feat: nmr-load-save prerelease with filters (#1965)

close #1948 #1943 
* fix: filter expno option name
* chore: remove null for brukerFilters
* call re or rr based on the type

package.json

@@ -80,7 +80,7 @@
     "ml-stat": "^1.3.3",
     "multiplet-analysis": "^2.0.0",
     "nmr-correlation": "^2.3.3",
-    "nmr-load-save": "^0.6.1",
+    "nmr-load-save": "^0.7.1",
     "nmr-processing": "^9.3.1",
     "nmredata": "^0.9.1",
     "numeral": "^2.0.6",

src/component/2d/FooterBanner.tsx

@@ -5,7 +5,7 @@ import { useContext, useMemo, Fragment } from 'react';
 import { MF } from 'react-mf';
 
 import { get1DDataXY } from '../../data/data1d/Spectrum1D/get1DDataXY';
-import { Data2D } from '../../data/types/data2d';
+import { Data2DFid, Data2DFt } from '../../data/types/data2d/Data2D';
 import { BrushContext } from '../EventsTrackers/BrushTracker';
 import { MouseContext } from '../EventsTrackers/MouseTracker';
 import { useChartData } from '../context/ChartContext';
@@ -228,9 +228,10 @@ function FooterBanner({ layout, data1D }) {
 
   const getZValue = () => {
     if (trackID === LAYOUT.CENTER_2D) {
-      const { maxX, maxY, minX, minY, z } = (
-        data[activeSpectrum.index].data as Data2D
-      ).rr as any;
+      const { info, data: spectraData } = data[activeSpectrum.index];
+      const { maxX, maxY, minX, minY, z } = info.isFid
+        ? (spectraData as Data2DFid).re
+        : ((spectraData as Data2DFt).rr as any);
 
       const xStep = (maxX - minX) / (z[0].length - 1);
       const yStep = (maxY - minY) / (z.length - 1);

src/component/2d/fid/FidCanvas.tsx

@@ -2,6 +2,7 @@ import { matrixZPivotRescale } from 'ml-spectra-processing';
 import { useEffect, useRef, useMemo } from 'react';
 
 import { Datum2D } from '../../../data/types/data2d';
+import { Data2DFid, Data2DFt } from '../../../data/types/data2d/Data2D';
 import { useChartData } from '../../context/ChartContext';
 import useSpectrum from '../../hooks/useSpectrum';
 import { get2DXScale, get2DYScale } from '../utilities/scale';
@@ -102,10 +103,16 @@ export function FidCanvas() {
 }
 
 function getImageData(spectrum: Datum2D) {
-  const matrix = matrixZPivotRescale(spectrum.data.rr.z, {
-    max: 255,
-    ArrayConstructor: Int16Array,
-  });
+  const { isFid } = spectrum.info;
+  const matrix = matrixZPivotRescale(
+    isFid
+      ? (spectrum.data as Data2DFid).re.z
+      : (spectrum.data as Data2DFt).rr.z,
+    {
+      max: 255,
+      ArrayConstructor: Int16Array,
+    },
+  );
   const WIDTH = matrix[0].length;
   const HEIGHT = matrix.length;
 

src/component/loader/DropZone.tsx

@@ -9,6 +9,7 @@ import { FaUpload } from 'react-icons/fa';
 import { useChartData } from '../context/ChartContext';
 import { useDispatch } from '../context/DispatchContext';
 import { LoaderProvider } from '../context/LoaderContext';
+import { usePreferences } from '../context/PreferencesContext';
 import { useAlert } from '../elements/popup/Alert';
 import { useCheckToolsVisibility } from '../hooks/useCheckToolsVisibility';
 import { SET_LOADING_FLAG, LOAD_DROP_FILES } from '../reducer/types/Types';
@@ -49,6 +50,7 @@ const containerStyle = css`
 function DropZone(props) {
   const { width, height } = useChartData();
   const dispatch = useDispatch();
+  const preferences = usePreferences();
   const isToolEnabled = useCheckToolsVisibility();
   const alert = useAlert();
 
@@ -58,7 +60,9 @@ function DropZone(props) {
     }
     try {
       const fileCollection = await fileCollectionFromFileList(files);
-      const data = await readDropFiles(fileCollection);
+
+      const { nmrLoaders: filter } = preferences.current;
+      const data = await readDropFiles(fileCollection, { filter });
       dispatch({ type: LOAD_DROP_FILES, payload: { data } });
     } catch (error: any) {
       alert.error(error.message);

src/component/modal/setting/ImportationFiltersTabContent.tsx

@@ -43,8 +43,8 @@ const BRUKER_LIST: ListItem[] = [
     fieldType: 'input',
   },
   {
-    label: 'Experimental Number',
-    name: 'bruker.experimentalNumber',
+    label: 'Experiment Number',
+    name: 'bruker.experimentNumber',
     fieldType: 'input',
   },
   {

src/component/reducer/actions/DomainActions.ts

@@ -5,6 +5,7 @@ import { get1DDataXY } from '../../../data/data1d/Spectrum1D/get1DDataXY';
 import { isSpectrum2D } from '../../../data/data2d/Spectrum2D';
 import { Datum1D } from '../../../data/types/data1d';
 import { Datum2D } from '../../../data/types/data2d';
+import { Data2DFid, Data2DFt } from '../../../data/types/data2d/Data2D';
 import nucleusToString from '../../utility/nucleusToString';
 import { State } from '../Reducer';
 import { DISPLAYER_MODE } from '../core/Constants';
@@ -87,7 +88,7 @@ function get2DDomain(state: State) {
   const spectrum =
     data.find((datum) => datum.id === activeSpectrum?.id) || null;
   if (spectrum?.info.isFid) {
-    const { minX, maxX, minY, maxY } = (spectrum as Datum2D).data.rr;
+    const { minX, maxX, minY, maxY } = (spectrum.data as Data2DFid).re;
     xArray = [minX, maxX];
     yArray = [minY, maxY];
   } else {
@@ -100,7 +101,8 @@ function get2DDomain(state: State) {
             datum.info.isFt,
         ) as Array<Datum2D>
       ).flatMap((datum: Datum2D) => {
-        return [datum.data.rr.minX, datum.data.rr.maxX];
+        const { minX, maxX } = (datum.data as Data2DFt).rr;
+        return [minX, maxX];
       });
 
       yArray = (
@@ -111,7 +113,8 @@ function get2DDomain(state: State) {
             d.info.isFt,
         ) as Array<Datum2D>
       ).flatMap((datum: Datum2D) => {
-        return [datum.data.rr.minY, datum.data.rr.maxY];
+        const { minY, maxY } = (datum.data as Data2DFt).rr;
+        return [minY, maxY];
       });
     } catch (error) {
       // TODO: handle error

src/component/reducer/actions/SpectrumsActions.ts

@@ -13,6 +13,7 @@ import {
 import { contoursManager } from '../../../data/data2d/Spectrum2D/contours';
 import { Datum1D } from '../../../data/types/data1d';
 import { Datum2D } from '../../../data/types/data2d';
+import { Data2DFid, Data2DFt } from '../../../data/types/data2d/Data2D';
 import { options } from '../../toolbar/ToolTypes';
 import groupByInfoKey from '../../utility/GroupByInfoKey';
 import { getSpectraByNucleus } from '../../utility/getSpectraByNucleus';
@@ -169,10 +170,10 @@ function addMissingProjectionHandler(draft, action) {
   if (activeSpectrum?.id) {
     const { index } = activeSpectrum;
     const datum2D = state.data[index];
-    const info = datum2D.info;
+    const { info, data } = datum2D;
     for (let n of nucleus) {
       const datum1D = getMissingProjection(
-        datum2D.data.rr,
+        info.isFid ? (data as Data2DFid).re : (data as Data2DFt).rr,
         n,
         info,
         draft.usedColors,

src/component/reducer/actions/ZonesActions.ts

@@ -15,6 +15,7 @@ import {
   detectZonesManual,
 } from '../../../data/data2d/Spectrum2D';
 import { Datum2D } from '../../../data/types/data2d';
+import { Data2DFid, Data2DFt } from '../../../data/types/data2d/Data2D';
 import {
   unlink,
   unlinkInAssignmentData,
@@ -66,8 +67,11 @@ function handleAutoZonesDetection(draft: Draft<State>, detectionOptions) {
 }
 function handleAutoSpectraZonesDetection(draft: Draft<State>) {
   for (const datum of draft.data) {
-    if (datum.info.dimension === 2) {
-      const { minX, maxX, minY, maxY } = (datum as Datum2D).data.rr;
+    const { info, data } = datum;
+    if (info.dimension === 2) {
+      const { minX, maxX, minY, maxY } = info.isFid
+        ? (data as Data2DFid).re
+        : (data as Data2DFt).rr;
       const detectionOptions = {
         selectedZone: { fromX: minX, toX: maxX, fromY: minY, toY: maxY },
         thresholdFactor: 1,

src/component/workspaces/Workspace.ts

@@ -148,8 +148,8 @@ export interface LoadersPreferences {
     onlyReal: boolean;
   };
   bruker: {
-    processingNumber: number | null;
-    experimentalNumber: number | null;
+    processingNumber?: number | number[];
+    experimentNumber?: number | number[];
     onlyFirstProcessedData: boolean;
   };
 }

src/component/workspaces/workspaceDefaultProperties.ts

@@ -80,8 +80,6 @@ export const workspaceDefaultProperties: Required<WorkspaceData> = {
       onlyReal: false,
     },
     bruker: {
-      processingNumber: null,
-      experimentalNumber: null,
       onlyFirstProcessedData: true,
     },
   },

src/data/data2d/Spectrum2D/contours.ts

@@ -162,6 +162,7 @@ function drawContours(
   level: number,
   datum: Datum2D,
   negative = false,
+  quadrant = 'rr',
 ): { contours: any; timeout: boolean } {
   const zoom = level / 2 + 1;
   const {
@@ -173,13 +174,13 @@ function drawContours(
     return getContours(zoom, {
       negative,
       nbLevels: numberOfNegativeLayer,
-      data: datum.data.rr,
+      data: datum.data[quadrant],
     });
   }
 
   return getContours(zoom, {
     nbLevels: numberOfPositiveLayer,
-    data: datum.data.rr,
+    data: datum.data[quadrant],
   });
 }
 

src/data/data2d/Spectrum2D/get2DSpectrumErrorValue.ts

@@ -1,12 +1,16 @@
 import { Datum2D } from '../../types/data2d';
+import { Data2DFid, Data2DFt } from '../../types/data2d/Data2D';
 
 export interface Zone2DError {
   x: number;
   y: number;
 }
 
 export function get2DSpectrumErrorValue(datum: Datum2D): Zone2DError {
-  const { minX, maxX, minY, maxY } = datum.data.rr;
+  const { data, info } = datum;
+  const { minX, maxX, minY, maxY } = info.isFid
+    ? (data as Data2DFid).re
+    : (data as Data2DFt).rr;
   const x = Math.abs(maxX - minX) / 10000;
   const y = Math.abs(maxY - minY) / 10000;
   return { x, y };

src/data/data2d/Spectrum2D/getSlice.ts

@@ -2,6 +2,7 @@ import { zoneToX } from 'ml-spectra-processing';
 
 import { initiateDatum1D } from '../../data1d/Spectrum1D';
 import { Datum2D } from '../../types/data2d';
+import { Data2DFid, Data2DFt } from '../../types/data2d/Data2D';
 
 /** get 2d projection
  * @param {number} x in ppm
@@ -14,7 +15,10 @@ interface SlicePosition {
 }
 
 export function getSlice(spectrum: Datum2D, position: SlicePosition) {
-  const data = spectrum.data.rr;
+  const { data: spectraData, info } = spectrum;
+  const data = info.isFid
+    ? (spectraData as Data2DFid).re
+    : (spectraData as Data2DFt).rr;
   const xStep = (data.maxX - data.minX) / (data.z[0].length - 1);
   const yStep = (data.maxY - data.minY) / (data.z.length - 1);
   const xIndex = Math.floor((position.x - data.minX) / xStep);
@@ -24,26 +28,23 @@ export function getSlice(spectrum: Datum2D, position: SlicePosition) {
   if (yIndex < 0 || yIndex >= data.z.length) return;
 
   let infoX = {
-    nucleus: spectrum.info.nucleus[0], // 1H, 13C, 19F, ...
+    nucleus: info.nucleus[0], // 1H, 13C, 19F, ...
     isFid: false,
     isComplex: false, // if isComplex is true that mean it contains real/ imaginary  x set, if not hid re/im button .
     dimension: 1,
   };
 
   let dataX = {
-    x: zoneToX(
-      { from: data.minX, to: data.maxX },
-      spectrum.data.rr.z[0].length,
-    ),
-    re: new Float64Array(spectrum.data.rr.z[0].length),
+    x: zoneToX({ from: data.minX, to: data.maxX }, data.z[0].length),
+    re: new Float64Array(data.z[0].length),
   };
 
-  for (let i = 0; i < spectrum.data.rr.z[0].length; i++) {
-    dataX.re[i] += spectrum.data.rr.z[yIndex][i];
+  for (let i = 0; i < data.z[0].length; i++) {
+    dataX.re[i] += data.z[yIndex][i];
   }
 
   let infoY = {
-    nucleus: spectrum.info.nucleus[1], // 1H, 13C, 19F, ...
+    nucleus: info.nucleus[1], // 1H, 13C, 19F, ...
     isFid: false,
     isComplex: false, // if isComplex is true that mean it contains real/ imaginary  x set, if not hid re/im button .
     dimension: 1,
@@ -56,7 +57,7 @@ export function getSlice(spectrum: Datum2D, position: SlicePosition) {
 
   let index = data.z.length - 1;
   for (let i = 0; i < data.z.length; i++) {
-    dataY.re[i] += spectrum.data.rr.z[index--][xIndex];
+    dataY.re[i] += data.z[index--][xIndex];
   }
   const horizontal = initiateDatum1D({ info: infoX, data: dataX }, {});
   const vertical = initiateDatum1D({ info: infoY, data: dataY }, {});

src/data/data2d/Spectrum2D/initiateDatum2D.ts

@@ -55,7 +55,7 @@ export function initiateDatum2D(options: any, usedColors = {}): Datum2D {
 function getData(datum, options) {
   if (datum.info.isFid) {
     const { re = defaultMinMax, im = defaultMinMax } = options.data;
-    return { rr: re, ii: im };
+    return { re, im };
   }
   return { rr: defaultMinMax, ...options.data };
 }

src/data/types/data2d/Data2D.ts

@@ -8,4 +8,16 @@ export interface MinMaxContent {
   maxZ: number;
 }
 
-export type Data2D = Record<'rr' | 'ii' | 'ri' | 'ir', MinMaxContent>;
+export type Data2D = Data2DFid | Data2DFt;
+
+export interface Data2DFid {
+  re: MinMaxContent;
+  im?: MinMaxContent;
+}
+
+export interface Data2DFt {
+  rr: MinMaxContent;
+  ri?: MinMaxContent;
+  ir?: MinMaxContent;
+  ii?: MinMaxContent;
+}