nmr-processing 9.7.8 → 9.8.0

package/lib/datum/data1d/filter1d/zeroFilling.js

@@ -11,26 +11,26 @@ function apply(datum1D, options) {
     if (!isApplicable(datum1D)) {
         throw new Error('zeroFilling not applicable on this data');
     }
-    let { nbPoints, factor = 2 } = options;
-    if (!nbPoints) {
-        nbPoints = 2 ** Math.round(Math.log2(datum1D.data.x.length * factor));
+    const { factor = 2 } = options;
+    const { nbPoints = 2 ** Math.round(Math.log2(datum1D.data.x.length * factor)), } = options;
+    if (!options.nbPoints) {
         const filter = datum1D.filters.find((filter) => filter.name === exports.id);
         if (filter) {
             filter.value = { nbPoints };
         }
     }
-    let digitalFilterApplied = datum1D.filters.some((e) => e.name === 'digitalFilter' && e.flag);
+    const digitalFilterApplied = datum1D.filters.some((e) => e.name === 'digitalFilter' && e.flag);
     const grpdly = datum1D.info?.digitalFilter || 0;
     const pointsToShift = digitalFilterApplied && grpdly > 0 ? Math.floor(grpdly) : 0;
     const { re, im, x } = datum1D.data;
-    let newRE = new Float64Array(nbPoints);
-    let newIM = new Float64Array(nbPoints);
-    let newX = new Float64Array(nbPoints);
+    const newRE = new Float64Array(nbPoints);
+    const newIM = new Float64Array(nbPoints);
+    const newX = new Float64Array(nbPoints);
     const length = Math.min(nbPoints, re.length);
     newRE.set(re.slice(0, length - pointsToShift));
     newIM.set(im.slice(0, length - pointsToShift));
     newX.set(x.slice(0, length - pointsToShift));
-    let diff = x[1] - x[0];
+    const diff = x[1] - x[0];
     let currentX = x[length - pointsToShift - 1];
     for (let i = length - pointsToShift; i < nbPoints; i++) {
         currentX += diff;

package/lib/datum/data1d/filter1d/zeroFilling.js.map

@@ -1 +1 @@
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+{"version":3,"file":"zeroFilling.js","sourceRoot":"","sources":["../../../../src/datum/data1d/filter1d/zeroFilling.ts"],"names":[],"mappings":";;;AAMa,QAAA,EAAE,GAAG,aAAa,CAAC;AACnB,QAAA,IAAI,GAAG,cAAc,CAAC;AACtB,QAAA,mBAAmB,GAAsC;IACpE,aAAa,EAAE,IAAI;IACnB,aAAa,EAAE,KAAK;CACrB,CAAC;AAUF,SAAgB,KAAK,CACnB,OAA2B,EAC3B,OAA2B;IAE3B,IAAI,CAAC,YAAY,CAAC,OAAO,CAAC,EAAE;QAC1B,MAAM,IAAI,KAAK,CAAC,yCAAyC,CAAC,CAAC;KAC5D;IAED,MAAM,EAAE,MAAM,GAAG,CAAC,EAAE,GAAG,OAAO,CAAC;IAC/B,MAAM,EACJ,QAAQ,GAAG,CAAC,IAAI,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,MAAM,GAAG,MAAM,CAAC,CAAC,GACtE,GAAG,OAAO,CAAC;IACZ,IAAI,CAAC,OAAO,CAAC,QAAQ,EAAE;QACrB,MAAM,MAAM,GAAG,OAAO,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,IAAI,KAAK,UAAE,CAAC,CAAC;QACpE,IAAI,MAAM,EAAE;YACV,MAAM,CAAC,KAAK,GAAG,EAAE,QAAQ,EAAE,CAAC;SAC7B;KACF;IAED,MAAM,oBAAoB,GAAG,OAAO,CAAC,OAAO,CAAC,IAAI,CAC/C,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,eAAe,IAAI,CAAC,CAAC,IAAI,CAC5C,CAAC;IAEF,MAAM,MAAM,GAAG,OAAO,CAAC,IAAI,EAAE,aAAa,IAAI,CAAC,CAAC;IAChD,MAAM,aAAa,GACjB,oBAAoB,IAAI,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IAE9D,MAAM,EAAE,EAAE,EAAE,EAAE,EAAE,CAAC,EAAE,GAAG,OAAO,CAAC,IAAI,CAAC;IAEnC,MAAM,KAAK,GAAG,IAAI,YAAY,CAAC,QAAQ,CAAC,CAAC;IACzC,MAAM,KAAK,GAAG,IAAI,YAAY,CAAC,QAAQ,CAAC,CAAC;IACzC,MAAM,IAAI,GAAG,IAAI,YAAY,CAAC,QAAQ,CAAC,CAAC;IAExC,MAAM,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,QAAQ,EAAE,EAAE,CAAC,MAAM,CAAC,CAAC;IAE7C,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,EAAE,MAAM,GAAG,aAAa,CAAC,CAAC,CAAC;IAC/C,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,CAAC,EAAE,MAAM,GAAG,aAAa,CAAC,CAAC,CAAC;IAC/C,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,MAAM,GAAG,aAAa,CAAC,CAAC,CAAC;IAE7C,MAAM,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;IACzB,IAAI,QAAQ,GAAG,CAAC,CAAC,MAAM,GAAG,aAAa,GAAG,CAAC,CAAC,CAAC;IAC7C,KAAK,IAAI,CAAC,GAAG,MAAM,GAAG,aAAa,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE;QACtD,QAAQ,IAAI,IAAI,CAAC;QACjB,IAAI,CAAC,CAAC,CAAC,GAAG,QAAQ,CAAC;KACpB;IAED,IAAI,aAAa,GAAG,CAAC,IAAI,aAAa,GAAG,QAAQ,EAAE;QACjD,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,MAAM,GAAG,aAAa,CAAC,EAAE,QAAQ,GAAG,aAAa,CAAC,CAAC;QACzE,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,MAAM,GAAG,aAAa,CAAC,EAAE,QAAQ,GAAG,aAAa,CAAC,CAAC;KAC1E;IAED,OAAO,CAAC,IAAI,GAAG,EAAE,GAAG,OAAO,CAAC,IAAI,EAAE,EAAE,EAAE,KAAK,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,IAAI,EAAE,CAAC;AACpE,CAAC;AApDD,sBAoDC;AAED,SAAgB,YAAY,CAC1B,OAA2B;IAE3B,IAAI,OAAO,CAAC,IAAI,EAAE,SAAS,IAAI,OAAO,CAAC,IAAI,EAAE,KAAK,EAAE;QAClD,OAAO,IAAI,CAAC;KACb;IACD,OAAO,KAAK,CAAC;AACf,CAAC;AAPD,oCAOC;AAED,SAAgB,MAAM,CACpB,cAAkC,EAClC,QAA4B;IAE5B,OAAO,QAAQ,CAAC,MAAM,CAAC;IAEvB,OAAO;QACL,IAAI,EAAE,IAAI;QACV,MAAM,EAAE,QAAQ;KACjB,CAAC;AACJ,CAAC;AAVD,wBAUC"}

package/lib/datum/data1d/utils/mapPeaks.js

@@ -32,7 +32,7 @@ function mapPeaks(peaks, spectrum, options = {}) {
     const { checkIsExisting = true, shiftTarget = 'origin' } = options;
     const shiftX = (0, getShiftX_1.getShiftX)(spectrum);
     const error = (0, getSpectrumErrorValue_1.getSpectrumErrorValue)(spectrum);
-    let newPeaks = [];
+    const newPeaks = [];
     for (const peak of peaks) {
         const peakDelta = getPeakDelta(peak, shiftTarget, shiftX);
         if (!checkIsExisting ||

package/lib/datum/data1d/utils/mapPeaks.js.map

@@ -1 +1 @@
-{"version":3,"file":"mapPeaks.js","sourceRoot":"","sources":["../../../../src/datum/data1d/utils/mapPeaks.ts"],"names":[],"mappings":";;;AAAA,uCAAkC;AAMlC,2CAAwC;AACxC,mEAAgE;AAEhE,SAAS,QAAQ,CAAC,IAAY,EAAE,QAAiB,EAAE,KAAa;IAC9D,sCAAsC;IACtC,KAAK,MAAM,EAAE,CAAC,EAAE,IAAI,QAAQ,CAAC,KAAK,EAAE,MAAM,IAAI,EAAE,EAAE;QAChD,IAAI,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,KAAK,EAAE;YAChC,OAAO,IAAI,CAAC;SACb;KACF;IACD,OAAO,KAAK,CAAC;AACf,CAAC;AAED,SAAS,YAAY,CAAC,IAAY,EAAE,WAAwB,EAAE,KAAa;IACzE,MAAM,EAAE,SAAS,GAAG,CAAC,EAAE,CAAC,EAAE,GAAG,IAAI,CAAC;IAClC,IAAI,WAAW,KAAK,QAAQ,EAAE;QAC5B,OAAO;YACL,SAAS,EAAE,CAAC,GAAG,KAAK;YACpB,CAAC;SACF,CAAC;KACH;SAAM;QACL,OAAO;YACL,SAAS;YACT,CAAC,EAAE,SAAS,GAAG,KAAK;SACrB,CAAC;KACH;AACH,CAAC;AAED,SAAgB,QAAQ,CACtB,KAAe,EACf,QAAiB,EACjB,UAAsB,EAAE;IAExB,MAAM,EAAE,eAAe,GAAG,IAAI,EAAE,WAAW,GAAG,QAAQ,EAAE,GAAG,OAAO,CAAC;IACnE,MAAM,MAAM,GAAG,IAAA,qBAAS,EAAC,QAAQ,CAAC,CAAC;IACnC,MAAM,KAAK,GAAG,IAAA,6CAAqB,EAAC,QAAQ,CAAC,CAAC;IAE9C,IAAI,QAAQ,GAAa,EAAE,CAAC;IAE5B,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE;QACxB,MAAM,SAAS,GAAG,YAAY,CAAC,IAAI,EAAE,WAAW,EAAE,MAAM,CAAC,CAAC;QAE1D,IACE,CAAC,eAAe;YAChB,CAAC,eAAe,IAAI,CAAC,QAAQ,CAAC,IAAI,EAAE,QAAQ,EAAE,KAAK,CAAC,CAAC,EACrD;YACA,QAAQ,CAAC,IAAI,CAAC;gBACZ,GAAG,IAAI;gBACP,EAAE,EAAE,IAAI,EAAE,EAAE,IAAI,IAAA,SAAE,GAAE;gBACpB,GAAG,SAAS;aACb,CAAC,CAAC;SACJ;KACF;IAED,OAAO,QAAQ,CAAC;AAClB,CAAC;AA3BD,4BA2BC"}
+{"version":3,"file":"mapPeaks.js","sourceRoot":"","sources":["../../../../src/datum/data1d/utils/mapPeaks.ts"],"names":[],"mappings":";;;AAAA,uCAAkC;AAMlC,2CAAwC;AACxC,mEAAgE;AAEhE,SAAS,QAAQ,CAAC,IAAY,EAAE,QAAiB,EAAE,KAAa;IAC9D,sCAAsC;IACtC,KAAK,MAAM,EAAE,CAAC,EAAE,IAAI,QAAQ,CAAC,KAAK,EAAE,MAAM,IAAI,EAAE,EAAE;QAChD,IAAI,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,KAAK,EAAE;YAChC,OAAO,IAAI,CAAC;SACb;KACF;IACD,OAAO,KAAK,CAAC;AACf,CAAC;AAED,SAAS,YAAY,CAAC,IAAY,EAAE,WAAwB,EAAE,KAAa;IACzE,MAAM,EAAE,SAAS,GAAG,CAAC,EAAE,CAAC,EAAE,GAAG,IAAI,CAAC;IAClC,IAAI,WAAW,KAAK,QAAQ,EAAE;QAC5B,OAAO;YACL,SAAS,EAAE,CAAC,GAAG,KAAK;YACpB,CAAC;SACF,CAAC;KACH;SAAM;QACL,OAAO;YACL,SAAS;YACT,CAAC,EAAE,SAAS,GAAG,KAAK;SACrB,CAAC;KACH;AACH,CAAC;AAED,SAAgB,QAAQ,CACtB,KAAe,EACf,QAAiB,EACjB,UAAsB,EAAE;IAExB,MAAM,EAAE,eAAe,GAAG,IAAI,EAAE,WAAW,GAAG,QAAQ,EAAE,GAAG,OAAO,CAAC;IACnE,MAAM,MAAM,GAAG,IAAA,qBAAS,EAAC,QAAQ,CAAC,CAAC;IACnC,MAAM,KAAK,GAAG,IAAA,6CAAqB,EAAC,QAAQ,CAAC,CAAC;IAE9C,MAAM,QAAQ,GAAa,EAAE,CAAC;IAE9B,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE;QACxB,MAAM,SAAS,GAAG,YAAY,CAAC,IAAI,EAAE,WAAW,EAAE,MAAM,CAAC,CAAC;QAE1D,IACE,CAAC,eAAe;YAChB,CAAC,eAAe,IAAI,CAAC,QAAQ,CAAC,IAAI,EAAE,QAAQ,EAAE,KAAK,CAAC,CAAC,EACrD;YACA,QAAQ,CAAC,IAAI,CAAC;gBACZ,GAAG,IAAI;gBACP,EAAE,EAAE,IAAI,EAAE,EAAE,IAAI,IAAA,SAAE,GAAE;gBACpB,GAAG,SAAS;aACb,CAAC,CAAC;SACJ;KACF;IAED,OAAO,QAAQ,CAAC;AAClB,CAAC;AA3BD,4BA2BC"}

package/lib/datum/data2d/Entry2D.d.ts

@@ -8,5 +8,5 @@ export interface Entry2D {
     originalInfo?: Record<string, any>;
     data: NmrData2D;
     originalData?: NmrData2D;
-    filters: Array<Filter>;
+    filters: Filter[];
 }

package/lib/datum/data2d/filter2d/fftDimension1.d.ts

@@ -0,0 +1,15 @@
+import { NmrData2DFid } from 'cheminfo-types';
+import { FilterDomainUpdateRules } from '../../FiltersManager';
+import { Entry2D } from '../Entry2D';
+import { DirectDimensionOptions } from '../../../xyz/util/fft2d/fftDirectDimension';
+export declare const id = "fftDimension1";
+export declare const name = "FFT Dimension 1";
+export declare const DOMAIN_UPDATE_RULES: Readonly<FilterDomainUpdateRules>;
+export declare function apply(datum2D: Entry2D, options: DirectDimensionOptions): void;
+export declare function isApplicable(datum2D: Entry2D): datum2D is Entry2D & {
+    data: Required<NmrData2DFid>;
+};
+export declare function reduce(): {
+    once: boolean;
+    reduce: undefined;
+};

package/lib/datum/data2d/filter2d/fftDimension1.js

@@ -0,0 +1,69 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.reduce = exports.isApplicable = exports.apply = exports.DOMAIN_UPDATE_RULES = exports.name = exports.id = void 0;
+const fftDirectDimension_1 = require("../../../xyz/util/fft2d/fftDirectDimension");
+const ml_spectra_processing_1 = require("ml-spectra-processing");
+exports.id = 'fftDimension1';
+exports.name = 'FFT Dimension 1';
+exports.DOMAIN_UPDATE_RULES = {
+    updateXDomain: true,
+    updateYDomain: true,
+};
+function apply(datum2D, options) {
+    if (!isApplicable(datum2D)) {
+        throw new Error('fft dimension 1 not applicable on this data');
+    }
+    // eslint-disable-next-line @typescript-eslint/no-unused-vars
+    const { data, info } = datum2D;
+    const { digitalFilter: digitalFilterValue = 0 } = info;
+    const fnMode = info.fnMode[1].toLowerCase();
+    const orderedData = fnMode === 'echo-antiecho'
+        ? echoQuadrature(data)
+        : {
+            re: data.re.z,
+            im: data.im.z,
+        };
+    const { zeroFilling = {} } = options;
+    const nbColumns = orderedData.re[0].length;
+    const { factor = 1 } = zeroFilling;
+    const nbPoints = zeroFilling?.nbPoints || 2 ** Math.round(Math.log2(nbColumns * factor));
+    const transformed = (0, fftDirectDimension_1.fftDirectDimension)(orderedData, {
+        fnMode,
+        ...options,
+        digitalFilterValue,
+        zeroFilling: { nbPoints },
+    });
+    datum2D.data.re.z = transformed.re.to2DArray().map(ml_spectra_processing_1.xEnsureFloat64);
+    datum2D.data.im.z = transformed.im.to2DArray().map(ml_spectra_processing_1.xEnsureFloat64);
+}
+exports.apply = apply;
+function isApplicable(datum2D) {
+    if (datum2D.info.isComplex && datum2D.info.isFid)
+        return true;
+    return false;
+}
+exports.isApplicable = isApplicable;
+function reduce() {
+    return {
+        once: true,
+        reduce: undefined,
+    };
+}
+exports.reduce = reduce;
+function echoQuadrature(data) {
+    const { re: { z: reMatrix }, im: { z: imMatrix }, } = data;
+    const newRe = [];
+    const newIm = [];
+    for (let i = 0; i < reMatrix.length; i += 2) {
+        const reCosine = reMatrix[i];
+        const imCosine = imMatrix[i];
+        const reSine = reMatrix[i + 1];
+        const imSine = imMatrix[i + 1];
+        newRe.push((0, ml_spectra_processing_1.xSubtract)((0, ml_spectra_processing_1.xMultiply)(imSine, -1), imCosine));
+        newRe.push((0, ml_spectra_processing_1.xSubtract)(reSine, reCosine));
+        newIm.push((0, ml_spectra_processing_1.xAdd)(reSine, reCosine));
+        newIm.push((0, ml_spectra_processing_1.xSubtract)(imSine, imCosine));
+    }
+    return { re: newRe, im: newIm };
+}
+//# sourceMappingURL=fftDimension1.js.map

package/lib/datum/data2d/filter2d/fftDimension1.js.map

@@ -0,0 +1 @@
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package/lib/datum/data2d/filter2d/fftDimension2.d.ts

@@ -0,0 +1,15 @@
+import { NmrData2DFid } from 'cheminfo-types';
+import { FilterDomainUpdateRules } from '../../FiltersManager';
+import { Entry2D } from '../Entry2D';
+import { IndirectDimensionOptions } from '../../../xyz/util/fft2d/fftIndirectDimension';
+export declare const id = "fftDimension2";
+export declare const name = "FFT Dimension 2";
+export declare const DOMAIN_UPDATE_RULES: Readonly<FilterDomainUpdateRules>;
+export declare function apply(datum2D: Entry2D, options: IndirectDimensionOptions): void;
+export declare function isApplicable(datum2D: Entry2D): datum2D is Entry2D & {
+    data: Required<NmrData2DFid>;
+};
+export declare function reduce(): {
+    once: boolean;
+    reduce: undefined;
+};

package/lib/datum/data2d/filter2d/fftDimension2.js

@@ -0,0 +1,78 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.reduce = exports.isApplicable = exports.apply = exports.DOMAIN_UPDATE_RULES = exports.name = exports.id = void 0;
+const fftIndirectDimension_1 = require("../../../xyz/util/fft2d/fftIndirectDimension");
+const ml_spectra_processing_1 = require("ml-spectra-processing");
+const getMinMaxXY_1 = require("../../../xyz/util/getMinMaxXY");
+exports.id = 'fftDimension2';
+exports.name = 'FFT Dimension 2';
+exports.DOMAIN_UPDATE_RULES = {
+    updateXDomain: true,
+    updateYDomain: true,
+};
+function apply(datum2D, options) {
+    if (!isApplicable(datum2D)) {
+        throw new Error('fft dimension 2 not applicable on this data');
+    }
+    const { data, info } = datum2D;
+    const fnMode = info.fnMode[1];
+    const orderedData = {
+        re: data.re.z,
+        im: data.im.z,
+    };
+    const { zeroFilling = {} } = options;
+    const nbRows = orderedData.re.length;
+    const { factor = 2 } = zeroFilling;
+    const nbPoints = zeroFilling?.nbPoints || 2 ** Math.round(Math.log2(nbRows * factor));
+    const transformed = (0, fftIndirectDimension_1.fftIndirectDimension)({
+        re: orderedData.re,
+        im: orderedData.im,
+    }, {
+        fnMode,
+        ...options,
+        zeroFilling: { nbPoints },
+    });
+    datum2D.data = {
+        ...getQuadrants(transformed, info),
+    };
+    const { isFid, isComplex, ...resInfo } = info;
+    datum2D.info = {
+        ...resInfo,
+        isFt: true,
+    };
+}
+exports.apply = apply;
+function getQuadrants(transformed, info) {
+    const quadrants = {};
+    const { fnMode } = info;
+    const minMaxXY = (0, getMinMaxXY_1.getMinMaxXY)(info);
+    const buildQuandrants = (keys) => {
+        for (const key of keys) {
+            quadrants[key] = {
+                z: transformed[key].to2DArray().map(ml_spectra_processing_1.xEnsureFloat64),
+                maxZ: transformed[key].max(),
+                minZ: transformed[key].min(),
+                ...minMaxXY,
+            };
+        }
+        return quadrants;
+    };
+    if (fnMode === 'QF') {
+        return buildQuandrants(['rr', 'ir']);
+    }
+    return buildQuandrants(['rr', 'ir', 'ri', 'ii']);
+}
+function isApplicable(datum2D) {
+    if (datum2D.info.isComplex && datum2D.info.isFid)
+        return true;
+    return false;
+}
+exports.isApplicable = isApplicable;
+function reduce() {
+    return {
+        once: true,
+        reduce: undefined,
+    };
+}
+exports.reduce = reduce;
+//# sourceMappingURL=fftDimension2.js.map

package/lib/datum/data2d/filter2d/fftDimension2.js.map

@@ -0,0 +1 @@
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package/lib/datum/data2d/utils/getShift.js

@@ -3,7 +3,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.getShift = void 0;
 const Filters_1 = require("../../Filters");
 function getShift(spectrum) {
-    let shift = { x: 0, y: 0 };
+    const shift = { x: 0, y: 0 };
     if (spectrum?.filters) {
         for (const filter of spectrum.filters) {
             if (filter.name === Filters_1.Filters.shift2DX.id) {

package/lib/datum/data2d/utils/getShift.js.map

@@ -1 +1 @@
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+{"version":3,"file":"getShift.js","sourceRoot":"","sources":["../../../../src/datum/data2d/utils/getShift.ts"],"names":[],"mappings":";;;AAAA,2CAAwC;AAQxC,SAAgB,QAAQ,CAAC,QAAiB;IACxC,MAAM,KAAK,GAAG,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC,EAAE,CAAC;IAC7B,IAAI,QAAQ,EAAE,OAAO,EAAE;QACrB,KAAK,MAAM,MAAM,IAAI,QAAQ,CAAC,OAAO,EAAE;YACrC,IAAI,MAAM,CAAC,IAAI,KAAK,iBAAO,CAAC,QAAQ,CAAC,EAAE,EAAE;gBACvC,KAAK,CAAC,CAAC,GAAG,MAAM,EAAE,IAAI,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC;aACjD;YACD,IAAI,MAAM,CAAC,IAAI,KAAK,iBAAO,CAAC,QAAQ,CAAC,EAAE,EAAE;gBACvC,KAAK,CAAC,CAAC,GAAG,MAAM,EAAE,IAAI,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC;aACjD;SACF;KACF;IAED,OAAO,KAAK,CAAC;AACf,CAAC;AAdD,4BAcC"}

package/lib/multiplicity/splitPatterns.js

@@ -16,7 +16,7 @@ function splitPatterns(multiplet) {
     if (/^\s*$/.exec(multiplet))
         return [];
     const regexp = new RegExp(possiblePatterns.join('|'), 'g');
-    let result = multiplet.match(regexp);
+    const result = multiplet.match(regexp);
     if (result)
         return result.map((entry) => entry.trim());
     return [multiplet];

package/lib/multiplicity/splitPatterns.js.map

@@ -1 +1 @@
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+{"version":3,"file":"splitPatterns.js","sourceRoot":"","sources":["../../src/multiplicity/splitPatterns.ts"],"names":[],"mappings":";;;AAAA,4EAAyE;AAEzE,IAAI,gBAAgB,GAAa,EAAE,CAAC;AACpC,KAAK,MAAM,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,IAAI,2CAAoB,EAAE;IAC1D,gBAAgB,CAAC,IAAI,CAAC,KAAK,EAAE,KAAK,EAAE,GAAG,KAAK,CAAC,CAAC;CAC/C;AACD,gBAAgB,GAAG,gBAAgB,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,MAAM,CAAC,CAAC;AAExE;;;;GAIG;AAEH,SAAgB,aAAa,CAAC,SAAiB;IAC7C,IAAI,OAAO,CAAC,IAAI,CAAC,SAAS,CAAC;QAAE,OAAO,EAAE,CAAC;IACvC,MAAM,MAAM,GAAG,IAAI,MAAM,CAAC,gBAAgB,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,GAAG,CAAC,CAAC;IAC3D,MAAM,MAAM,GAAG,SAAS,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC;IACvC,IAAI,MAAM;QAAE,OAAO,MAAM,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;IACvD,OAAO,CAAC,SAAS,CAAC,CAAC;AACrB,CAAC;AAND,sCAMC"}

package/lib/peaks/peaksFilterImpurities.js

@@ -7,15 +7,16 @@ const toCheck = ['solvent', 'h2o', 'tms'];
  * Try to remove peaks of impurities.
  */
 function peaksFilterImpurities(peakList, options = {}) {
-    let { solvent, error = 0.025, remove = false } = options;
-    if (solvent) {
+    const { error = 0.025, remove = false } = options;
+    if (options.solvent) {
+        let { solvent } = options;
         if (solvent === '(cd3)2so')
             solvent = 'dmso';
         if (solvent === 'meod')
             solvent = 'cd3od';
-        let solventImpurities = impurities_1.impurities[solvent];
-        for (let impurity of toCheck) {
-            let impurityShifts = solventImpurities[impurity];
+        const solventImpurities = impurities_1.impurities[solvent];
+        for (const impurity of toCheck) {
+            const impurityShifts = solventImpurities[impurity];
             checkImpurity(peakList, impurityShifts, {
                 error,
                 remove,
@@ -27,7 +28,7 @@ function peaksFilterImpurities(peakList, options = {}) {
 }
 exports.peaksFilterImpurities = peaksFilterImpurities;
 function checkImpurity(peakList, impurity, options) {
-    let { name, error, remove } = options;
+    const { name, error, remove } = options;
     let j, tolerance, difference;
     let i = impurity.length;
     while (i--) {

package/lib/peaks/peaksFilterImpurities.js.map

@@ -1 +1 @@
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package/lib/peaks/peaksToRanges.js

@@ -47,8 +47,8 @@ const assignSignal = (peak, frequency, nucleus) => {
  * This function clustering peaks and calculate the integration value for each range from the peak list returned from extractPeaks function.
  */
 function peaksToRanges(data, peakList, options = {}) {
-    let { integrationSum = 100, joinOverlapRanges = true, clean = 0.4, compile = true, integralType = 'sum', frequency = 400, frequencyCluster = 16, keepPeaks = false, nucleus = '1H', } = options;
-    let signalOptions = {
+    const { integrationSum = 100, joinOverlapRanges = true, clean = 0.4, compile = true, integralType = 'sum', frequency = 400, frequencyCluster = 16, keepPeaks = false, nucleus = '1H', } = options;
+    const signalOptions = {
         integrationSum,
         integralType,
         frequencyCluster,
@@ -61,7 +61,7 @@ function peaksToRanges(data, peakList, options = {}) {
         data.x = data.x.reverse();
         data.y = data.y.reverse();
     }
-    let signals = detectSignals(data, peakList, signalOptions);
+    const signals = detectSignals(data, peakList, signalOptions);
     if (clean) {
         for (let i = 0; i < signals.length; i++) {
             if (Math.abs(signals[i].integralData.value) < clean) {
@@ -73,7 +73,7 @@ function peaksToRanges(data, peakList, options = {}) {
         let nHi, sum;
         for (let i = 0; i < signals.length; i++) {
             signals[i] = jAnalyzer_1.default.compilePattern(signals[i]);
-            let signal = signals[i];
+            const signal = signals[i];
             if (signal.maskPattern &&
                 signal.multiplicity !== 'm' &&
                 signal.multiplicity !== '') {
@@ -81,11 +81,11 @@ function peaksToRanges(data, peakList, options = {}) {
                 // Create a new signal with the removed peaks
                 nHi = 0;
                 sum = 0;
-                let peaksO = [];
+                const peaksO = [];
                 for (let j = signal.maskPattern.length - 1; j >= 0; j--) {
                     sum += computeArea(signal.peaks[j], frequency);
                     if (!signal.maskPattern[j]) {
-                        let peakR = signal.peaks.splice(j, 1)[0];
+                        const peakR = signal.peaks.splice(j, 1)[0];
                         peaksO.push({
                             x: peakR.x,
                             y: peakR.intensity,
@@ -101,12 +101,12 @@ function peaksToRanges(data, peakList, options = {}) {
                 if (peaksO.length > 0) {
                     nHi = (nHi * signal.integralData.value) / sum;
                     signal.integralData.value -= nHi;
-                    let peaks1 = [];
+                    const peaks1 = [];
                     for (let j = peaksO.length - 1; j >= 0; j--) {
                         peaks1.push(peaksO[j]);
                     }
                     signalOptions.integrationSum = Math.abs(nHi);
-                    let ranges = detectSignals(data, peaks1, signalOptions);
+                    const ranges = detectSignals(data, peaks1, signalOptions);
                     for (const range of ranges) {
                         signals.push(range);
                     }
@@ -128,7 +128,7 @@ function peaksToRanges(data, peakList, options = {}) {
     }
     let ranges = [];
     for (let i = 0; i < signals.length; i++) {
-        let signal = signals[i];
+        const signal = signals[i];
         const range = {
             id: (0, uuid_1.v4)(),
             from: signal.integralData.from,
@@ -176,21 +176,21 @@ exports.peaksToRanges = peaksToRanges;
  * @private
  */
 function detectSignals(data, peakList, options = {}) {
-    let { integrationSum = 100, integralType = 'sum', frequencyCluster = 16, frequency = 400, nucleus = '1H', } = options;
+    const { frequencyCluster = 16, integrationSum = 100, integralType = 'sum', frequency = 400, nucleus = '1H', } = options;
     let signal1D = assignSignal(peakList[0], frequency, nucleus);
     let peaks;
-    let signals = [];
+    const signals = [];
     let prevPeak = { x: Number.MIN_SAFE_INTEGER };
-    frequencyCluster /= frequency;
+    const distantToClustering = frequencyCluster / frequency;
     for (const peak of peakList) {
-        if (Math.abs(peak.x - prevPeak.x) > frequencyCluster) {
+        if (Math.abs(peak.x - prevPeak.x) > distantToClustering) {
             signal1D = assignSignal(peak, frequency, nucleus);
             if (peak.kind)
                 signal1D.kind = peak.kind;
             signals.push(signal1D);
         }
         else {
-            let tmp = peak.x + peak.width / frequency;
+            const tmp = peak.x + peak.width / frequency;
             signal1D.stopX = Math.max(signal1D.stopX, tmp);
             signal1D.startX = Math.min(signal1D.startX, tmp);
             signal1D.nbPeaks++;
@@ -206,13 +206,13 @@ function detectSignals(data, peakList, options = {}) {
         }
         prevPeak = peak;
     }
-    for (let signal of signals) {
+    for (const signal of signals) {
         peaks = signal.peaks;
-        let integration = signal.integralData;
+        const integration = signal.integralData;
         let chemicalShift = 0;
         let integralPeaks = 0;
         for (const peak of peaks) {
-            let area = computeArea(peak, frequency);
+            const area = computeArea(peak, frequency);
             chemicalShift += peak.x * area;
             integralPeaks += area;
         }

package/lib/peaks/peaksToRanges.js.map

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package/lib/peaks/solventSuppression.js

@@ -15,17 +15,17 @@ function solventSuppression(peakList, solvent, options = {}) {
     const xValues = peaks.map((peak) => peak.x);
     const { markSolventPeaks = false, solventZoneExtension = 1.2 } = options;
     for (const solventSignal of solvent) {
-        let solventXYPeaks = solventSignal.peaks
+        const solventXYPeaks = solventSignal.peaks
             ? solventSignal.peaks
             : getSolventPeaks(solventSignal);
         solventXYPeaks.sort((a, b) => a.x - b.x);
-        let upIndex = (0, ml_spectra_processing_1.xFindClosestIndex)(xValues, solventXYPeaks[solventXYPeaks.length - 1].x + solventZoneExtension);
-        let lowIndex = (0, ml_spectra_processing_1.xFindClosestIndex)(xValues, solventXYPeaks[0].x - solventZoneExtension);
+        const upIndex = (0, ml_spectra_processing_1.xFindClosestIndex)(xValues, solventXYPeaks[solventXYPeaks.length - 1].x + solventZoneExtension);
+        const lowIndex = (0, ml_spectra_processing_1.xFindClosestIndex)(xValues, solventXYPeaks[0].x - solventZoneExtension);
         const nearPeaks = peaks.filter((peak, index) => index >= lowIndex && index <= upIndex);
         const amplitudeResiduals = [];
         const deltaResiduals = [];
         const positionResiduals = [];
-        for (let peak of nearPeaks) {
+        for (const peak of nearPeaks) {
             const { peaks: shiftedSolventPeaks, delta: currentDelta } = getShiftedSolventPeaks(peak, solventSignal, solventXYPeaks);
             const closestPeaks = getClosestPeaks(shiftedSolventPeaks, nearPeaks);
             let deltaResidual = 0;
@@ -57,7 +57,7 @@ function solventSuppression(peakList, solvent, options = {}) {
         });
         let minIndex = -1;
         let minScore = Number.MAX_SAFE_INTEGER;
-        let score = [];
+        const score = [];
         for (let i = 0; i < deltaResiduals.length; i++) {
             const value = (amplitudeResiduals[i] / maxAmplitude +
                 deltaResiduals[i] / maxDelta +
@@ -84,13 +84,13 @@ function solventSuppression(peakList, solvent, options = {}) {
             return peaks;
         }
         if (markSolventPeaks) {
-            for (let index of rowAssignments) {
+            for (const index of rowAssignments) {
                 peaks[index + lowIndex].kind = 'solvent';
             }
         }
         else {
             rowAssignments.sort((a, b) => b - a);
-            for (let index of rowAssignments) {
+            for (const index of rowAssignments) {
                 peaks.splice(index + lowIndex, 1);
             }
         }
@@ -99,8 +99,8 @@ function solventSuppression(peakList, solvent, options = {}) {
 }
 exports.solventSuppression = solventSuppression;
 function getSolventPeaks(signal, options = {}) {
-    let signals = (0, addDummySignals_1.addDummySignals)([signal]);
-    let spinSystem = (0, signalsToSpinSystem_1.signalsToSpinSystem)(signals);
+    const signals = (0, addDummySignals_1.addDummySignals)([signal]);
+    const spinSystem = (0, signalsToSpinSystem_1.signalsToSpinSystem)(signals);
     const { frequency = 400, maxClusterSize = 8 } = options;
     spinSystem.clusters = (0, splitSpinSystem_1.splitSpinSystem)(spinSystem, {
         frequency,
@@ -118,7 +118,7 @@ function getShiftedSolventPeaks(peak, solventSignal, solventXYPeaks) {
     }
     const maxIntensity = shiftedSolventPeaks.reduce((max, current) => (current.y > max ? current.y : max), shiftedSolventPeaks[0].y);
     let currentDelta = 0;
-    for (let shiftedSolventPeak of shiftedSolventPeaks) {
+    for (const shiftedSolventPeak of shiftedSolventPeaks) {
         shiftedSolventPeak.x += deltaPPM;
         shiftedSolventPeak.y /= maxIntensity;
         currentDelta += shiftedSolventPeak.x;
@@ -137,7 +137,7 @@ function getClosestPeaks(shiftedSolventPeaks, nearPeaks) {
         return [];
     const assignmentPeaks = [];
     let maxValue = Number.MIN_SAFE_INTEGER;
-    for (let index of rowAssignments) {
+    for (const index of rowAssignments) {
         if (maxValue < nearPeaks[index].y)
             maxValue = nearPeaks[index].y;
         assignmentPeaks.push({ ...nearPeaks[index] });

package/lib/peaks/solventSuppression.js.map

@@ -1 +1 @@
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package/lib/peaks/util/addMissingIDs.js.map

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