[Proposal] Revised OME-Zarr data type hierarchy and interface

packages/omezarr/src/index.ts

@@ -1,6 +1,10 @@
 export {
     buildOmeZarrSliceRenderer,
     buildAsyncOmezarrRenderer,
+    makeRGBColorChannels,
+    makeRenderSettings,
+    toZarrDataSpecifier,
+    type Decoder,
     type VoxelTileImage,
     type RenderSettings,
     type RenderSettingsChannel,
@@ -25,37 +29,33 @@ export {
     type OmeZarrOmeroChannelWindow,
     type OmeZarrOmeroChannel,
     type OmeZarrOmero,
-    type OmeZarrAttrs,
-    type OmeZarrArrayMetadata,
+    type OmeZarrData,
+    OmeZarrArrayTransform,
     OmeZarrAxisSchema,
     OmeZarrCoordinateTranslationSchema,
     OmeZarrCoordinateScaleSchema,
     OmeZarrCoordinateTransformSchema,
     OmeZarrDatasetSchema,
+    OmeZarrGroupTransform,
     OmeZarrMultiscaleSchema,
     OmeZarrOmeroChannelWindowSchema,
     OmeZarrOmeroChannelSchema,
     OmeZarrOmeroSchema,
-    OmeZarrAttrsSchema,
-    OmeZarrMetadata,
-    type DehydratedOmeZarrArray,
-    type DehydratedOmeZarrMetadata,
 } from './zarr/types';
 export {
-    loadMetadata,
-    loadZarrArrayFile,
-    loadZarrAttrsFile,
-    pickBestScale,
-    loadSlice,
-    sizeInUnits,
-    sizeInVoxels,
-    nextSliceStep,
-    planeSizeInVoxels,
-    type ZarrRequest,
-} from './zarr/loading';
+    CachedOmeZarrConnection,
+    type OmeZarrConnection,
+    type ZarrDataSpecifier,
+} from './zarr/connection';
 
-export { type CancelRequest, type ZarrSliceRequest, makeOmeZarrSliceLoaderWorker } from './sliceview/worker-loader';
-export { decoderFactory } from './zarr/cache-lower';
+export {
+    type OmeZarrLevelSpecifier,
+    type OmeZarrMultiscaleSpecifier,
+    OmeZarrMetadata,
+} from './zarr/metadata';
+export { OmeZarrLevel } from './zarr/level';
+export {} from './zarr/omezarr-transforms';
+// export { decoderFactory } from './zarr/cache-lower';
 export { setupFetchDataWorker } from './zarr/cached-loading/fetch-data.worker-loader';
 export {
     type TransferrableRequestInit,

packages/omezarr/src/sliceview/loader.test-data.ts

@@ -0,0 +1,253 @@
+import { OmeZarrMetadata } from '../zarr/metadata';
+
+export const exampleOmeZarr: OmeZarrMetadata = new OmeZarrMetadata(
+    new URL('https://allen-genetic-tools.s3.us-west-2.amazonaws.com/tissuecyte/1263343692/ome-zarr/'),
+    {
+        nodeType: 'group',
+        zarrFormat: 3,
+        attributes: {
+            multiscales: [
+                {
+                    name: 'test',
+                    version: '2',
+                    axes: [
+                        {
+                            name: 'c',
+                            type: 'channel',
+                            unit: 'millimeter',
+                        },
+                        {
+                            name: 'z',
+                            type: 'space',
+                            unit: 'millimeter',
+                        },
+                        {
+                            name: 'y',
+                            type: 'space',
+                            unit: 'millimeter',
+                        },
+                        {
+                            name: 'x',
+                            type: 'space',
+                            unit: 'millimeter',
+                        },
+                    ],
+                    datasets: [
+                        {
+                            coordinateTransformations: [
+                                {
+                                    scale: [1, 0.1, 0.00035, 0.00035],
+                                    type: 'scale',
+                                },
+                                {
+                                    translation: [0, 0, 0, 0],
+                                    type: 'translation',
+                                },
+                            ],
+                            path: '0',
+                        },
+                        {
+                            coordinateTransformations: [
+                                {
+                                    scale: [1, 0.1, 0.0007, 0.0007],
+                                    type: 'scale',
+                                },
+                                {
+                                    translation: [0, 0, 0.00035, 0.00035],
+                                    type: 'translation',
+                                },
+                            ],
+                            path: '1',
+                        },
+                        {
+                            coordinateTransformations: [
+                                {
+                                    scale: [1, 0.1, 0.0014, 0.0014],
+                                    type: 'scale',
+                                },
+                                {
+                                    translation: [0, 0, 0.00105, 0.00105],
+                                    type: 'translation',
+                                },
+                            ],
+                            path: '2',
+                        },
+                        {
+                            coordinateTransformations: [
+                                {
+                                    scale: [1, 0.1, 0.0028, 0.0028],
+                                    type: 'scale',
+                                },
+                                {
+                                    translation: [0, 0, 0.00245, 0.00245],
+                                    type: 'translation',
+                                },
+                            ],
+                            path: '3',
+                        },
+                        {
+                            coordinateTransformations: [
+                                {
+                                    scale: [1, 0.1, 0.0056, 0.0056],
+                                    type: 'scale',
+                                },
+                                {
+                                    translation: [0, 0, 0.00525, 0.00525],
+                                    type: 'translation',
+                                },
+                            ],
+                            path: '4',
+                        },
+                        {
+                            coordinateTransformations: [
+                                {
+                                    scale: [1, 0.1, 0.0112, 0.0112],
+                                    type: 'scale',
+                                },
+                                {
+                                    translation: [0, 0, 0.01085, 0.01085],
+                                    type: 'translation',
+                                },
+                            ],
+                            path: '5',
+                        },
+                        {
+                            coordinateTransformations: [
+                                {
+                                    scale: [1, 0.1, 0.0224, 0.0224],
+                                    type: 'scale',
+                                },
+                                {
+                                    translation: [0, 0, 0.02205, 0.02205],
+                                    type: 'translation',
+                                },
+                            ],
+                            path: '6',
+                        },
+                        {
+                            coordinateTransformations: [
+                                {
+                                    scale: [1, 0.1, 0.0448, 0.0448],
+                                    type: 'scale',
+                                },
+                                {
+                                    translation: [0, 0, 0.044449999999999996, 0.044449999999999996],
+                                    type: 'translation',
+                                },
+                            ],
+                            path: '7',
+                        },
+                        {
+                            coordinateTransformations: [
+                                {
+                                    scale: [1, 0.1, 0.0896, 0.0896],
+                                    type: 'scale',
+                                },
+                                {
+                                    translation: [0, 0, 0.08925, 0.08925],
+                                    type: 'translation',
+                                },
+                            ],
+                            path: '8',
+                        },
+                        {
+                            coordinateTransformations: [
+                                {
+                                    scale: [1, 0.1, 0.1792, 0.1792],
+                                    type: 'scale',
+                                },
+                                {
+                                    translation: [0, 0, 0.17885, 0.17885],
+                                    type: 'translation',
+                                },
+                            ],
+                            path: '9',
+                        },
+                    ],
+                },
+            ],
+        },
+    },
+    {
+        '/0': {
+            nodeType: 'array',
+            path: '0',
+            chunkShape: [],
+            dataType: 'float32',
+            shape: [3, 142, 29998, 39998],
+            attributes: {},
+        },
+        '/1': {
+            nodeType: 'array',
+            path: '1',
+            chunkShape: [],
+            dataType: 'float32',
+            shape: [3, 142, 14999, 19999],
+            attributes: {},
+        },
+        '/2': {
+            nodeType: 'array',
+            path: '2',
+            chunkShape: [],
+            dataType: 'float32',
+            shape: [3, 142, 7499, 9999],
+            attributes: {},
+        },
+        '/3': {
+            nodeType: 'array',
+            path: '2',
+            chunkShape: [],
+            dataType: 'float32',
+            shape: [3, 142, 3749, 4999],
+            attributes: {},
+        },
+        '/4': {
+            nodeType: 'array',
+            path: '2',
+            chunkShape: [],
+            dataType: 'float32',
+            shape: [3, 142, 1874, 2499],
+            attributes: {},
+        },
+        '/5': {
+            nodeType: 'array',
+            path: '2',
+            chunkShape: [],
+            dataType: 'float32',
+            shape: [3, 142, 937, 1249],
+            attributes: {},
+        },
+        '/6': {
+            nodeType: 'array',
+            path: '2',
+            chunkShape: [],
+            dataType: 'float32',
+            shape: [3, 142, 468, 624],
+            attributes: {},
+        },
+        '/7': {
+            nodeType: 'array',
+            path: '2',
+            chunkShape: [],
+            dataType: 'float32',
+            shape: [3, 142, 234, 312],
+            attributes: {},
+        },
+        '/8': {
+            nodeType: 'array',
+            path: '2',
+            chunkShape: [],
+            dataType: 'float32',
+            shape: [3, 142, 117, 156],
+            attributes: {},
+        },
+        '/9': {
+            nodeType: 'array',
+            path: '2',
+            chunkShape: [],
+            dataType: 'float32',
+            shape: [3, 142, 58, 78],
+            attributes: {},
+        },
+    },
+);