feat: improve 1D apodization (#3260)

* fix: typo in the type name * fix: add shape to manual peak added * fix: apodization 1D options * chore: correct use of generalized lorentzian * chore: update format apodization * chore: update nmr deps * chore: include gamma * fix: split back apodization 2D into dimensions * chore: force nmr-load-save v13.0.2 * chore: fix prettier * chore: work in progress to new splitted FilterManages * Update package.json Co-authored-by: Luc Patiny <[email protected]> * chore: use pre release nmr-processing * chore: work in progress refactor * chore: adapt defaultApodizationOptions but there is a bug in nmr-processing * chore: refactor to use both Filters1DManager n Filters2DManager * chore: missing typing corrections * chore: refactor FiltersActions * refactor: adaptation to Filters with types * chore: pass draft data directly to the filter * refactor: adapt to typed Filters * chore: update pre-release nmr-processing * chore: update nmr-processing and nmr-load-save to pre-release * refactor: filters and types * chore: update nmr-processing and nmr-load-save * refactor: apodization line component * feat: improve apodization * fix: apodization guide line * chore: update nmr-processing and nmr-load-save * fix: autprocessing filter and getFilterLabel by name * chore: prerelease nmr-processing fixing filters * fix: show filter error message and set background color red * chore(eslint): disable switch-exhaustiveness-check rule * chore: update nmr-processing * chore: fix eslint * chore: update nmr-load-save to version 2.0.1 * test: fix apodization test * refactor: repalce useWatch hook with watch * refactor: prevent change the line boroadening if the exponential filter not activated * fix: remove Nucleus/Nuclei from types * fix eslint * fix: matrix generation types --------- Co-authored-by: hamed musallam <[email protected]> Co-authored-by: Michaël Zasso <[email protected]> Co-authored-by: Luc Patiny <[email protected]>
cheminfo · Nov 20, 2024 · 797fea4 · 797fea4
1 parent e5071fe
commit 797fea4
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diff --git a/.vscode/settings.json b/.vscode/settings.json
@@ -1,4 +1,4 @@
 {
   "typescript.tsdk": "node_modules/typescript/lib",
-  "references.preferredLocation": "view"
+  "references.preferredLocation": "view",
 }
diff --git a/eslint.config.js b/eslint.config.js
@@ -26,12 +26,7 @@ export default [
   },
   {
     rules: {
-      //todo remove the following rules once fixed: https://github.com/eslint/eslint/issues/19134
-      // start 
-      '@typescript-eslint/no-unused-expressions': 'off',
-      '@typescript-eslint/dot-notation': 'off',
-      '@typescript-eslint/no-empty-function': 'off',
-      //end
+      '@typescript-eslint/switch-exhaustiveness-check': 'off',
       'import/default': 'off',
       'import/no-unresolved': 'off',
       'react-refresh/only-export-components': 'off',

diff --git a/package-lock.json b/package-lock.json
diff --git a/package.json b/package.json
@@ -88,8 +88,8 @@
     "ml-tree-similarity": "^2.2.0",
     "multiplet-analysis": "^2.1.2",
     "nmr-correlation": "^2.3.3",
-    "nmr-load-save": "^1.2.0",
-    "nmr-processing": "^12.12.3",
+    "nmr-load-save": "^2.0.4",
+    "nmr-processing": "^14.0.3",
     "nmredata": "^0.9.11",
     "numeral": "^2.0.6",
     "openchemlib": "^8.17.0",

diff --git a/src/component/1d/ApodizationLine.tsx b/src/component/1d/ApodizationLine.tsx
@@ -1,7 +1,11 @@
+import merge from 'lodash/merge.js';
 import type { Spectrum1D } from 'nmr-load-save';
-import { apodization, Filters } from 'nmr-processing';
+import {
+  Filters1D,
+  createApodizationWindowData,
+  default1DApodization,
+} from 'nmr-processing';
 
-import { defaultApodizationOptions } from '../../data/constants/DefaultApodizationOptions.js';
 import { useChartData } from '../context/ChartContext.js';
 import { useScaleChecked } from '../context/ScaleContext.js';
 import { useActiveSpectrum } from '../hooks/useActiveSpectrum.js';
@@ -26,11 +30,11 @@ function useWindowYScale() {
   });
 }
 
-function ApodizationLine() {
+export function ApodizationLine() {
   const {
     toolOptions: {
       selectedTool,
-      data: { apodizationOptions },
+      data: { apodizationOptions: externalApodizationOptions },
     },
   } = useChartData();
   const activeSpectrum = useActiveSpectrum();
@@ -39,44 +43,25 @@ function ApodizationLine() {
   const xyReduce = useXYReduce(XYReducerDomainAxis.XAxis);
   const scaleY = useWindowYScale();
 
-  if (!activeSpectrum?.id || selectedTool !== Filters.apodization.id) {
+  if (!activeSpectrum?.id || selectedTool !== Filters1D.apodization.name) {
     return null;
   }
 
   const paths = () => {
     const pathBuilder = new PathBuilder();
-    const { re, im = [], x } = spectrum.data;
-
-    const { lineBroadening, gaussBroadening, lineBroadeningCenter } =
-      apodizationOptions || defaultApodizationOptions;
+    const { re, x } = spectrum.data;
 
+    const apodizationOptions = merge(
+      default1DApodization,
+      externalApodizationOptions,
+    );
     const length = re.length;
     const dw = (x[length - 1] - x[0]) / (length - 1);
-    const { windowData: y } = apodization(
-      { re, im },
-      {
-        apply: false,
-        compose: {
-          length,
-          shapes: [
-            {
-              start: 0,
-              shape: {
-                kind: 'lorentzToGauss',
-                options: {
-                  length,
-                  dw,
-                  exponentialHz:
-                    gaussBroadening > 0 ? lineBroadening : -lineBroadening,
-                  gaussianHz: gaussBroadening,
-                  center: lineBroadeningCenter,
-                },
-              },
-            },
-          ],
-        },
-      },
-    );
+
+    const y = createApodizationWindowData({
+      windowOptions: { dw, length },
+      shapes: apodizationOptions,
+    });
 
     if (x && y) {
       const pathPoints = xyReduce({ x, y });
@@ -102,5 +87,3 @@ function ApodizationLine() {
     />
   );
 }
-
-export default ApodizationLine;
diff --git a/src/component/1d/Chart1D.tsx b/src/component/1d/Chart1D.tsx
@@ -1,7 +1,7 @@
 import SpectrumInfoBlock from '../1d-2d/components/SpectrumInfoBlock.js';
 import { usePreferences } from '../context/PreferencesContext.js';
 
-import ApodizationLine from './ApodizationLine.js';
+import { ApodizationLine } from './ApodizationLine.js';
 import ExclusionZonesAnnotations from './ExclusionZonesAnnotations.js';
 import LinesSeries from './LinesSeries.js';
 import SimilarityTree from './SimilarityTree.js';

diff --git a/src/component/1d/ExclusionZoneAnnotation.tsx b/src/component/1d/ExclusionZoneAnnotation.tsx
@@ -1,6 +1,6 @@
 /** @jsxImportSource @emotion/react */
 import { css } from '@emotion/react';
-import { Filters } from 'nmr-processing';
+import { Filters1D } from 'nmr-processing';
 import { memo } from 'react';
 
 import type { ExclusionZone } from '../../data/types/data1d/ExclusionZone.js';
@@ -31,7 +31,7 @@ function ExclusionZoneAnnotation({
 }: ExclusionZoneProps) {
   const { scaleX, scaleY } = useScaleChecked();
   const type =
-    filterId === Filters.signalProcessing.id
+    filterId === Filters1D.signalProcessing.name
       ? HighlightEventSource.MATRIX_GENERATION_EXCLUSION_ZONE
       : HighlightEventSource.EXCLUSION_ZONE;
   const highlight = useHighlight([], {
@@ -50,7 +50,7 @@ function ExclusionZoneAnnotation({
         width={`${scaleX()(zone.from) - scaleX()(zone.to)}`}
         height="10px"
         style={{
-          fill: filterId === Filters.signalProcessing.id ? 'gray' : color,
+          fill: filterId === Filters1D.signalProcessing.name ? 'gray' : color,
           opacity,
         }}
         {...highlight.onHover}

diff --git a/src/component/1d/ExclusionZonesAnnotations.tsx b/src/component/1d/ExclusionZonesAnnotations.tsx
@@ -1,5 +1,5 @@
 import type { Spectrum1D } from 'nmr-load-save';
-import { Filters } from 'nmr-processing';
+import { Filters1D } from 'nmr-processing';
 import { memo } from 'react';
 
 import type { ExclusionZone } from '../../data/types/data1d/ExclusionZone.js';
@@ -76,11 +76,14 @@ function getExclusionZones(
 ): Array<{ id: string; zones: ExclusionZone[] }> {
   const zones: Array<{ id: string; zones: ExclusionZone[] }> = [];
   for (const filter of data.filters) {
-    if (filter.name === Filters.exclusionZones.id && filter.flag) {
-      zones.push({ id: Filters.exclusionZones.id, zones: filter.value });
-    } else if (filter.name === Filters.signalProcessing.id && filter.flag) {
+    if (filter.name === Filters1D.exclusionZones.name && filter.enabled) {
+      zones.push({ id: Filters1D.exclusionZones.name, zones: filter.value });
+    } else if (
+      filter.name === Filters1D.signalProcessing.name &&
+      filter.enabled
+    ) {
       zones.push({
-        id: Filters.signalProcessing.id,
+        id: Filters1D.signalProcessing.name,
         zones: filter.value.exclusionsZones,
       });
     }

diff --git a/src/component/1d/matrix/useMatrix.ts b/src/component/1d/matrix/useMatrix.ts
@@ -1,14 +1,11 @@
 import type { NumberArray } from 'cheminfo-types';
 import type { Spectrum } from 'nmr-load-save';
-import { Filters } from 'nmr-processing';
 import { useMemo } from 'react';
 
 import { isSpectrum1D } from '../../../data/data1d/Spectrum1D/index.js';
 import { useChartData } from '../../context/ChartContext.js';
 import useSpectraByActiveNucleus from '../../hooks/useSpectraPerNucleus.js';
 
-const { signalProcessing } = Filters;
-
 /**
  * This method will slice the array from the fromIndex to the toIndex and add the first and last element of the original array
  * if needed
@@ -53,9 +50,9 @@ export function useMatrix() {
     for (let i = 0; i < spectra.length; i++) {
       const spectrum = spectra[i];
       const filter = spectrum.filters.find(
-        (filter) => filter.name === signalProcessing.id,
+        (filter) => filter.name === 'signalProcessing',
       );
-      if (isSpectrum1D(spectrum) && filter?.flag) {
+      if (isSpectrum1D(spectrum) && filter?.enabled) {
         matrixY[i] = spectrum.data.re;
       }
     }

diff --git a/src/component/1d/multiAnalysis/MultiAnalysisRanges.tsx b/src/component/1d/multiAnalysis/MultiAnalysisRanges.tsx
@@ -1,5 +1,5 @@
 import type { SpectraAnalysisColumns } from 'nmr-load-save';
-import { AnalysisColumnsTypes } from 'nmr-load-save';
+import { ANALYSIS_COLUMN_TYPES } from 'nmr-load-save';
 import { memo } from 'react';
 
 import { useChartData } from '../../context/ChartContext.js';
@@ -19,7 +19,7 @@ function MultiAnalysisRangesInner({
   activeTab,
 }: MultiAnalysisRangesInnerProps) {
   const ranges = Object.keys(columns).filter(
-    (key) => columns[key].type !== AnalysisColumnsTypes.FORMULA,
+    (key) => columns[key].type !== ANALYSIS_COLUMN_TYPES.FORMULA,
   );
 
   if (!ranges || ranges.length === 0) {

diff --git a/src/component/2d/1d-tracer/phase-correction-traces/SpectrumPhaseTrace.tsx b/src/component/2d/1d-tracer/phase-correction-traces/SpectrumPhaseTrace.tsx
@@ -1,5 +1,5 @@
 import type { Spectrum1D, Spectrum2D } from 'nmr-load-save';
-import { Filters } from 'nmr-processing';
+import { Filters1D } from 'nmr-processing';
 import type { ReactNode } from 'react';
 
 import { getSlice } from '../../../../data/data2d/Spectrum2D/index.js';
@@ -143,7 +143,7 @@ function InnerSpectrumPhaseTrace(props: InnerSpectrumPhaseTraceProps) {
     info: { isComplex: true, isFid: false },
   };
 
-  Filters.phaseCorrection.apply(spectrum as unknown as Spectrum1D, {
+  Filters1D.phaseCorrection.apply(spectrum as Spectrum1D, {
     ph0,
     ph1,
   });

diff --git a/src/component/2d/utilities/DimensionLayout.ts b/src/component/2d/utilities/DimensionLayout.ts
@@ -51,9 +51,7 @@ interface StartEndProps {
   endY?: number;
 }
 
-type DimensionType = {
-  [key in Layout]: Required<StartEndProps>;
-};
+type DimensionType = Record<Layout, Required<StartEndProps>>;
 
 function getLayoutID(
   dimension: DimensionType,

diff --git a/src/component/elements/Sections.tsx b/src/component/elements/Sections.tsx
@@ -13,11 +13,13 @@ import { createContext, useContext, useMemo } from 'react';
 interface SelectionsContextState {
   overflow: boolean;
   renderActiveSectionContentOnly: boolean;
+  matchContentHeight: boolean;
 }
 
 const selectionState: SelectionsContextState = {
   overflow: false,
   renderActiveSectionContentOnly: false,
+  matchContentHeight: false,
 };
 
 const SectionsContext = createContext<SelectionsContextState>(selectionState);
@@ -36,10 +38,13 @@ interface ActiveProps {
   overflow?: boolean;
 }
 
-const Container = styled.div<{ overflow: boolean }>(
-  ({ overflow }) => `
+const Container = styled.div<{
+  overflow: boolean;
+  matchContentHeight: boolean;
+}>(
+  ({ overflow, matchContentHeight }) => `
   width: 100%;
-  height: 100%;
+  height: ${matchContentHeight ? 'auto' : '100%'};
   display: flex;
   flex-direction: column;
   overflow: ${overflow ? 'auto' : 'hidden'};
@@ -139,6 +144,7 @@ interface BaseSectionProps {
   rightElement?: ReactNode | ((isOpen) => ReactNode);
   leftElement?: ReactNode | ((isOpen) => ReactNode);
   headerStyle?: CSSProperties;
+  arrowProps?: { style?: CSSProperties; hide?: boolean };
 }
 
 interface SectionItemProps extends BaseSectionProps {
@@ -147,28 +153,31 @@ interface SectionItemProps extends BaseSectionProps {
   children?: ReactNode | ((options: { isOpen?: boolean }) => ReactNode);
   isOpen: boolean;
   sticky?: boolean;
-  matchContentHeight?: boolean;
 }
 
 interface SectionProps {
   children?: ReactNode;
   overflow?: boolean;
   renderActiveSectionContentOnly?: boolean;
+  matchContentHeight?: boolean;
 }
 
 export function Sections(props: SectionProps) {
   const {
     children,
     overflow = false,
     renderActiveSectionContentOnly = false,
+    matchContentHeight = false,
   } = props;
 
   const state = useMemo(() => {
-    return { overflow, renderActiveSectionContentOnly };
-  }, [overflow, renderActiveSectionContentOnly]);
+    return { overflow, renderActiveSectionContentOnly, matchContentHeight };
+  }, [overflow, renderActiveSectionContentOnly, matchContentHeight]);
   return (
     <SectionsContext.Provider value={state}>
-      <Container overflow={overflow}>{children}</Container>
+      <Container overflow={overflow} matchContentHeight={matchContentHeight}>
+        {children}
+      </Container>
     </SectionsContext.Provider>
   );
 }
@@ -196,10 +205,10 @@ function SectionItem(props: SectionItemProps) {
     headerStyle,
     isOpen,
     sticky = false,
-    matchContentHeight = false,
+    arrowProps = { hide: false, style: {} },
   } = props;
 
-  const { overflow } = useSections();
+  const { overflow, matchContentHeight } = useSections();
 
   return (
     <SectionWrapper
@@ -216,6 +225,7 @@ function SectionItem(props: SectionItemProps) {
         leftElement={leftElement}
         headerStyle={headerStyle}
         sticky={sticky}
+        arrowProps={arrowProps}
       />
       <Wrapper isOpen={isOpen}>{children}</Wrapper>
     </SectionWrapper>
@@ -260,6 +270,7 @@ function MainSectionHeader(props: MainSectionHeaderProps) {
     leftElement,
     headerStyle = {},
     sticky,
+    arrowProps,
   } = props;
   return (
     <Header
@@ -292,7 +303,13 @@ function MainSectionHeader(props: MainSectionHeaderProps) {
             ? rightElement(isOpen)
             : rightElement}
         </ElementsContainer>
-        <OpenIcon icon="chevron-right" isOpen={isOpen} />
+        {!arrowProps?.hide && (
+          <OpenIcon
+            icon="chevron-right"
+            isOpen={isOpen}
+            style={arrowProps?.style}
+          />
+        )}
       </ElementsContainer>
     </Header>
   );