Merge pull request #1676 from silx-kit/complex-auxiliaries

Support complex auxiliaries

.eslintrc.cjs

@@ -10,6 +10,7 @@ module.exports = createConfig(__dirname, getDependencies(), [
       'testing-library/await-async-utils': 'off', // Cypress has its own way of dealing with asynchronicity
       'testing-library/prefer-screen-queries': 'off', // Cypress provides `cy` object instead of `screen`
       'sonarjs/no-duplicate-string': 'off', // incompatible with Cypress testing syntax
+      'sonarjs/cognitive-complexity': 'off', // allow long `describe` and `context` functions
       'unicorn/numeric-separators-style': 'off', // not supported
     },
   },

.github/workflows/lint-test.yml

@@ -95,7 +95,7 @@ jobs:
         uses: actions/cache@v4
         with:
           path: ~/.cache/pypoetry/virtualenvs
-          key: poetry-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+          key: poetry-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}-0 # increment to reset cache
 
       - name: Create Poetry environments 📜
         if: steps.poetry-venvs.outputs.cache-hit != 'true'

cypress/e2e/app.cy.ts

@@ -297,7 +297,7 @@ describe('/mock', () => {
       cy.findByRole('figure', { name: 'NeXus 2D' }).should('be.visible');
     });
 
-    it('visualize dataset with "spectrum" interpretation as NxSpectrum', () => {
+    it('visualize dataset with "spectrum" interpretation as NxLine', () => {
       cy.selectExplorerNode('nexus_entry');
       cy.selectExplorerNode('spectrum');
 
@@ -312,7 +312,7 @@ describe('/mock', () => {
       cy.get('svg[data-type="abscissa"] svg').should('have.text', 'X (nm)');
 
       if (Cypress.env('TAKE_SNAPSHOTS')) {
-        cy.matchImageSnapshot('nxspectrum');
+        cy.matchImageSnapshot('nxline');
       }
     });
 
@@ -348,7 +348,7 @@ describe('/mock', () => {
       );
     });
 
-    it('visualize dataset with log scales on both axes on NxSpectrum with SILX_style', () => {
+    it('visualize dataset with log scales on both axes on NxLine with SILX_style', () => {
       cy.selectExplorerNode('nexus_entry');
       cy.selectExplorerNode('log_spectrum');
 
@@ -365,7 +365,7 @@ describe('/mock', () => {
       }
     });
 
-    it('visualize signal and auxiliary signals datasets as NxSpectrum', () => {
+    it('visualize signal and auxiliary signals datasets as NxLine', () => {
       cy.selectExplorerNode('nexus_entry');
       cy.selectExplorerNode('spectrum_with_aux');
 
@@ -399,6 +399,32 @@ describe('/mock', () => {
       }
     });
 
+    it('visualize 2D complex signal as NxImage', () => {
+      cy.selectExplorerNode('nexus_entry');
+      cy.selectExplorerNode('complex');
+
+      cy.findByRole('heading', {
+        name: 'nexus_entry / complex',
+      }).should('be.visible');
+
+      if (Cypress.env('TAKE_SNAPSHOTS')) {
+        cy.matchImageSnapshot('nximage_complex_2d');
+      }
+    });
+
+    it('visualize 2D complex signal with "spectrum" interpretation and auxiliaries as NxLine', () => {
+      cy.selectExplorerNode('nexus_entry');
+      cy.selectExplorerNode('complex_spectrum');
+
+      cy.findByRole('heading', {
+        name: 'nexus_entry / complex_spectrum',
+      }).should('be.visible');
+
+      if (Cypress.env('TAKE_SNAPSHOTS')) {
+        cy.matchImageSnapshot('nxline_complex_2d_aux');
+      }
+    });
+
     it('visualize dataset with "rgb-image" interpretation as NxRGB', () => {
       cy.selectExplorerNode('nexus_entry');
       cy.selectExplorerNode('rgb-image');

packages/app/src/providers/mock/mock-file.ts

@@ -228,6 +228,8 @@ export function makeMockFile(): GroupWithChildren {
             signal: withNxAttr(array('twoD_cplx'), {
               interpretation: 'spectrum',
             }),
+            auxiliary: { secondary_cplx: array('secondary_cplx') },
+            auxAttr: ['secondary_cplx'],
           }),
           nxData('rgb-image', {
             signal: withImageAttr(

packages/app/src/vis-packs/core/complex/MappedComplexLineVis.tsx

@@ -1,23 +1,30 @@
-import { LineVis, useDomain, useSafeDomain, useVisDomain } from '@h5web/lib';
-import type { H5WebComplex } from '@h5web/shared/hdf5-models';
+import {
+  LineVis,
+  useCombinedDomain,
+  useDomain,
+  useDomains,
+  useSafeDomain,
+  useVisDomain,
+} from '@h5web/lib';
+import type { ArrayValue, ComplexType } from '@h5web/shared/hdf5-models';
 import type { AxisMapping } from '@h5web/shared/nexus-models';
 import type { NumArray } from '@h5web/shared/vis-models';
-import { ComplexVisType } from '@h5web/shared/vis-models';
-import { useMemo } from 'react';
 import { createPortal } from 'react-dom';
 
 import type { DimensionMapping } from '../../../dimension-mapper/models';
 import visualizerStyles from '../../../visualizer/Visualizer.module.css';
-import { useMappedArray, useSlicedDimsAndMapping } from '../hooks';
 import type { LineConfig } from '../line/config';
 import { DEFAULT_DOMAIN } from '../utils';
 import ComplexLineToolbar from './ComplexLineToolbar';
+import { useMappedComplexArrays } from './hooks';
 import type { ComplexLineConfig } from './lineConfig';
-import { COMPLEX_VIS_TYPE_LABELS, getPhaseAmplitudeValues } from './utils';
+import { COMPLEX_VIS_TYPE_LABELS } from './utils';
 
 interface Props {
-  value: H5WebComplex[];
+  value: ArrayValue<ComplexType>;
   valueLabel?: string;
+  auxLabels?: string[];
+  auxValues?: ArrayValue<ComplexType>[];
   dims: number[];
   dimMapping: DimensionMapping;
   axisLabels?: AxisMapping<string>;
@@ -32,6 +39,8 @@ function MappedComplexLineVis(props: Props) {
   const {
     value,
     valueLabel,
+    auxLabels = [],
+    auxValues = [],
     dims,
     dimMapping,
     axisLabels,
@@ -46,21 +55,20 @@ function MappedComplexLineVis(props: Props) {
   const { customDomain, yScaleType, xScaleType, curveType, showGrid } =
     lineConfig;
 
-  const [slicedDims, slicedMapping] = useSlicedDimsAndMapping(dims, dimMapping);
-  const { phaseValues, amplitudeValues } = useMemo(
-    () => getPhaseAmplitudeValues(value),
-    [value],
+  const [dataArray, ...auxArrays] = useMappedComplexArrays(
+    [value, ...auxValues],
+    dims,
+    dimMapping,
+    visType,
   );
 
-  const dataArray = useMappedArray(
-    visType === ComplexVisType.Amplitude ? amplitudeValues : phaseValues,
-    slicedDims,
-    slicedMapping,
-  );
+  const dataDomain = useDomain(dataArray, yScaleType);
+  const auxDomains = useDomains(auxArrays, yScaleType);
+  const combinedDomain =
+    useCombinedDomain([dataDomain, ...auxDomains]) || DEFAULT_DOMAIN;
 
-  const dataDomain = useDomain(dataArray, yScaleType) || DEFAULT_DOMAIN;
-  const visDomain = useVisDomain(customDomain, dataDomain);
-  const [safeDomain] = useSafeDomain(visDomain, dataDomain, yScaleType);
+  const visDomain = useVisDomain(customDomain, combinedDomain);
+  const [safeDomain] = useSafeDomain(visDomain, combinedDomain, yScaleType);
 
   const xDimIndex = dimMapping.indexOf('x');
   const ordinateLabel = valueLabel
@@ -72,7 +80,7 @@ function MappedComplexLineVis(props: Props) {
       {toolbarContainer &&
         createPortal(
           <ComplexLineToolbar
-            dataDomain={dataDomain}
+            dataDomain={combinedDomain}
             config={config}
             lineConfig={lineConfig}
           />,
@@ -93,6 +101,10 @@ function MappedComplexLineVis(props: Props) {
         }}
         ordinateLabel={ordinateLabel}
         title={title}
+        auxiliaries={auxArrays.map((array, i) => ({
+          label: auxLabels[i],
+          array,
+        }))}
         testid={dimMapping.toString()}
       />
     </>

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

@@ -0,0 +1,40 @@
+import { ComplexVisType } from '@h5web/lib';
+import type { H5WebComplex } from '@h5web/shared/hdf5-models';
+import type { ComplexLineVisType } from '@h5web/shared/vis-models';
+import type { NdArray } from 'ndarray';
+import { useMemo } from 'react';
+
+import type { DimensionMapping } from '../../../dimension-mapper/models';
+import { useSlicedDimsAndMapping } from '../hooks';
+import { applyMapping, getBaseArray } from '../utils';
+import { getPhaseAmplitudeValues } from './utils';
+
+export function useMappedComplexArrays(
+  values: H5WebComplex[][],
+  dims: number[],
+  mapping: DimensionMapping,
+  complexVisType: ComplexLineVisType,
+): NdArray<number[]>[] {
+  const [slicedDims, slicedMapping] = useSlicedDimsAndMapping(dims, mapping);
+
+  const phaseAmplitudeValues = useMemo(
+    () => values.map(getPhaseAmplitudeValues),
+    [...values], // eslint-disable-line react-hooks/exhaustive-deps
+  );
+
+  const baseArrays = useMemo(() => {
+    return phaseAmplitudeValues.map((paValues) =>
+      getBaseArray(
+        complexVisType === ComplexVisType.Phase
+          ? paValues.phaseValues
+          : paValues.amplitudeValues,
+        slicedDims,
+      ),
+    );
+  }, [complexVisType, slicedDims, phaseAmplitudeValues]);
+
+  return useMemo(
+    () => baseArrays.map((ndArr) => applyMapping(ndArr, slicedMapping)),
+    [baseArrays, slicedMapping],
+  );
+}

packages/app/src/vis-packs/core/complex/lineConfig.tsx

@@ -1,3 +1,4 @@
+import type { ComplexLineVisType } from '@h5web/shared/vis-models';
 import { ComplexVisType } from '@h5web/shared/vis-models';
 import { createContext, useContext, useState } from 'react';
 import type { StoreApi } from 'zustand';
@@ -6,8 +7,6 @@ import { persist } from 'zustand/middleware';
 
 import type { ConfigProviderProps } from '../../models';
 
-type ComplexLineVisType = ComplexVisType.Phase | ComplexVisType.Amplitude;
-
 export interface ComplexLineConfig {
   visType: ComplexLineVisType;
   setVisType: (visType: ComplexLineVisType) => void;

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

@@ -20,7 +20,7 @@ function NxComplexSpectrumContainer(props: VisContainerProps) {
   const nxData = useNxData(entity);
   assertComplexNxData(nxData);
 
-  const { signalDef, axisDefs, silxStyle } = nxData;
+  const { signalDef, axisDefs, auxDefs, silxStyle } = nxData;
   const signalDims = signalDef.dataset.shape;
 
   const [dimMapping, setDimMapping] = useDimMappingState(signalDims, 1);
@@ -50,12 +50,14 @@ function NxComplexSpectrumContainer(props: VisContainerProps) {
           nxData={nxData}
           selection={getSliceSelection(dimMapping)}
           render={(nxValues) => {
-            const { signal, axisValues, title } = nxValues;
+            const { signal, axisValues, auxValues, title } = nxValues;
 
             return (
               <MappedComplexLineVis
                 value={signal}
                 valueLabel={signalDef.label}
+                auxLabels={auxDefs.map((def) => def?.label)}
+                auxValues={auxValues}
                 dims={signalDims}
                 dimMapping={dimMapping}
                 axisLabels={axisLabels}

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

@@ -19,8 +19,8 @@ function NxSpectrumContainer(props: VisContainerProps) {
 
   const nxData = useNxData(entity);
   assertNumericNxData(nxData);
-  const { signalDef, axisDefs, auxDefs, silxStyle } = nxData;
 
+  const { signalDef, axisDefs, auxDefs, silxStyle } = nxData;
   const signalDims = signalDef.dataset.shape;
   const errorDims = signalDef.errorDataset?.shape;
 

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

@@ -6,13 +6,15 @@ import type { NxData } from './models';
 export function assertNumericNxData(
   nxData: NxData,
 ): asserts nxData is NxData<NumericType> {
-  const { signalDef } = nxData;
+  const { signalDef, auxDefs } = nxData;
   assertNumericType(signalDef.dataset);
+  auxDefs.forEach((def) => assertNumericType(def.dataset));
 }
 
 export function assertComplexNxData(
   nxData: NxData,
 ): asserts nxData is NxData<ComplexType> {
-  const { signalDef } = nxData;
+  const { signalDef, auxDefs } = nxData;
   assertComplexType(signalDef.dataset);
+  auxDefs.forEach((def) => assertComplexType(def.dataset));
 }

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

@@ -1,4 +1,3 @@
-import { isDefined } from '@h5web/shared/guards';
 import type { GroupWithChildren } from '@h5web/shared/hdf5-models';
 
 import type { DimensionMapping } from '../../dimension-mapper/models';
@@ -7,8 +6,8 @@ import { useValuesInCache } from '../core/hooks';
 import type { NxData } from './models';
 import {
   assertNxDataGroup,
-  findAssociatedDatasets,
   findAuxErrorDataset,
+  findAuxiliaryDatasets,
   findAxesDatasets,
   findErrorDataset,
   findSignalDataset,
@@ -23,11 +22,7 @@ export function useNxData(group: GroupWithChildren): NxData {
   assertNxDataGroup(group, attrValuesStore);
   const signalDataset = findSignalDataset(group, attrValuesStore);
   const axisDatasets = findAxesDatasets(group, signalDataset, attrValuesStore);
-  const auxSignals = findAssociatedDatasets(
-    group,
-    'auxiliary_signals',
-    attrValuesStore,
-  ).filter(isDefined);
+  const auxSignals = findAuxiliaryDatasets(group, attrValuesStore);
 
   return {
     titleDataset: findTitleDataset(group),

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

@@ -38,7 +38,6 @@ type WithError<T extends DatasetDef> = T & {
   errorDataset?: NumArrayDataset;
 };
 
-export type AuxDef = WithError<DatasetDef<NumericType>>;
 export type AxisDef = DatasetDef<NumericType>;
 
 export interface SilxStyle {
@@ -51,7 +50,7 @@ export interface NxData<
 > {
   titleDataset?: Dataset<ScalarShape, StringType>;
   signalDef: WithError<DatasetDef<T>>;
-  auxDefs: AuxDef[];
+  auxDefs: WithError<DatasetDef<T>>[];
   axisDefs: AxisMapping<AxisDef>;
   silxStyle: SilxStyle;
 }
@@ -60,7 +59,7 @@ export interface NxValues<T extends NumericType | ComplexType> {
   title: string;
   signal: ArrayValue<T>;
   errors?: NumArray;
-  auxValues: NumArray[];
+  auxValues: ArrayValue<T>[];
   auxErrors: (NumArray | undefined)[];
   axisValues: AxisMapping<NumArray>;
 }