAA;AAClD,wBAAwB;AACxB,OAAO,EACL,aAAa,EACb,wBAAwB,EACxB,oBAAoB,EACpB,uBAAuB,EACvB,kBAAkB,EAClB,uBAAuB,EACvB,iBAAiB,EACjB,0BAA0B,EAC1B,eAAe,EACf,uBAAuB,EACvB,8BAA8B,EAC9B,kBAAkB,EAClB,eAAe,EACf,eAAe,EACf,wBAAwB,EACxB,oBAAoB,EACpB,kBAAkB,GACnB,MAAM,iBAAiB,CAAA;AAOxB,gDAAgD;AAChD,OAAO,EAAE,mBAAmB,EAAE,MAAM,aAAa,CAAA;AAEjD,uCAAuC;AACvC,OAAO,EAAE,QAAQ,EAAE,MAAM,eAAe,CAAA;AAGxC,OAAO,EAAE,oBAAoB,EAAE,gBAAgB,EAAE,MAAM,gBAAgB,CAAA;AACvE,aAAa;AACb,OAAO,EAAE,cAAc,EAAE,MAAM,qBAAqB,CAAA;AACpD,mBAAmB;AACnB,OAAO,EAAE,cAAc,EAAE,eAAe,EAAE,MAAM,sBAAsB,CAAA;AAEtE,gCAAgC;AAChC,OAAO,EACL,mBAAmB,EACnB,uBAAuB,EACvB,aAAa,EACb,uBAAuB,EACvB,wBAAwB,EACxB,cAAc,EACd,kBAAkB,EAClB,gBAAgB,GACjB,MAAM,yBAAyB,CAAA;AAsBhC,iEAAiE;AACjE,iBAAiB;AACjB,OAAO,EACL,gBAAgB,EAChB,cAAc,EACd,gBAAgB,EAChB,mBAAmB,EACnB,wBAAwB,EACxB,UAAU,EACV,aAAa,EACb,qBAAqB,EACrB,iBAAiB,EACjB,UAAU,GACX,MAAM,YAAY,CAAA;AACnB,mBAAmB;AACnB,OAAO,EACL,kBAAkB,EAClB,oBAAoB,EACpB,yBAAyB,EACzB,uBAAuB,EACvB,kBAAkB,EAClB,qBAAqB,GACtB,MAAM,mBAAmB,CAAA;AAC1B,uBAAuB;AACvB,OAAO,EACL,cAAc,EACd,eAAe,EACf,eAAe,EACf,iBAAiB,EACjB,YAAY,EACZ,kBAAkB,EAClB,eAAe,EACf,iBAAiB,EACjB,YAAY,EACZ,kBAAkB,GACnB,MAAM,wBAAwB,CAAA;AAM/B,OAAO,EACL,wBAAwB,EACxB,kBAAkB,EAClB,qBAAqB,EACrB,mBAAmB,GACpB,MAAM,wBAAwB,CAAA;AAC/B,4BAA4B;AAC5B,OAAO,EACL,iBAAiB,EACjB,uBAAuB,EACvB,uBAAuB,EACvB,eAAe,GAChB,MAAM,qBAAqB,CAAA"}

package/dist/types.d.ts

@@ -153,6 +153,24 @@ export interface OMEZarrNVImageOptions {
      * This option has no effect on 3D volumes (images with a `"z"` axis).
      */
     flipY2D?: boolean;
+    /**
+     * Initial time index to display (default: 0, or `omero.defaultT` if available).
+     *
+     * Only relevant for datasets with a `"t"` (time) dimension. Ignored
+     * when the dataset has no time axis.
+     */
+    timeIndex?: number;
+    /**
+     * Number of adjacent time frames to pre-fetch in each direction (default: 2).
+     *
+     * When the user navigates to time index `t`, frames
+     * `[t - timePrefetchCount, t + timePrefetchCount]` are fetched in the
+     * background so that subsequent scrubbing can swap frames instantly from
+     * the cache. Set to `0` to disable pre-fetching.
+     *
+     * Only relevant for datasets with a `"t"` (time) dimension.
+     */
+    timePrefetchCount?: number;
 }
 /**
  * Result of fetching a region from the zarr store.
@@ -266,6 +284,48 @@ export declare const NiftiDataType: {
     readonly RGBA32: 2304;
 };
 export type NiftiDataTypeCode = (typeof NiftiDataType)[keyof typeof NiftiDataType];
+/**
+ * Time units supported by OME-Zarr NGFF.
+ *
+ * Matches the UDUNITS-2 time units recognized by the OME-Zarr
+ * specification for the `"time"` axis type.
+ */
+export type TimeUnit = "attosecond" | "centisecond" | "day" | "decisecond" | "exasecond" | "femtosecond" | "gigasecond" | "hectosecond" | "hour" | "kilosecond" | "megasecond" | "microsecond" | "millisecond" | "minute" | "nanosecond" | "petasecond" | "picosecond" | "second" | "terasecond" | "yoctosecond" | "yottasecond" | "zeptosecond" | "zettasecond";
+/**
+ * Time axis metadata extracted from OME-Zarr multiscales.
+ *
+ * Present only when the dataset has a `"t"` dimension. Contains
+ * the number of time points, physical time step, and unit
+ * information needed for time navigation.
+ */
+export interface TimeAxisInfo {
+    /** Number of time points (from the zarr array shape along `"t"`) */
+    readonly count: number;
+    /** Index of the `"t"` dimension in `NgffImage.dims` */
+    readonly dimIndex: number;
+    /** Physical time step between adjacent indices (from `scale.t`) */
+    readonly step: number;
+    /** Time origin offset (from `translation.t`) */
+    readonly origin: number;
+    /** Time unit (e.g., `"second"`, `"millisecond"`), or `undefined` if not specified */
+    readonly unit: TimeUnit | undefined;
+}
+/**
+ * A pre-fetched 3D frame ready for instant buffer swap.
+ *
+ * Used by the time frame cache to avoid re-fetching when scrubbing
+ * through adjacent time points.
+ */
+export interface CachedTimeFrame {
+    /** The typed array pixel data for this frame */
+    data: TypedArray;
+    /** Spatial shape in `[z, y, x]` order */
+    shape: [number, number, number];
+    /** The resolution level this was fetched at */
+    levelIndex: number;
+    /** The chunk-aligned pixel region this was fetched for */
+    region: ChunkAlignedRegion;
+}
 /**
  * Information about a channel (component) dimension in the image.
  */

package/dist/types.d.ts.map

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package/dist/types.js.map

@@ -1 +1 @@
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package/dist/utils/affine.d.ts

@@ -23,8 +23,18 @@ export declare function createAffineFromOMEZarr(scale: Record<string, number>, t
 /**
  * Create an affine matrix from an NgffImage.
  *
- * @param ngffImage - The NgffImage containing scale and translation
- * @returns 4x4 affine matrix
+ * If the image has RFC-4 anatomical orientation metadata
+ * (`axesOrientations`), the affine column vectors and translations
+ * are sign-flipped so the matrix encodes direction relative to
+ * the NIfTI RAS+ convention. This allows NiiVue's `calculateRAS()`
+ * to correctly determine the anatomical layout.
+ *
+ * When no orientation metadata is present, the matrix is identical
+ * to a plain scale + translation affine (backward-compatible).
+ *
+ * @param ngffImage - The NgffImage containing scale, translation,
+ *   and optional `axesOrientations`
+ * @returns 4x4 affine matrix with orientation signs applied
  */
 export declare function createAffineFromNgffImage(ngffImage: NgffImage): mat4;
 /**

package/dist/utils/affine.d.ts.map

@@ -1 +1 @@
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package/dist/utils/affine.js

@@ -1,6 +1,7 @@
 // SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
 // SPDX-License-Identifier: MIT
 import { mat4 } from "gl-matrix";
+import { applyOrientationToAffine } from "./orientation.js";
 /**
  * Create a 4x4 affine transformation matrix from OME-Zarr scale and translation.
  *
@@ -60,11 +61,22 @@ export function createAffineFromOMEZarr(scale, translation) {
 /**
  * Create an affine matrix from an NgffImage.
  *
- * @param ngffImage - The NgffImage containing scale and translation
- * @returns 4x4 affine matrix
+ * If the image has RFC-4 anatomical orientation metadata
+ * (`axesOrientations`), the affine column vectors and translations
+ * are sign-flipped so the matrix encodes direction relative to
+ * the NIfTI RAS+ convention. This allows NiiVue's `calculateRAS()`
+ * to correctly determine the anatomical layout.
+ *
+ * When no orientation metadata is present, the matrix is identical
+ * to a plain scale + translation affine (backward-compatible).
+ *
+ * @param ngffImage - The NgffImage containing scale, translation,
+ *   and optional `axesOrientations`
+ * @returns 4x4 affine matrix with orientation signs applied
  */
 export function createAffineFromNgffImage(ngffImage) {
-    return createAffineFromOMEZarr(ngffImage.scale, ngffImage.translation);
+    const affine = createAffineFromOMEZarr(ngffImage.scale, ngffImage.translation);
+    return applyOrientationToAffine(affine, ngffImage.axesOrientations);
 }
 /**
  * Convert an affine matrix to a flat array for NIfTI header.

package/dist/utils/affine.js.map

@@ -1 +1 @@
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package/dist/utils/orientation.d.ts

@@ -0,0 +1,157 @@
+import type { AnatomicalOrientation } from "@fideus-labs/ngff-zarr";
+import type { mat4 } from "gl-matrix";
+/**
+ * Mapping from an array axis orientation to the physical (RAS) row
+ * and sign it should occupy in the NIfTI affine.
+ *
+ * - `physicalRow`: which row of the 4x4 affine the scale/translation
+ *   should be placed in (0 = R/L, 1 = A/P, 2 = S/I)
+ * - `sign`: `1` if the orientation is in the RAS+ direction,
+ *   `-1` if opposite
+ */
+export interface OrientationMapping {
+    readonly physicalRow: 0 | 1 | 2;
+    readonly sign: 1 | -1;
+}
+/**
+ * Sign multipliers for each spatial axis, used to encode anatomical
+ * orientation into the NIfTI affine matrix.
+ *
+ * A value of `1` means the axis increases in the RAS+ direction
+ * (Right, Anterior, Superior). A value of `-1` means it increases
+ * in the opposite direction (Left, Posterior, Inferior).
+ *
+ * @deprecated Use {@link getOrientationMapping} for full permutation
+ *   support. This interface only captures sign, not axis permutations.
+ */
+export interface OrientationSigns {
+    readonly x: 1 | -1;
+    readonly y: 1 | -1;
+    readonly z: 1 | -1;
+}
+/**
+ * Get the orientation mapping (physical row + RAS sign) for a single
+ * axis orientation.
+ *
+ * For unknown/exotic orientations, returns `undefined`.
+ *
+ * @param orientation - The anatomical orientation for one axis
+ * @returns The physical row and sign, or `undefined` if not a standard
+ *   L/R, A/P, or S/I orientation
+ */
+export declare function getOrientationInfo(orientation: AnatomicalOrientation): OrientationMapping | undefined;
+/**
+ * Get orientation mappings for all three spatial axes.
+ *
+ * Each mapping tells you which physical (RAS) row the array axis
+ * maps to and what sign to apply. This supports both sign flips
+ * (e.g. LPS) and axis permutations (e.g. when the OME-Zarr y axis
+ * encodes S/I instead of A/P).
+ *
+ * When no orientation metadata is present, returns the identity
+ * mapping: x→row 0 sign +1, y→row 1 sign +1, z→row 2 sign +1.
+ *
+ * @param axesOrientations - Orientation metadata from
+ *   `NgffImage.axesOrientations`, or `undefined`
+ * @returns Mappings for x, y, and z axes
+ *
+ * @example
+ * ```typescript
+ * // LPS data: x→row0 sign-1, y→row1 sign-1, z→row2 sign+1
+ * getOrientationMapping(LPS)
+ *
+ * // Permuted (mri.nii.gz): x→row0 sign-1, y→row2 sign-1, z→row1 sign+1
+ * getOrientationMapping(permutedOrientations)
+ * ```
+ */
+export declare function getOrientationMapping(axesOrientations: Record<string, AnatomicalOrientation> | undefined): {
+    x: OrientationMapping;
+    y: OrientationMapping;
+    z: OrientationMapping;
+};
+/**
+ * Compute RAS+ sign multipliers from RFC-4 anatomical orientation metadata.
+ *
+ * For each spatial axis, determines whether the axis direction is aligned
+ * with (+1) or opposite to (-1) the NIfTI RAS+ convention:
+ * - x: positive = left-to-right (R), negative = right-to-left (L)
+ * - y: positive = posterior-to-anterior (A), negative = anterior-to-posterior (P)
+ * - z: positive = inferior-to-superior (S), negative = superior-to-inferior (I)
+ *
+ * Only the 6 standard L/R, A/P, I/S orientations are handled. Exotic
+ * orientations (dorsal/ventral, rostral/caudal, etc.) are treated as
+ * unknown and default to +1.
+ *
+ * **Note**: This function only returns sign information, not axis
+ * permutation. For full permutation support, use
+ * {@link getOrientationMapping} and {@link applyOrientationToAffine}.
+ *
+ * @param axesOrientations - Orientation metadata from `NgffImage.axesOrientations`,
+ *   or `undefined` if no orientation metadata is present
+ * @returns Sign multipliers for x, y, and z axes
+ *
+ * @example
+ * ```typescript
+ * import { LPS, RAS } from "@fideus-labs/ngff-zarr"
+ *
+ * // LPS data: x and y are anti-RAS+
+ * getOrientationSigns(LPS)
+ * // => { x: -1, y: -1, z: 1 }
+ *
+ * // RAS data: all axes are RAS+
+ * getOrientationSigns(RAS)
+ * // => { x: 1, y: 1, z: 1 }
+ *
+ * // No orientation: defaults to all positive
+ * getOrientationSigns(undefined)
+ * // => { x: 1, y: 1, z: 1 }
+ * ```
+ */
+export declare function getOrientationSigns(axesOrientations: Record<string, AnatomicalOrientation> | undefined): OrientationSigns;
+/**
+ * Apply anatomical orientation to an affine matrix in place.
+ *
+ * Builds a rotation/permutation matrix from the orientation metadata
+ * and applies it to the affine's 3x3 rotation/scale submatrix. This
+ * supports both simple sign flips (e.g. LPS where axes align with
+ * physical axes but directions differ) and full axis permutations
+ * (e.g. when OME-Zarr y axis encodes S/I instead of A/P).
+ *
+ * The input affine is expected to be a diagonal scale+translation
+ * matrix in gl-matrix column-major format, as produced by
+ * `createAffineFromOMEZarr()`:
+ *
+ * ```
+ * | sx  0   0  tx |
+ * | 0   sy  0  ty |
+ * | 0   0   sz tz |
+ * | 0   0   0  1  |
+ * ```
+ *
+ * **3x3 submatrix**: Each column's scale is placed in the row
+ * corresponding to the physical RAS axis the array axis maps to,
+ * with the appropriate sign:
+ *
+ * ```
+ * Column j (array axis j):
+ *   row = physicalRow for axis j
+ *   affine[j*4 + row] = sign * scale_j
+ * ```
+ *
+ * **Translation column**: Sign-flipped for LPS→RAS conversion but
+ * NOT row-permuted. This is because `itkImageToNgffImage` stores
+ * the ITK LPS origin values in array-axis-label order without
+ * transforming them through the direction matrix. The label
+ * assignment (x/y/z) follows the reversed ITK axis indices, so the
+ * physical meaning of each translation value matches its original
+ * LPS axis, regardless of axis permutation.
+ *
+ * When `axesOrientations` is `undefined`, the affine is left
+ * unchanged (backward-compatible identity mapping).
+ *
+ * @param affine - 4x4 affine matrix (column-major, modified in place)
+ * @param axesOrientations - Orientation metadata from `NgffImage.axesOrientations`
+ * @returns The same affine matrix (for chaining)
+ */
+export declare function applyOrientationToAffine(affine: mat4, axesOrientations: Record<string, AnatomicalOrientation> | undefined): mat4;
+//# sourceMappingURL=orientation.d.ts.map

package/dist/utils/orientation.d.ts.map

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