@fideus-labs/ngff-zarr 0.0.1 → 0.1.0

package/esm/schemas/coordinate_systems.js

@@ -0,0 +1,140 @@
+// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
+// SPDX-License-Identifier: MIT
+import { z } from "zod";
+import { AxisSchema } from "./rfc4.js";
+// RFC5: Coordinate Systems and Transformations
+// Coordinate System schema
+export const CoordinateSystemSchema = z.object({
+    name: z.string().min(1), // MUST be non-empty and unique
+    axes: z.array(AxisSchema), // Array of axes that define the coordinate system
+});
+// Identity transformation
+export const IdentityTransformationSchema = z.object({
+    type: z.literal("identity"),
+    input: z.union([z.string(), z.array(z.string())]).optional(),
+    output: z.union([z.string(), z.array(z.string())]).optional(),
+    name: z.string().optional(),
+});
+// Map Axis transformation (axis permutation)
+export const MapAxisTransformationSchema = z.object({
+    type: z.literal("mapAxis"),
+    mapAxis: z.record(z.string(), z.string()), // Dictionary mapping axis names
+    input: z.union([z.string(), z.array(z.string())]).optional(),
+    output: z.union([z.string(), z.array(z.string())]).optional(),
+    name: z.string().optional(),
+});
+// Translation transformation
+export const TranslationTransformationSchema = z
+    .object({
+    type: z.literal("translation"),
+    translation: z.array(z.number()).optional(),
+    path: z.string().optional(), // For binary data
+    input: z.union([z.string(), z.array(z.string())]).optional(),
+    output: z.union([z.string(), z.array(z.string())]).optional(),
+    name: z.string().optional(),
+})
+    .refine((data) => data.translation !== undefined || data.path !== undefined, {
+    message: "Either translation array or path must be provided",
+});
+// Scale transformation
+export const ScaleTransformationSchema = z
+    .object({
+    type: z.literal("scale"),
+    scale: z.array(z.number()).optional(),
+    path: z.string().optional(), // For binary data
+    input: z.union([z.string(), z.array(z.string())]).optional(),
+    output: z.union([z.string(), z.array(z.string())]).optional(),
+    name: z.string().optional(),
+})
+    .refine((data) => data.scale !== undefined || data.path !== undefined, {
+    message: "Either scale array or path must be provided",
+});
+// Affine transformation
+export const AffineTransformationSchema = z
+    .object({
+    type: z.literal("affine"),
+    affine: z.array(z.array(z.number())).optional(), // 2D array for matrix
+    path: z.string().optional(), // For binary data
+    input: z.union([z.string(), z.array(z.string())]).optional(),
+    output: z.union([z.string(), z.array(z.string())]).optional(),
+    name: z.string().optional(),
+})
+    .refine((data) => data.affine !== undefined || data.path !== undefined, {
+    message: "Either affine matrix or path must be provided",
+});
+// Rotation transformation
+export const RotationTransformationSchema = z
+    .object({
+    type: z.literal("rotation"),
+    rotation: z.array(z.number()).optional(),
+    path: z.string().optional(), // For binary data
+    input: z.union([z.string(), z.array(z.string())]).optional(),
+    output: z.union([z.string(), z.array(z.string())]).optional(),
+    name: z.string().optional(),
+})
+    .refine((data) => data.rotation !== undefined || data.path !== undefined, {
+    message: "Either rotation array or path must be provided",
+});
+// Forward declaration for recursive types
+const BaseCoordinateTransformationSchema = z.union([
+    IdentityTransformationSchema,
+    MapAxisTransformationSchema,
+    TranslationTransformationSchema,
+    ScaleTransformationSchema,
+    AffineTransformationSchema,
+    RotationTransformationSchema,
+]);
+// Sequence transformation (for chaining transformations)
+export const SequenceTransformationSchema = z.object({
+    type: z.literal("sequence"),
+    transformations: z.array(BaseCoordinateTransformationSchema),
+    input: z.union([z.string(), z.array(z.string())]).optional(),
+    output: z.union([z.string(), z.array(z.string())]).optional(),
+    name: z.string().optional(),
+});
+// Inverse transformation
+export const InverseTransformationSchema = z.object({
+    type: z.literal("inverseOf"),
+    transformation: BaseCoordinateTransformationSchema,
+    input: z.union([z.string(), z.array(z.string())]).optional(),
+    output: z.union([z.string(), z.array(z.string())]).optional(),
+    name: z.string().optional(),
+});
+// Bijection transformation (forward and inverse)
+export const BijectionTransformationSchema = z.object({
+    type: z.literal("bijection"),
+    forward: BaseCoordinateTransformationSchema,
+    inverse: BaseCoordinateTransformationSchema,
+    input: z.union([z.string(), z.array(z.string())]).optional(),
+    output: z.union([z.string(), z.array(z.string())]).optional(),
+    name: z.string().optional(),
+});
+// By dimension transformation
+export const ByDimensionTransformationSchema = z.object({
+    type: z.literal("byDimension"),
+    transformations: z.array(BaseCoordinateTransformationSchema),
+    input: z.union([z.string(), z.array(z.string())]).optional(),
+    output: z.union([z.string(), z.array(z.string())]).optional(),
+    name: z.string().optional(),
+});
+// Complete coordinate transformation schema (union of all types)
+export const CoordinateTransformationSchema = z.union([
+    IdentityTransformationSchema,
+    MapAxisTransformationSchema,
+    TranslationTransformationSchema,
+    ScaleTransformationSchema,
+    AffineTransformationSchema,
+    RotationTransformationSchema,
+    SequenceTransformationSchema,
+    InverseTransformationSchema,
+    BijectionTransformationSchema,
+    ByDimensionTransformationSchema,
+]);
+// Array coordinate system schema
+export const ArrayCoordinateSystemSchema = z.object({
+    name: z.string().min(1),
+    axes: z.array(z.object({
+        name: z.string(),
+        type: z.literal("array"),
+    })),
+});

package/esm/schemas/index.d.ts

@@ -0,0 +1,9 @@
+export * from "./units.js";
+export * from "./methods.js";
+export { type AnatomicalOrientation, AnatomicalOrientationSchema, type AnatomicalOrientationValues, AnatomicalOrientationValuesSchema, type Axes as RFC4Axes, type AxesNames, AxesNamesSchema, AxesSchema as RFC4AxesSchema, type Axis as RFC4Axis, AxisSchema as RFC4AxisSchema, type AxisType, AxisTypeSchema, type BaseAxis, BaseAxisSchema, type ChannelAxis, ChannelAxisSchema, type Orientation, OrientationSchema, type SpaceAxesNames, SpaceAxesNamesSchema, type SpaceAxis, SpaceAxisSchema, type SpaceUnit, SpaceUnitSchema, type TimeAxis, TimeAxisSchema, type TimeUnit, TimeUnitSchema, } from "./rfc4.js";
+export * from "./coordinate_systems.js";
+export { AxisSchema, DatasetSchema, IdentitySchema, MetadataSchema, OmeroChannelSchema, OmeroSchema, OmeroWindowSchema, ScaleSchema, TransformSchema, TranslationSchema, } from "./zarr_metadata.js";
+export { AxisSchemaV05, type AxisV05, type CoordinateTransformation as OmeZarrCoordinateTransformation, DatasetSchemaV01, DatasetSchemaV05, type DatasetV01, type DatasetV05, type Image, ImageSchema, ImageSchemaV01, ImageSchemaV05, type ImageV01, type ImageV05, type LabelColor, LabelColorSchema, type LabelProperty, LabelPropertySchema, LabelSchemaV04, type LabelV04, type Multiscales, MultiscalesSchema, MultiscalesSchemaV01, MultiscalesSchemaV05, type MultiscalesV01, type MultiscalesV05, type OmeMetadata, OmeMetadataSchema, type Omero as OmeZarrOmero, type OmeroChannel as OmeZarrOmeroChannel, OmeroChannelSchema as OmeZarrOmeroChannelSchema, OmeroSchema as OmeZarrOmeroSchema, type OmeroWindow as OmeZarrOmeroWindow, OmeroWindowSchema as OmeZarrOmeroWindowSchema, type OmeSeries, OmeSeriesSchema, OmeZarrCoordinateTransformationSchema, type OmeZarrMetadata, OmeZarrMetadataSchema, type OmeZarrVersion, OmeZarrVersion01Schema, OmeZarrVersion02Schema, OmeZarrVersion03Schema, OmeZarrVersion04Schema, OmeZarrVersion05Schema, OmeZarrVersionSchema, type PlateAcquisition, PlateAcquisitionSchema, type PlateColumn, PlateColumnSchema, type PlateRow, PlateRowSchema, PlateSchemaV05, type PlateV05, type PlateWell, PlateWellSchema, type WellImage, WellImageSchema, WellSchemaV05, type WellV05, } from "./ome_zarr.js";
+export * from "./ngff_image.js";
+export * from "./multiscales.js";
+//# sourceMappingURL=index.d.ts.map

package/esm/schemas/index.d.ts.map

@@ -0,0 +1 @@
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package/esm/schemas/index.js

@@ -0,0 +1,38 @@
+// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
+// SPDX-License-Identifier: MIT
+// Re-export all schemas with explicit naming to avoid conflicts
+export * from "./units.js";
+export * from "./methods.js";
+// RFC4 schemas
+export { AnatomicalOrientationSchema, AnatomicalOrientationValuesSchema, AxesNamesSchema, AxesSchema as RFC4AxesSchema, AxisSchema as RFC4AxisSchema, AxisTypeSchema, BaseAxisSchema, ChannelAxisSchema, OrientationSchema, SpaceAxesNamesSchema, SpaceAxisSchema, SpaceUnitSchema, TimeAxisSchema, TimeUnitSchema, } from "./rfc4.js";
+// Coordinate systems (RFC5)
+export * from "./coordinate_systems.js";
+// Zarr metadata schemas (with RFC4 integration)
+export { AxisSchema, DatasetSchema, IdentitySchema, MetadataSchema, OmeroChannelSchema, OmeroSchema, OmeroWindowSchema, ScaleSchema, TransformSchema, TranslationSchema, } from "./zarr_metadata.js";
+// OME-Zarr specification schemas
+export { 
+// Axis schemas
+AxisSchemaV05, 
+// Dataset schemas
+DatasetSchemaV01, DatasetSchemaV05, ImageSchema, 
+// Image schemas
+ImageSchemaV01, ImageSchemaV05, 
+// Label schemas
+LabelColorSchema, LabelPropertySchema, LabelSchemaV04, MultiscalesSchema, 
+// Multiscales schemas
+MultiscalesSchemaV01, MultiscalesSchemaV05, OmeMetadataSchema, OmeroChannelSchema as OmeZarrOmeroChannelSchema, OmeroSchema as OmeZarrOmeroSchema, 
+// Core schemas
+OmeroWindowSchema as OmeZarrOmeroWindowSchema, 
+// OME metadata schemas
+OmeSeriesSchema, OmeZarrCoordinateTransformationSchema, 
+// Comprehensive schema
+OmeZarrMetadataSchema, OmeZarrVersion01Schema, OmeZarrVersion02Schema, OmeZarrVersion03Schema, OmeZarrVersion04Schema, OmeZarrVersion05Schema, 
+// Version schemas
+OmeZarrVersionSchema, 
+// Plate schemas
+PlateAcquisitionSchema, PlateColumnSchema, PlateRowSchema, PlateSchemaV05, PlateWellSchema, 
+// Well schemas
+WellImageSchema, WellSchemaV05, } from "./ome_zarr.js";
+// NGFF Image and Multiscales
+export * from "./ngff_image.js";
+export * from "./multiscales.js";

package/esm/schemas/methods.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"methods.d.ts","sourceRoot":"","sources":["../../src/schemas/methods.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAExB,eAAO,MAAM,aAAa,EAAE,CAAC,CAAC,UAI5B,CAAC"}
+{"version":3,"file":"methods.d.ts","sourceRoot":"","sources":["../../src/schemas/methods.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAExB,eAAO,MAAM,aAAa,EAAE,CAAC,CAAC,UAI5B,CAAC"}

package/esm/schemas/methods.js

@@ -1,3 +1,5 @@
+// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
+// SPDX-License-Identifier: MIT
 import { z } from "zod";
 export const MethodsSchema = z.enum([
     "itkwasm_gaussian",

package/esm/schemas/multiscales.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"multiscales.d.ts","sourceRoot":"","sources":["../../src/schemas/multiscales.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAKxB,eAAO,MAAM,eAAe,EAAE,CAAC,CAAC,UAK9B,CAAC;AAEH,eAAO,MAAM,wBAAwB,EAAE,CAAC,CAAC,UAQvC,CAAC"}
+{"version":3,"file":"multiscales.d.ts","sourceRoot":"","sources":["../../src/schemas/multiscales.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAKxB,eAAO,MAAM,eAAe,EAAE,CAAC,CAAC,UAK9B,CAAC;AAEH,eAAO,MAAM,wBAAwB,EAAE,CAAC,CAAC,UAQvC,CAAC"}

package/esm/schemas/multiscales.js

@@ -1,3 +1,5 @@
+// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
+// SPDX-License-Identifier: MIT
 import { z } from "zod";
 import { NgffImageOptionsSchema } from "./ngff_image.js";
 import { MetadataSchema } from "./zarr_metadata.js";

package/esm/schemas/ngff_image.d.ts

@@ -1,8 +1,14 @@
 import { z } from "zod";
 import { UnitsSchema } from "./units.js";
-import { LazyArrayMetadataSchema } from "./lazy_array.js";
+declare const ZarrArraySchema: z.ZodObject<{
+    shape: z.ZodArray<z.ZodNumber>;
+    dtype: z.ZodString;
+    chunks: z.ZodArray<z.ZodNumber>;
+    path: z.ZodOptional<z.ZodString>;
+    name: z.ZodOptional<z.ZodString>;
+}>;
 export declare const NgffImageOptionsSchema: z.ZodObject<{
-    data: typeof LazyArrayMetadataSchema;
+    data: typeof ZarrArraySchema;
     dims: z.ZodArray<z.ZodString>;
     scale: z.ZodRecord<z.ZodString, z.ZodNumber>;
     translation: z.ZodRecord<z.ZodString, z.ZodNumber>;
@@ -10,4 +16,5 @@ export declare const NgffImageOptionsSchema: z.ZodObject<{
     axesUnits: z.ZodOptional<z.ZodRecord<z.ZodString, typeof UnitsSchema>>;
     computedCallbacks: z.ZodDefault<z.ZodArray<z.ZodAny>>;
 }>;
+export {};
 //# sourceMappingURL=ngff_image.d.ts.map

package/esm/schemas/ngff_image.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"ngff_image.d.ts","sourceRoot":"","sources":["../../src/schemas/ngff_image.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AACxB,OAAO,EAAE,WAAW,EAAE,MAAM,YAAY,CAAC;AACzC,OAAO,EAAE,uBAAuB,EAAE,MAAM,iBAAiB,CAAC;AAE1D,eAAO,MAAM,sBAAsB,EAAE,CAAC,CAAC,SAAS,CAAC;IAC/C,IAAI,EAAE,OAAO,uBAAuB,CAAC;IACrC,IAAI,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;IAC9B,KAAK,EAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,EAAE,CAAC,CAAC,SAAS,CAAC,CAAC;IAC7C,WAAW,EAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,EAAE,CAAC,CAAC,SAAS,CAAC,CAAC;IACnD,IAAI,EAAE,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;IAChC,SAAS,EAAE,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,EAAE,OAAO,WAAW,CAAC,CAAC,CAAC;IACvE,iBAAiB,EAAE,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC;CACvD,CAQC,CAAC"}
+{"version":3,"file":"ngff_image.d.ts","sourceRoot":"","sources":["../../src/schemas/ngff_image.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AACxB,OAAO,EAAE,WAAW,EAAE,MAAM,YAAY,CAAC;AAGzC,QAAA,MAAM,eAAe,EAAE,CAAC,CAAC,SAAS,CAAC;IACjC,KAAK,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;IAC/B,KAAK,EAAE,CAAC,CAAC,SAAS,CAAC;IACnB,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;IAChC,IAAI,EAAE,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;IACjC,IAAI,EAAE,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;CAClC,CAMC,CAAC;AAEH,eAAO,MAAM,sBAAsB,EAAE,CAAC,CAAC,SAAS,CAAC;IAC/C,IAAI,EAAE,OAAO,eAAe,CAAC;IAC7B,IAAI,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;IAC9B,KAAK,EAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,EAAE,CAAC,CAAC,SAAS,CAAC,CAAC;IAC7C,WAAW,EAAE,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,EAAE,CAAC,CAAC,SAAS,CAAC,CAAC;IACnD,IAAI,EAAE,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;IAChC,SAAS,EAAE,CAAC,CAAC,WAAW,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,SAAS,EAAE,OAAO,WAAW,CAAC,CAAC,CAAC;IACvE,iBAAiB,EAAE,CAAC,CAAC,UAAU,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC;CACvD,CAQC,CAAC"}

package/esm/schemas/ngff_image.js

@@ -1,8 +1,17 @@
+// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
+// SPDX-License-Identifier: MIT
 import { z } from "zod";
 import { UnitsSchema } from "./units.js";
-import { LazyArrayMetadataSchema } from "./lazy_array.js";
+// Since NgffImage now uses zarr.Array directly, we create a basic schema for validation
+const ZarrArraySchema = z.object({
+    shape: z.array(z.number()),
+    dtype: z.string(),
+    chunks: z.array(z.number()),
+    path: z.string().optional(),
+    name: z.string().optional(),
+});
 export const NgffImageOptionsSchema = z.object({
-    data: LazyArrayMetadataSchema,
+    data: ZarrArraySchema,
     dims: z.array(z.string()),
     scale: z.record(z.string(), z.number()),
     translation: z.record(z.string(), z.number()),