Fix values provided by H5Grove

packages/app/src/providers/h5grove/h5grove-api.ts

@@ -6,13 +6,20 @@ import type {
   GroupWithChildren,
   UnresolvedEntity,
 } from '@h5web/shared';
-import { assertDataset, buildEntityPath, EntityKind } from '@h5web/shared';
+import {
+  hasScalarShape,
+  hasArrayShape,
+  assertDataset,
+  buildEntityPath,
+  EntityKind,
+  assertNonNullShape,
+} from '@h5web/shared';
 import { isString } from 'lodash';
 
 import { ProviderApi } from '../api';
 import type { ValuesStoreParams } from '../models';
 import { ProviderError } from '../models';
-import { convertDtype, handleAxiosError } from '../utils';
+import { convertDtype, flattenValue, handleAxiosError } from '../utils';
 import type {
   H5GroveAttribute,
   H5GroveAttrValuesResponse,
@@ -41,17 +48,22 @@ export class H5GroveApi extends ProviderApi {
   public async getValue(
     params: ValuesStoreParams
   ): Promise<H5GroveDataResponse> {
-    const { path } = params;
+    const { path, selection } = params;
     const entity = await this.getEntity(path);
     assertDataset(entity);
+    assertNonNullShape(entity);
 
     const DTypedArray = typedArrayFromDType(entity.type);
-    if (!DTypedArray) {
-      return this.fetchData(params);
+    if (DTypedArray) {
+      const buffer = await this.fetchBinaryData(params);
+      const array = new DTypedArray(buffer);
+      return hasScalarShape(entity) ? array[0] : [...array];
     }
 
-    const buffer = await this.fetchBinaryData(params);
-    return new DTypedArray(buffer);
+    const value = await this.fetchData(params);
+    return hasArrayShape(entity)
+      ? flattenValue(value, entity, selection)
+      : value;
   }
 
   private async fetchEntity(path: string): Promise<H5GroveEntityResponse> {
@@ -114,7 +126,7 @@ export class H5GroveApi extends ProviderApi {
     params: ValuesStoreParams
   ): Promise<ArrayBuffer> {
     const { data } = await this.cancellableFetchValue<ArrayBuffer>(
-      `/data/`,
+      '/data/',
       params,
       { ...params, format: 'bin' },
       'arraybuffer'

packages/app/src/providers/hsds/hsds-api.ts

@@ -17,7 +17,7 @@ import {
 import { ProviderApi } from '../api';
 import type { ValuesStoreParams } from '../models';
 import { ProviderError } from '../models';
-import { handleAxiosError } from '../utils';
+import { flattenValue, handleAxiosError } from '../utils';
 import type {
   HsdsDatasetResponse,
   HsdsDatatypeResponse,
@@ -33,7 +33,7 @@ import type {
   HsdsId,
 } from './models';
 import {
-  assertHsdsDataset,
+  assertNonNullHsdsDataset,
   isHsdsGroup,
   convertHsdsShape,
   convertHsdsType,
@@ -111,18 +111,14 @@ export class HsdsApi extends ProviderApi {
     const { path } = params;
 
     const entity = await this.getEntity(path);
-    assertHsdsDataset(entity);
+    assertNonNullHsdsDataset(entity);
 
     const value = await this.fetchValue(entity.id, params);
 
     // https://github.com/HDFGroup/hsds/issues/88
     // HSDS does not reduce the number of dimensions when selecting indices
     // Therefore the flattening must be done on all dimensions regardless of the selection
-    if (hasArrayShape(entity)) {
-      return (value as unknown[]).flat(entity.shape.length - 1);
-    }
-
-    return value;
+    return hasArrayShape(entity) ? flattenValue(value, entity) : value;
   }
 
   private async fetchRootId(): Promise<HsdsId> {

packages/app/src/providers/hsds/utils.ts

@@ -8,8 +8,16 @@ import type {
   ComplexType,
   DType,
   Attribute,
+  ScalarShape,
+  ArrayShape,
+} from '@h5web/shared';
+import {
+  isGroup,
+  isDataset,
+  DTypeClass,
+  Endianness,
+  hasNonNullShape,
 } from '@h5web/shared';
-import { isGroup, isDataset, DTypeClass, Endianness } from '@h5web/shared';
 
 import type {
   HsdsType,
@@ -34,11 +42,11 @@ export function assertHsdsEntity(entity: Entity): asserts entity is HsdsEntity {
   }
 }
 
-export function assertHsdsDataset(
+export function assertNonNullHsdsDataset(
   entity: HsdsEntity
-): asserts entity is HsdsEntity<Dataset> {
-  if (!isHsdsDataset(entity)) {
-    throw new Error('Expected entity to be HSDS dataset');
+): asserts entity is HsdsEntity<Dataset<ScalarShape | ArrayShape>> {
+  if (!isHsdsDataset(entity) || !hasNonNullShape(entity)) {
+    throw new Error('Expected entity to be HSDS dataset with non-null shape');
   }
 }
 

packages/app/src/providers/utils.ts

@@ -1,5 +1,5 @@
-import type { DType } from '@h5web/shared';
-import { Endianness, DTypeClass } from '@h5web/shared';
+import type { ArrayShape, Dataset, DType } from '@h5web/shared';
+import { Endianness, DTypeClass, assertArray } from '@h5web/shared';
 import axios from 'axios';
 
 import type { ProviderError } from './models';
@@ -81,6 +81,17 @@ export function convertDtype(dtype: string): DType {
   }
 }
 
+export function flattenValue(
+  value: unknown,
+  dataset: Dataset<ArrayShape>,
+  selection?: string
+): unknown[] {
+  assertArray(value);
+  const slicedDims = selection?.split(',').filter((s) => s.includes(':'));
+  const dims = slicedDims || dataset.shape;
+  return value.flat(dims.length - 1);
+}
+
 export async function handleAxiosError<T>(
   func: () => Promise<T>,
   getErrorToThrow: (

packages/app/src/vis-packs/core/hooks.ts

@@ -5,6 +5,8 @@ import {
   ScaleType,
   getBounds,
   getValidDomainForScale,
+  assertDatasetValue,
+  assertNonNullShape,
 } from '@h5web/shared';
 import type { NdArray } from 'ndarray';
 import { useContext, useMemo } from 'react';
@@ -45,11 +47,17 @@ export function useDatasetValue(
     return undefined;
   }
 
+  // Dataset with null shape has no value to fetch
+  assertNonNullShape(dataset);
+
   // If `dimMapping` is not provided or has no slicing dimension, the entire dataset will be fetched
-  return valuesStore.get({
+  const value = valuesStore.get({
     path: dataset.path,
     selection: getSliceSelection(dimMapping),
   });
+
+  assertDatasetValue(value, dataset);
+  return value;
 }
 
 export function useDatasetValues<D extends Dataset>(
@@ -60,7 +68,15 @@ export function useDatasetValues(datasets: Dataset[]): Record<string, unknown> {
   const { valuesStore } = useContext(ProviderContext);
 
   return Object.fromEntries(
-    datasets.map(({ name, path }) => [name, valuesStore.get({ path })])
+    datasets.map((dataset) => {
+      assertNonNullShape(dataset);
+
+      const { name, path } = dataset;
+      const value = valuesStore.get({ path });
+      assertDatasetValue(value, dataset);
+
+      return [name, value];
+    })
   );
 }
 
@@ -95,14 +111,12 @@ export const useCombinedDomain = createMemo(getCombinedDomain);
 const useBaseArray = createMemo(getBaseArray);
 const useApplyMapping = createMemo(applyMapping);
 
-export function useMappedArray<T extends unknown[] | undefined>(
-  value: T,
+export function useMappedArray<T, U extends T[] | undefined>(
+  value: U,
   dims: number[],
   mapping: DimensionMapping,
   autoScale?: boolean
-): T extends (infer U)[]
-  ? [NdArray<U[]>, NdArray<U[]>]
-  : [undefined, undefined];
+): U extends T[] ? [NdArray<U>, NdArray<U>] : [undefined, undefined];
 
 export function useMappedArray<T>(
   value: T[] | undefined,

packages/app/src/vis-packs/core/utils.ts

@@ -10,10 +10,10 @@ import { getAttributeValue } from '../../utils';
 
 export const DEFAULT_DOMAIN: Domain = [0.1, 1];
 
-export function getBaseArray<T extends unknown[] | undefined>(
-  value: T,
+export function getBaseArray<T, U extends T[] | undefined>(
+  value: U,
   rawDims: number[]
-): T extends (infer U)[] ? NdArray<U[]> : undefined;
+): U extends T[] ? NdArray<U> : undefined;
 
 export function getBaseArray<T>(
   value: T[] | undefined,
@@ -22,10 +22,10 @@ export function getBaseArray<T>(
   return value && ndarray(value, rawDims);
 }
 
-export function applyMapping<T extends NdArray<unknown[]> | undefined>(
-  baseArray: T,
+export function applyMapping<T, U extends NdArray<T[]> | undefined>(
+  baseArray: U,
   mapping: (number | Axis | ':')[]
-): T extends NdArray<infer U> ? NdArray<U> : undefined;
+): U extends NdArray<T[]> ? U : undefined;
 
 export function applyMapping<T>(
   baseArray: NdArray<T[]> | undefined,

packages/app/src/vis-packs/nexus/containers/NxComplexImageContainer.tsx

@@ -1,25 +1,21 @@
-import type { H5WebComplex } from '@h5web/shared';
-import {
-  assertComplexType,
-  assertGroupWithChildren,
-  assertMinDims,
-} from '@h5web/shared';
+import { assertGroupWithChildren, assertMinDims } from '@h5web/shared';
 
 import DimensionMapper from '../../../dimension-mapper/DimensionMapper';
 import VisBoundary from '../../VisBoundary';
 import MappedComplexVis from '../../core/complex/MappedComplexVis';
 import { useDimMappingState } from '../../hooks';
 import type { VisContainerProps } from '../../models';
 import NxValuesFetcher from '../NxValuesFetcher';
-import { getNxData, getDatasetLabel } from '../utils';
+import { getNxData, getDatasetLabel, assertComplexSignal } from '../utils';
 
 function NxComplexImageContainer(props: VisContainerProps) {
   const { entity } = props;
   assertGroupWithChildren(entity);
 
   const nxData = getNxData(entity);
+  assertComplexSignal(nxData);
+
   const { signalDataset, silxStyle } = nxData;
-  assertComplexType(signalDataset);
   assertMinDims(signalDataset, 2);
 
   const { shape: dims } = signalDataset;
@@ -40,7 +36,7 @@ function NxComplexImageContainer(props: VisContainerProps) {
             const { signal, axisMapping, title } = nxValues;
             return (
               <MappedComplexVis
-                value={signal as H5WebComplex[]}
+                value={signal}
                 dims={dims}
                 dimMapping={dimMapping}
                 axisMapping={axisMapping}

packages/app/src/vis-packs/nexus/containers/NxImageContainer.tsx

@@ -1,24 +1,21 @@
-import {
-  assertGroupWithChildren,
-  assertNumericType,
-  assertMinDims,
-} from '@h5web/shared';
+import { assertGroupWithChildren, assertMinDims } from '@h5web/shared';
 
 import DimensionMapper from '../../../dimension-mapper/DimensionMapper';
 import VisBoundary from '../../VisBoundary';
 import MappedHeatmapVis from '../../core/heatmap/MappedHeatmapVis';
 import { useDimMappingState } from '../../hooks';
 import type { VisContainerProps } from '../../models';
 import NxValuesFetcher from '../NxValuesFetcher';
-import { getNxData, getDatasetLabel } from '../utils';
+import { getNxData, getDatasetLabel, assertNumericSignal } from '../utils';
 
 function NxImageContainer(props: VisContainerProps) {
   const { entity } = props;
   assertGroupWithChildren(entity);
 
   const nxData = getNxData(entity);
+  assertNumericSignal(nxData);
+
   const { signalDataset, silxStyle } = nxData;
-  assertNumericType(signalDataset);
   assertMinDims(signalDataset, 2);
 
   const { shape: dims } = signalDataset;
@@ -39,7 +36,7 @@ function NxImageContainer(props: VisContainerProps) {
             const { signal, axisMapping, title } = nxValues;
             return (
               <MappedHeatmapVis
-                value={signal as number[]}
+                value={signal}
                 dims={dims}
                 dimMapping={dimMapping}
                 axisMapping={axisMapping}

packages/app/src/vis-packs/nexus/containers/NxRgbContainer.tsx

@@ -1,7 +1,6 @@
 import { RgbVis } from '@h5web/lib';
 import {
   assertGroupWithChildren,
-  assertNumericType,
   assertNumDims,
   DTypeClass,
 } from '@h5web/shared';
@@ -11,15 +10,16 @@ import VisBoundary from '../../VisBoundary';
 import { useRgbVisConfig } from '../../core/rgb/config';
 import type { VisContainerProps } from '../../models';
 import NxValuesFetcher from '../NxValuesFetcher';
-import { getNxData, getDatasetLabel } from '../utils';
+import { getNxData, getDatasetLabel, assertNumericSignal } from '../utils';
 
 function NxRgbContainer(props: VisContainerProps) {
   const { entity } = props;
   assertGroupWithChildren(entity);
 
   const nxData = getNxData(entity);
+  assertNumericSignal(nxData);
+
   const { signalDataset } = nxData;
-  assertNumericType(signalDataset);
   assertNumDims(signalDataset, 3);
 
   const { shape: dims } = signalDataset;
@@ -37,7 +37,7 @@ function NxRgbContainer(props: VisContainerProps) {
           const { signal, title } = nxValues;
           return (
             <RgbVis
-              value={signal as number[]}
+              value={signal}
               dims={dims}
               floatFormat={signalDataset.type.class === DTypeClass.Float}
               title={title || getDatasetLabel(signalDataset)}

packages/app/src/vis-packs/nexus/utils.ts

@@ -1,6 +1,7 @@
 import {
   assertArray,
   assertArrayShape,
+  assertComplexType,
   assertDataset,
   assertDefined,
   assertNumericOrComplexType,
@@ -182,3 +183,15 @@ export function getDatasetLabel(dataset: Dataset): string {
 
   return dataset.name;
 }
+
+export function assertNumericSignal(
+  nxData: NxData
+): asserts nxData is NxData<NumericType> {
+  assertNumericType(nxData.signalDataset);
+}
+
+export function assertComplexSignal(
+  nxData: NxData
+): asserts nxData is NxData<ComplexType> {
+  assertComplexType(nxData.signalDataset);
+}