nmr-processing 8.2.0 → 8.4.0

package/lib/utilities/rangeFromSignal.js

@@ -2,15 +2,15 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.rangeFromSignal = void 0;
 const couplingValues_1 = require("../constants/couplingValues");
-function rangeFromSignal(signal, options = {}) {
+function rangeFromSignal(signal, options) {
     const { nucleus = '1h', frequency = 400 } = options;
     const { tolerance = getTolerance(nucleus) / frequency } = options;
-    let halfWidth = (signal.js || []).reduce((total, j) => {
-        const { coupling, multiplicity = 'd' } = j;
-        return total + (couplingValues_1.couplingValues[multiplicity] * coupling) / frequency;
-    }, 0) /
-        2 +
-        tolerance;
+    let halfWidth = 0;
+    for (const js of signal.js || []) {
+        const { coupling, multiplicity = 'd' } = js;
+        halfWidth += (couplingValues_1.couplingValues[multiplicity] * coupling) / frequency;
+    }
+    halfWidth = tolerance + halfWidth / 2;
     return {
         from: signal.delta - halfWidth,
         to: signal.delta + halfWidth,

package/lib/utilities/rangeFromSignal.js.map

@@ -1 +1 @@
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package/lib/utilities/resurrectRange.js

@@ -37,13 +37,10 @@ function resurrectRange(part, options = {}) {
                 signal.multiplicity = multiplicity;
             }
         }
-        else {
-            // looks like a real multiplicity, s, d, dd, etc..
-            if (!isARange) {
-                // a complex signal
-                signal.delta = from;
-                signal.multiplicity = multiplicity;
-            }
+        else if (!isARange) {
+            // a complex signal
+            signal.delta = from;
+            signal.multiplicity = multiplicity;
         }
     }
     const jCouplings = insideParts

package/lib/utilities/resurrectRange.js.map

@@ -1 +1 @@
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package/lib/xy/xyAutoPeaksPicking.d.ts

@@ -22,6 +22,11 @@ export interface OptionsXYAutoPeaksPicking extends Partial<GetPeakListOptions> {
      * @default 3
      */
     thresholdFactor?: number;
+    /**
+     * If it is true, it check for negative peaks.
+     * @default true
+     */
+    lookPositive?: boolean;
     /**
      * If it is true, it check for negative peaks.
      * @default false

package/lib/xy/xyAutoPeaksPicking.js

@@ -4,13 +4,15 @@ exports.xyAutoPeaksPicking = void 0;
 const ml_gsd_1 = require("ml-gsd");
 const ml_spectra_processing_1 = require("ml-spectra-processing");
 function xyAutoPeaksPicking(data, options = {}) {
-    const { from, to, noiseLevel, thresholdFactor = 3, minMaxRatio = 0.05, broadRatio = 0.00025, useSanPlot = false, smoothY = true, optimize = false, factorLimits = 4, realTopDetection = true, shape = { kind: 'gaussian' }, optimization = { kind: 'lm' }, broadWidth = 0.25, sgOptions = {}, lookNegative = false, } = options;
+    const { from, to, noiseLevel, thresholdFactor = 3, minMaxRatio = 0.05, broadRatio = 0.00025, useSanPlot = false, smoothY = true, optimize = false, factorLimits = 4, realTopDetection = true, shape = { kind: 'gaussian' }, optimization = { kind: 'lm' }, broadWidth = 0.25, sgOptions = {}, lookPositive = true, lookNegative = false, } = options;
     const { windowSize = 9, polynomial = 3 } = sgOptions;
+    if (data.x.length < windowSize)
+        return [];
+    if (!lookPositive && !lookNegative)
+        return [];
     if (from !== undefined && to !== undefined) {
         data = (0, ml_spectra_processing_1.xyExtract)(data, { zones: [{ from, to }] });
     }
-    if (data.x.length < windowSize)
-        return [];
     const cutOff = getCutOff(data.y, { noiseLevel, useSanPlot, thresholdFactor });
     let getPeakOptions = {
         shape,
@@ -26,7 +28,10 @@ function xyAutoPeaksPicking(data, options = {}) {
         optimization,
         realTopDetection,
     };
-    let peaks = getPeakList(data, getPeakOptions);
+    const peaks = [];
+    if (lookPositive) {
+        peaks.push(...getPeakList(data, getPeakOptions));
+    }
     if (lookNegative) {
         getPeakOptions.noiseLevel = cutOff.negative;
         getPeakOptions.maxCriteria = false;

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+{"version":3,"file":"xyAutoPeaksPicking.js","sourceRoot":"","sources":["../../src/xy/xyAutoPeaksPicking.ts"],"names":[],"mappings":";;;AACA,mCAAgF;AAMhF,iEAI+B;AA0D/B,SAAgB,kBAAkB,CAChC,IAAY,EACZ,UAAqC,EAAE;IAEvC,MAAM,EACJ,IAAI,EACJ,EAAE,EACF,UAAU,EACV,eAAe,GAAG,CAAC,EACnB,WAAW,GAAG,IAAI,EAClB,UAAU,GAAG,OAAO,EACpB,UAAU,GAAG,KAAK,EAClB,OAAO,GAAG,IAAI,EACd,QAAQ,GAAG,KAAK,EAChB,YAAY,GAAG,CAAC,EAChB,gBAAgB,GAAG,IAAI,EACvB,KAAK,GAAG,EAAE,IAAI,EAAE,UAAU,EAAE,EAC5B,YAAY,GAAG,EAAE,IAAI,EAAE,IAAI,EAAE,EAC7B,UAAU,GAAG,IAAI,EACjB,SAAS,GAAG,EAAE,EACd,YAAY,GAAG,IAAI,EACnB,YAAY,GAAG,KAAK,GACrB,GAAG,OAAO,CAAC;IAEZ,MAAM,EAAE,UAAU,GAAG,CAAC,EAAE,UAAU,GAAG,CAAC,EAAE,GAAG,SAAS,CAAC;IAErD,IAAI,IAAI,CAAC,CAAC,CAAC,MAAM,GAAG,UAAU;QAAE,OAAO,EAAE,CAAC;IAE1C,IAAI,CAAC,YAAY,IAAI,CAAC,YAAY;QAAE,OAAO,EAAE,CAAC;IAE9C,IAAI,IAAI,KAAK,SAAS,IAAI,EAAE,KAAK,SAAS,EAAE;QAC1C,IAAI,GAAG,IAAA,iCAAS,EAAC,IAAI,EAAE,EAAE,KAAK,EAAE,CAAC,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,CAAC;KACnD;IAED,MAAM,MAAM,GAAG,SAAS,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,UAAU,EAAE,UAAU,EAAE,eAAe,EAAE,CAAC,CAAC;IAE9E,IAAI,cAAc,GAAuB;QACvC,KAAK;QACL,UAAU;QACV,QAAQ;QACR,YAAY;QACZ,WAAW,EAAE,IAAI;QACjB,SAAS,EAAE,EAAE,UAAU,EAAE,UAAU,EAAE;QACrC,WAAW;QACX,UAAU;QACV,UAAU,EAAE,MAAM,CAAC,QAAQ;QAC3B,OAAO;QACP,YAAY;QACZ,gBAAgB;KACjB,CAAC;IAEF,MAAM,KAAK,GAAG,EAAE,CAAC;IACjB,IAAI,YAAY,EAAE;QAChB,KAAK,CAAC,IAAI,CAAC,GAAG,WAAW,CAAC,IAAI,EAAE,cAAc,CAAC,CAAC,CAAC;KAClD;IAED,IAAI,YAAY,EAAE;QAChB,cAAc,CAAC,UAAU,GAAG,MAAM,CAAC,QAAQ,CAAC;QAC5C,cAAc,CAAC,WAAW,GAAG,KAAK,CAAC;QACnC,KAAK,CAAC,IAAI,CAAC,GAAG,WAAW,CAAC,IAAI,EAAE,cAAc,CAAC,CAAC,CAAC;KAClD;IACD,OAAO,KAAK,CAAC;AACf,CAAC;AA9DD,gDA8DC;AAED,SAAS,WAAW,CAAC,IAAY,EAAE,OAA2B;IAC5D,MAAM,EACJ,KAAK,EACL,UAAU,EACV,QAAQ,EACR,WAAW,EACX,YAAY,EACZ,SAAS,EACT,WAAW,EACX,UAAU,EACV,UAAU,EACV,OAAO,EACP,YAAY,EACZ,gBAAgB,GACjB,GAAG,OAAO,CAAC;IAEZ,IAAI,QAAQ,GAAG,IAAA,YAAG,EAAC,IAAI,EAAE;QACvB,SAAS;QACT,WAAW;QACX,WAAW;QACX,UAAU;QACV,OAAO;QACP,gBAAgB;KACjB,CAAC,CAAC;IAEH,IAAI,UAAU,EAAE;QACd,QAAQ,GAAG,IAAA,uBAAc,EAAC,QAAQ,EAAE;YAClC,UAAU;YACV,UAAU;YACV,KAAK;YACL,YAAY;SACb,CAAC,CAAC;KACJ;IAED,IAAI,QAAQ,EAAE;QACZ,OAAO,IAAA,sBAAa,EAAC,IAAI,EAAE,QAAQ,EAAE;YACnC,KAAK;YACL,YAAY;YACZ,YAAY;SACb,CAAC,CAAC;KACJ;IAED,OAAO,IAAA,2BAAkB,EAAC,QAAQ,EAAE,EAAE,KAAK,EAAE,CAAC,CAAC;AACjD,CAAC;AAED,SAAS,SAAS,CAAC,IAA6B,EAAE,OAAyB;IACzE,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,eAAe,EAAE,GAAG,OAAO,CAAC;IAE5D,MAAM,YAAY,GAAG,CAAC,UAAkB,EAAE,EAAE,CAC1C,OAAO,UAAU,KAAK,QAAQ;QAC5B,CAAC,CAAC,EAAE,QAAQ,EAAE,UAAU,EAAE,QAAQ,EAAE,CAAC,UAAU,EAAE;QACjD,CAAC,CAAC,UAAU,CAAC;IAEjB,IAAI,UAAU,EAAE;QACd,OAAO,YAAY,CAAC,UAAU,CAAC,CAAC;KACjC;SAAM;QACL,OAAO,UAAU;YACf,CAAC,CAAC,IAAA,qCAAa,EAAC,IAAI,EAAE,EAAE,SAAS,EAAE,eAAe,EAAE,CAAC;YACrD,CAAC,CAAC,YAAY,CAAC,IAAA,uCAAe,EAAC,IAAI,CAAC,GAAG,eAAe,CAAC,CAAC;KAC3D;AACH,CAAC"}

package/lib-esm/apodization/apodization.js

@@ -0,0 +1,14 @@
+import { applyWindow } from './applyWindow';
+import { compose } from './compose';
+export function apodization(data, options) {
+    const { compose: composeOptions, pointsToShift } = options;
+    const windowData = compose(composeOptions);
+    const applyWindowOptions = {
+        windowData,
+        pointsToShift,
+    };
+    const re = applyWindow(data.re, applyWindowOptions);
+    const im = applyWindow(data.im, applyWindowOptions);
+    return { re, im, windowData };
+}
+//# sourceMappingURL=apodization.js.map

package/lib-esm/apodization/apodization.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"apodization.js","sourceRoot":"","sources":["../../src/apodization/apodization.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,WAAW,EAAE,MAAM,eAAe,CAAC;AAC5C,OAAO,EAAE,OAAO,EAAgB,MAAM,WAAW,CAAC;AAiBlD,MAAM,UAAU,WAAW,CAAC,IAAc,EAAE,OAA2B;IACrE,MAAM,EAAE,OAAO,EAAE,cAAc,EAAE,aAAa,EAAE,GAAG,OAAO,CAAC;IAC3D,MAAM,UAAU,GAAG,OAAO,CAAC,cAAc,CAAC,CAAC;IAE3C,MAAM,kBAAkB,GAAG;QACzB,UAAU;QACV,aAAa;KACd,CAAC;IAEF,MAAM,EAAE,GAAG,WAAW,CAAC,IAAI,CAAC,EAAE,EAAE,kBAAkB,CAAC,CAAC;IACpD,MAAM,EAAE,GAAG,WAAW,CAAC,IAAI,CAAC,EAAE,EAAE,kBAAkB,CAAC,CAAC;IAEpD,OAAO,EAAE,EAAE,EAAE,EAAE,EAAE,UAAU,EAAE,CAAC;AAChC,CAAC"}

package/lib-esm/apodization/applyWindow.js

@@ -0,0 +1,16 @@
+/**
+ * pure function that applies a window function to the input data.
+ */
+export function applyWindow(data, options) {
+    const dataLength = data.length;
+    const { windowData, start = 0, length = dataLength, pointsToShift = 0, output = new Float64Array(data), } = options;
+    const firstEndPoint = Math.min(start + length, dataLength - pointsToShift);
+    for (let i = start, j = 0; i < firstEndPoint; i++) {
+        output[i] *= windowData[j++];
+    }
+    for (let i = dataLength - 1, j = 0; i > dataLength - pointsToShift - 1; i--) {
+        output[i] *= windowData[j++];
+    }
+    return output;
+}
+//# sourceMappingURL=applyWindow.js.map

package/lib-esm/apodization/applyWindow.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"applyWindow.js","sourceRoot":"","sources":["../../src/apodization/applyWindow.ts"],"names":[],"mappings":"AA0BA;;GAEG;AACH,MAAM,UAAU,WAAW,CAAC,IAAiB,EAAE,OAA2B;IACxE,MAAM,UAAU,GAAG,IAAI,CAAC,MAAM,CAAC;IAE/B,MAAM,EACJ,UAAU,EACV,KAAK,GAAG,CAAC,EACT,MAAM,GAAG,UAAU,EACnB,aAAa,GAAG,CAAC,EACjB,MAAM,GAAG,IAAI,YAAY,CAAC,IAAI,CAAC,GAChC,GAAG,OAAO,CAAC;IAEZ,MAAM,aAAa,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,GAAG,MAAM,EAAE,UAAU,GAAG,aAAa,CAAC,CAAC;IAC3E,KAAK,IAAI,CAAC,GAAG,KAAK,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,aAAa,EAAE,CAAC,EAAE,EAAE;QACjD,MAAM,CAAC,CAAC,CAAC,IAAI,UAAU,CAAC,CAAC,EAAE,CAAC,CAAC;KAC9B;IAED,KAAK,IAAI,CAAC,GAAG,UAAU,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,GAAG,aAAa,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE;QAC3E,MAAM,CAAC,CAAC,CAAC,IAAI,UAAU,CAAC,CAAC,EAAE,CAAC,CAAC;KAC9B;IAED,OAAO,MAAM,CAAC;AAChB,CAAC"}

package/lib-esm/apodization/compose.js

@@ -0,0 +1,21 @@
+import { applyWindow } from './applyWindow';
+import { getFunction } from './getFunction';
+import { getData } from './utils/getData';
+export function compose(shapeOptions) {
+    const { length: dataLength, shapes = [] } = shapeOptions;
+    let data = new Float64Array(dataLength).fill(1);
+    shapes.forEach((options) => {
+        const { shape, start = 0 } = options;
+        const { options: shapeOptions } = shape;
+        const length = 'length' in shapeOptions ? shapeOptions.length : dataLength - start;
+        const windowData = getData(getFunction(shape), length);
+        applyWindow(data, {
+            windowData,
+            length,
+            start,
+            output: data,
+        });
+    });
+    return data;
+}
+//# sourceMappingURL=compose.js.map

package/lib-esm/apodization/compose.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"compose.js","sourceRoot":"","sources":["../../src/apodization/compose.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,eAAe,CAAC;AAC5C,OAAO,EAAE,WAAW,EAAE,MAAM,eAAe,CAAC;AAE5C,OAAO,EAAE,OAAO,EAAE,MAAM,iBAAiB,CAAC;AAyB1C,MAAM,UAAU,OAAO,CAAC,YAA0B;IAChD,MAAM,EAAE,MAAM,EAAE,UAAU,EAAE,MAAM,GAAG,EAAE,EAAE,GAAG,YAAY,CAAC;IACzD,IAAI,IAAI,GAAG,IAAI,YAAY,CAAC,UAAU,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;IAChD,MAAM,CAAC,OAAO,CAAC,CAAC,OAAO,EAAE,EAAE;QACzB,MAAM,EAAE,KAAK,EAAE,KAAK,GAAG,CAAC,EAAE,GAAG,OAAO,CAAC;QACrC,MAAM,EAAE,OAAO,EAAE,YAAY,EAAE,GAAG,KAAK,CAAC;QACxC,MAAM,MAAM,GACV,QAAQ,IAAI,YAAY,CAAC,CAAC,CAAC,YAAY,CAAC,MAAM,CAAC,CAAC,CAAC,UAAU,GAAG,KAAK,CAAC;QAEtE,MAAM,UAAU,GAAG,OAAO,CAAC,WAAW,CAAC,KAAK,CAAC,EAAE,MAAM,CAAC,CAAC;QACvD,WAAW,CAAC,IAAI,EAAE;YAChB,UAAU;YACV,MAAM;YACN,KAAK;YACL,MAAM,EAAE,IAAI;SACb,CAAC,CAAC;IACL,CAAC,CAAC,CAAC;IACH,OAAO,IAAI,CAAC;AACd,CAAC"}

package/lib-esm/apodization/getFunction.js

@@ -0,0 +1,14 @@
+import { exponential } from './shapes/exponential';
+import { lorentzToGauss } from './shapes/lorentzToGauss';
+export function getFunction(shape) {
+    const { kind, options } = shape;
+    switch (kind) {
+        case 'exponential':
+            return exponential(options);
+        case 'lorentzToGauss':
+            return lorentzToGauss(options);
+        default:
+            throw Error(`Unknown distribution ${kind}`);
+    }
+}
+//# sourceMappingURL=getFunction.js.map

package/lib-esm/apodization/getFunction.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"getFunction.js","sourceRoot":"","sources":["../../src/apodization/getFunction.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,WAAW,EAAE,MAAM,sBAAsB,CAAC;AACnD,OAAO,EAAE,cAAc,EAAE,MAAM,yBAAyB,CAAC;AAEzD,MAAM,UAAU,WAAW,CAAC,KAAsB;IAChD,MAAM,EAAE,IAAI,EAAE,OAAO,EAAE,GAAG,KAAK,CAAC;IAChC,QAAQ,IAAI,EAAE;QACZ,KAAK,aAAa;YAChB,OAAO,WAAW,CAAC,OAAO,CAAC,CAAC;QAC9B,KAAK,gBAAgB;YACnB,OAAO,cAAc,CAAC,OAAO,CAAC,CAAC;QACjC;YACE,MAAM,KAAK,CAAC,wBAAwB,IAAc,EAAE,CAAC,CAAC;KACzD;AACH,CAAC"}

package/lib-esm/apodization/shapes/WindowFunctions.js

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=WindowFunctions.js.map

package/lib-esm/apodization/shapes/WindowFunctions.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"WindowFunctions.js","sourceRoot":"","sources":["../../../src/apodization/shapes/WindowFunctions.ts"],"names":[],"mappings":""}

package/lib-esm/apodization/shapes/exponential.js

@@ -0,0 +1,6 @@
+export function exponential(options) {
+    const { lb, dw } = options;
+    const coefExp = -lb * Math.PI * dw;
+    return (i) => Math.exp(coefExp * i);
+}
+//# sourceMappingURL=exponential.js.map

package/lib-esm/apodization/shapes/exponential.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"exponential.js","sourceRoot":"","sources":["../../../src/apodization/shapes/exponential.ts"],"names":[],"mappings":"AAWA,MAAM,UAAU,WAAW,CAAC,OAA2B;IACrD,MAAM,EAAE,EAAE,EAAE,EAAE,EAAE,GAAG,OAAO,CAAC;IAC3B,MAAM,OAAO,GAAG,CAAC,EAAE,GAAG,IAAI,CAAC,EAAE,GAAG,EAAE,CAAC;IACnC,OAAO,CAAC,CAAS,EAAE,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC,OAAO,GAAG,CAAC,CAAC,CAAC;AAC9C,CAAC"}

package/lib-esm/apodization/shapes/lorentzToGauss.js

@@ -0,0 +1,11 @@
+export function lorentzToGauss(options) {
+    const { dw, length, gaussianHz = 0, exponentialHz = 0, center = 0 } = options;
+    if (center > 1 || center < 0) {
+        throw new Error('The center of gaussian shape should be inside of the window function: 0 - 1');
+    }
+    const C5 = Math.pow(0.6 * Math.PI * gaussianHz * dw, 2);
+    const C2 = center * (length - 1);
+    const C6 = Math.PI * dw * exponentialHz;
+    return (i) => Math.exp(i * C6 - Math.pow(C2 - i, 2) * C5);
+}
+//# sourceMappingURL=lorentzToGauss.js.map

package/lib-esm/apodization/shapes/lorentzToGauss.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"lorentzToGauss.js","sourceRoot":"","sources":["../../../src/apodization/shapes/lorentzToGauss.ts"],"names":[],"mappings":"AA0BA,MAAM,UAAU,cAAc,CAAC,OAA8B;IAC3D,MAAM,EAAE,EAAE,EAAE,MAAM,EAAE,UAAU,GAAG,CAAC,EAAE,aAAa,GAAG,CAAC,EAAE,MAAM,GAAG,CAAC,EAAE,GAAG,OAAO,CAAC;IAE9E,IAAI,MAAM,GAAG,CAAC,IAAI,MAAM,GAAG,CAAC,EAAE;QAC5B,MAAM,IAAI,KAAK,CACb,6EAA6E,CAC9E,CAAC;KACH;IAED,MAAM,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,GAAG,IAAI,CAAC,EAAE,GAAG,UAAU,GAAG,EAAE,EAAE,CAAC,CAAC,CAAC;IACxD,MAAM,EAAE,GAAG,MAAM,GAAG,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;IACjC,MAAM,EAAE,GAAG,IAAI,CAAC,EAAE,GAAG,EAAE,GAAG,aAAa,CAAC;IAExC,OAAO,CAAC,CAAS,EAAE,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,GAAG,CAAC,EAAE,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC;AACpE,CAAC"}

package/lib-esm/apodization/utils/getData.js

@@ -0,0 +1,17 @@
+/**
+ * generate and scale the data of a window function
+ */
+export function getData(func, length) {
+    const data = new Float64Array(length);
+    let max = Number.MIN_SAFE_INTEGER;
+    for (let i = 0; i < length; i++) {
+        const value = func(i);
+        data[i] = value;
+        if (value > max)
+            max = value;
+    }
+    for (let i = 0; i < length; i++)
+        data[i] /= max;
+    return data;
+}
+//# sourceMappingURL=getData.js.map

package/lib-esm/apodization/utils/getData.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"getData.js","sourceRoot":"","sources":["../../../src/apodization/utils/getData.ts"],"names":[],"mappings":"AAAA;;GAEG;AACH,MAAM,UAAU,OAAO,CAAC,IAA2B,EAAE,MAAc;IACjE,MAAM,IAAI,GAAG,IAAI,YAAY,CAAC,MAAM,CAAC,CAAC;IACtC,IAAI,GAAG,GAAG,MAAM,CAAC,gBAAgB,CAAC;IAClC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE;QAC/B,MAAM,KAAK,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC;QACtB,IAAI,CAAC,CAAC,CAAC,GAAG,KAAK,CAAC;QAChB,IAAI,KAAK,GAAG,GAAG;YAAE,GAAG,GAAG,KAAK,CAAC;KAC9B;IAED,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE;QAAE,IAAI,CAAC,CAAC,CAAC,IAAI,GAAG,CAAC;IAChD,OAAO,IAAI,CAAC;AACd,CAAC"}

package/lib-esm/assignment/utils/buildAssignments.js

@@ -1,4 +1,4 @@
-import treeSet from 'ml-tree-set';
+import TreeSet from 'ml-tree-set';
 import { createMapPossibleAssignments } from './createMapPossibleAssignments';
 import { exploreTreeRec } from './exploreTreeRec';
 const comparator = (a, b) => {
@@ -10,7 +10,7 @@ export async function buildAssignments(props) {
     let date = new Date();
     let timeStart = date.getTime();
     let store = {
-        solutions: new treeSet(comparator),
+        solutions: new TreeSet(comparator),
         nSolutions: 0,
     };
     let nSources = joinedSignals.length;
@@ -37,7 +37,7 @@ export async function buildAssignments(props) {
     const diaIDPeerPossibleAssignment = Object.keys(possibleAssignmentMap);
     let partial = fillPartial(nSources);
     store = {
-        solutions: new treeSet(comparator),
+        solutions: new TreeSet(comparator),
         nSolutions: 0,
     };
     exploreTreeRec({

package/lib-esm/assignment/utils/exploreTreeRec.js

@@ -51,7 +51,7 @@ function addSolution(store, props) {
     store.nSolutions++;
     let solution = {
         assignment: JSON.parse(JSON.stringify(partial)),
-        score: score,
+        score,
     };
     if (store.nSolutions >= maxSolutions) {
         if (solution.score > store.solutions.last().score) {

package/lib-esm/assignment/utils/exploreTreeRec.js.map

@@ -1 +1 @@
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+{"version":3,"file":"exploreTreeRec.js","sourceRoot":"","sources":["../../../src/assignment/utils/exploreTreeRec.ts"],"names":[],"mappings":"AAQA,OAAO,EAAE,YAAY,EAAE,MAAM,gBAAgB,CAAC;AAgB9C,MAAM,UAAU,cAAc,CAC5B,KAA0B,EAC1B,YAAoB,EACpB,OAA6B,EAC7B,KAAuB;IAEvB,MAAM,EACJ,QAAQ,EACR,eAAe,EACf,OAAO,EACP,SAAS,EACT,YAAY,EACZ,OAAO,EACP,WAAW,EACX,eAAe,EACf,mBAAmB,EACnB,qBAAqB,EACrB,yBAAyB,EACzB,2BAA2B,GAC5B,GAAG,KAAK,CAAC;IAEV,MAAM,WAAW,GAAG,IAAI,IAAI,EAAE,CAAC;IAC/B,IAAI,WAAW,CAAC,OAAO,EAAE,GAAG,SAAS,GAAG,OAAO,EAAE;QAC/C,IAAI,KAAK,CAAC,iBAAiB,CAAC,CAAC;QAC7B,OAAO,KAAK,CAAC;KACd;IAED,MAAM,KAAK,GAAG,2BAA2B,CAAC,YAAY,CAAC,CAAC;IACxD,MAAM,mBAAmB,GAAG,qBAAqB,CAAC,KAAK,CAAC,CAAC;IACzD,KAAK,IAAI,QAAQ,IAAI,mBAAmB,EAAE;QACxC,OAAO,CAAC,YAAY,CAAC,GAAG,QAAQ,CAAC;QACjC,IAAI,KAAK,GAAG,YAAY,CAAC,OAAO,EAAE;YAChC,yBAAyB;YACzB,2BAA2B;YAC3B,mBAAmB;YACnB,eAAe;YACf,WAAW;YACX,OAAO;SACR,CAAC,CAAC;QAEH,IAAI,KAAK,KAAK,CAAC,EAAE;YACf,IAAI,QAAQ,KAAK,GAAG,EAAE;gBACpB,OAAO,CAAC,YAAY,CAAC,GAAG,IAAI,CAAC;aAC9B;YACD,SAAS;SACV;QAED,IAAI,YAAY,KAAK,QAAQ,GAAG,CAAC,IAAI,KAAK,IAAI,eAAe,EAAE;YAC7D,WAAW,CAAC,KAAK,EAAE,EAAE,WAAW,EAAE,OAAO,EAAE,KAAK,EAAE,YAAY,EAAE,CAAC,CAAC;SACnE;aAAM,IAAI,YAAY,GAAG,QAAQ,GAAG,CAAC,EAAE;YACtC,cAAc,CACZ;gBACE,QAAQ;gBACR,eAAe;gBACf,OAAO;gBACP,SAAS;gBACT,YAAY;gBACZ,OAAO;gBACP,WAAW;gBACX,eAAe;gBACf,mBAAmB;gBACnB,qBAAqB;gBACrB,yBAAyB;gBACzB,2BAA2B;aAC5B,EACD,YAAY,GAAG,CAAC,EAChB,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,CAAC,EACnC,KAAK,CACN,CAAC;SACH;KACF;AACH,CAAC;AAcD,SAAS,WAAW,CAAC,KAAuB,EAAE,KAAuB;IACnE,IAAI,EAAE,KAAK,EAAE,YAAY,EAAE,OAAO,EAAE,WAAW,EAAE,GAAG,KAAK,CAAC;IAC1D,KAAK,IAAI,uBAAuB,CAAC,OAAO,EAAE,WAAW,CAAC,CAAC;IACvD,KAAK,CAAC,UAAU,EAAE,CAAC;IACnB,IAAI,QAAQ,GAAuB;QACjC,UAAU,EAAE,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,OAAO,CAAC,CAAC;QAC/C,KAAK;KACN,CAAC;IAEF,IAAI,KAAK,CAAC,UAAU,IAAI,YAAY,EAAE;QACpC,IAAI,QAAQ,CAAC,KAAK,GAAG,KAAK,CAAC,SAAS,CAAC,IAAI,EAAE,CAAC,KAAK,EAAE;YACjD,KAAK,CAAC,SAAS,CAAC,QAAQ,EAAE,CAAC;YAC3B,KAAK,CAAC,SAAS,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC;SAC/B;KACF;SAAM;QACL,KAAK,CAAC,SAAS,CAAC,GAAG,CAAC,QAAQ,CAAC,CAAC;QAC9B,KAAK,CAAC,UAAU,EAAE,CAAC;KACpB;AACH,CAAC;AAED,SAAS,uBAAuB,CAC9B,OAA6B,EAC7B,WAAqC;IAErC,MAAM,SAAS,GAAG,MAAM,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,MAAM,CAAC;IAClD,IAAI,WAAW,GAAG,IAAI,GAAG,CAAC,OAAO,CAAC,CAAC;IACnC,IAAI,kBAAkB,GAAG,SAAS,GAAG,WAAW,CAAC,IAAI,CAAC;IACtD,OAAO,kBAAkB,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,kBAAkB,CAAC,CAAC,CAAC,CAAC,CAAC;AAC7D,CAAC"}

package/lib-esm/assignment/utils/getAssignment/buildAssignments.js

@@ -1,4 +1,4 @@
-import treeSet from 'ml-tree-set';
+import TreeSet from 'ml-tree-set';
 import { getConnectivityMatrix } from 'openchemlib-utils';
 import { predictCarbon } from '../../../prediction/predictCarbon';
 import { predictProton } from '../../../prediction/predictProton';
@@ -33,7 +33,7 @@ export async function buildAssignments(props) {
     let timeStart = date.getTime();
     let lowerBoundScore = minScore;
     let store = {
-        solutions: new treeSet(comparator),
+        solutions: new TreeSet(comparator),
         nSolutions: 0,
     };
     const pathLengthMatrix = getConnectivityMatrix(molecule, {
@@ -87,7 +87,7 @@ export async function buildAssignments(props) {
         }
         let sourceOfPartials = getSourceOfPartials(store, infoByAtomType, atomTypesToPredict);
         store = {
-            solutions: new treeSet(comparator),
+            solutions: new TreeSet(comparator),
             nSolutions: 0,
         };
         for (let partial of sourceOfPartials) {

package/lib-esm/index.js

@@ -29,4 +29,5 @@ export * from './databases/carbonImpurities';
 export * from './databases/protonImpurities';
 export * from './peaks/solventSuppression';
 export * from './ranges/markSolventSignal';
+export * from './apodization/apodization';
 //# sourceMappingURL=index.js.map

package/lib-esm/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,cAAc,oBAAoB,CAAC;AACnC,cAAc,wBAAwB,CAAC;AACvC,cAAc,8BAA8B,CAAC;AAE7C,cAAc,+BAA+B,CAAC;AAE9C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,0BAA0B,CAAC;AACzC,cAAc,0BAA0B,CAAC;AACzC,cAAc,0BAA0B,CAAC;AACzC,cAAc,yBAAyB,CAAC;AACxC,cAAc,gCAAgC,CAAC;AAE/C,cAAc,+BAA+B,CAAC;AAC9C,cAAc,gCAAgC,CAAC;AAC/C,cAAc,6BAA6B,CAAC;AAE5C,cAAc,sBAAsB,CAAC;AACrC,cAAc,qBAAqB,CAAC;AAEpC,cAAc,2BAA2B,CAAC;AAC1C,cAAc,uBAAuB,CAAC;AACtC,cAAc,wBAAwB,CAAC;AAEvC,cAAc,uBAAuB,CAAC;AACtC,cAAc,6BAA6B,CAAC;AAC5C,cAAc,0BAA0B,CAAC;AAEzC,cAAc,yBAAyB,CAAC;AACxC,cAAc,0BAA0B,CAAC;AAEzC,cAAc,2BAA2B,CAAC;AAC1C,cAAc,uBAAuB,CAAC;AAEtC,cAAc,yBAAyB,CAAC;AACxC,cAAc,8BAA8B,CAAC;AAC7C,cAAc,8BAA8B,CAAC;AAE7C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,4BAA4B,CAAC"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA,cAAc,oBAAoB,CAAC;AACnC,cAAc,wBAAwB,CAAC;AACvC,cAAc,8BAA8B,CAAC;AAE7C,cAAc,+BAA+B,CAAC;AAE9C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,0BAA0B,CAAC;AACzC,cAAc,0BAA0B,CAAC;AACzC,cAAc,0BAA0B,CAAC;AACzC,cAAc,yBAAyB,CAAC;AACxC,cAAc,gCAAgC,CAAC;AAE/C,cAAc,+BAA+B,CAAC;AAC9C,cAAc,gCAAgC,CAAC;AAC/C,cAAc,6BAA6B,CAAC;AAE5C,cAAc,sBAAsB,CAAC;AACrC,cAAc,qBAAqB,CAAC;AAEpC,cAAc,2BAA2B,CAAC;AAC1C,cAAc,uBAAuB,CAAC;AACtC,cAAc,wBAAwB,CAAC;AAEvC,cAAc,uBAAuB,CAAC;AACtC,cAAc,6BAA6B,CAAC;AAC5C,cAAc,0BAA0B,CAAC;AAEzC,cAAc,yBAAyB,CAAC;AACxC,cAAc,0BAA0B,CAAC;AAEzC,cAAc,2BAA2B,CAAC;AAC1C,cAAc,uBAAuB,CAAC;AAEtC,cAAc,yBAAyB,CAAC;AACxC,cAAc,8BAA8B,CAAC;AAC7C,cAAc,8BAA8B,CAAC;AAE7C,cAAc,4BAA4B,CAAC;AAC3C,cAAc,4BAA4B,CAAC;AAE3C,cAAc,2BAA2B,CAAC"}

package/lib-esm/peaks/peaksToRanges.js

@@ -76,7 +76,7 @@ export function peaksToRanges(data, peakList, options = {}) {
                 let peaksO = [];
                 for (let j = signal.maskPattern.length - 1; j >= 0; j--) {
                     sum += computeArea(signal.peaks[j]);
-                    if (signal.maskPattern[j] === false) {
+                    if (!signal.maskPattern[j]) {
                         let peakR = signal.peaks.splice(j, 1)[0];
                         peaksO.push({
                             x: peakR.x,

package/lib-esm/peaks/peaksToRanges.js.map

@@ -1 +1 @@
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package/lib-esm/peaks/solventSuppression.js

@@ -17,9 +17,7 @@ export function solventSuppression(peakList, solvent, options = {}) {
         solventXYPeaks.sort((a, b) => a.x - b.x);
         let upIndex = xFindClosestIndex(xValues, solventXYPeaks[solventXYPeaks.length - 1].x + solventZoneExtension);
         let lowIndex = xFindClosestIndex(xValues, solventXYPeaks[0].x - solventZoneExtension);
-        if (upIndex === lowIndex)
-            continue;
-        const nearPeaks = peaks.slice(lowIndex, upIndex + 1);
+        const nearPeaks = peaks.filter((peak, index) => index >= lowIndex && index <= upIndex);
         const amplitudeResiduals = [];
         const deltaResiduals = [];
         const positionResiduals = [];
@@ -45,9 +43,14 @@ export function solventSuppression(peakList, solvent, options = {}) {
             deltaResiduals.push(deltaResidual);
             positionResiduals.push(positionResidual);
         }
-        const maxAmplitude = xMaxValue(amplitudeResiduals);
-        const maxDelta = xMaxValue(deltaResiduals);
-        const maxPosition = xMaxValue(positionResiduals);
+        const [maxAmplitude, maxDelta, maxPosition] = [
+            amplitudeResiduals,
+            deltaResiduals,
+            positionResiduals,
+        ].map((data) => {
+            const max = xMaxValue(data);
+            return max === 0 ? 1 : max;
+        });
         let minIndex = -1;
         let minScore = Number.MAX_SAFE_INTEGER;
         let score = [];
@@ -63,7 +66,7 @@ export function solventSuppression(peakList, solvent, options = {}) {
                 minScore = value;
             }
         }
-        if (minScore < 0) {
+        if (minScore < 0 || minIndex < 0) {
             new Error('There is not a correct match with the pattern');
             return peaks;
         }

package/lib-esm/peaks/solventSuppression.js.map

@@ -1 +1 @@
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package/lib-esm/peaks/util/jAnalyzer.js

@@ -53,10 +53,8 @@ export default {
                 if (peaks.length === 1 && n === 0) {
                     validPattern = true;
                 }
-                else {
-                    if (peaks.length <= 1) {
-                        continue;
-                    }
+                else if (peaks.length <= 1) {
+                    continue;
                 }
                 // 1.3 Establish a range for the Heights Hi [peaks.intensity*0.85,peaks.intensity*1.15];
                 let ranges = getRanges(peaks);
@@ -321,7 +319,7 @@ function getRanges(peaks) {
         }
         currentIndex[i] = 0;
     }
-    return { values: ranges, currentIndex: currentIndex, active: 0 };
+    return { values: ranges, currentIndex, active: 0 };
 }
 /**
  * Performs a symmetrization of the signal by using different aproximations to the center.
@@ -438,22 +436,22 @@ function symmetrize(signalInput, maxError, iteration, key) {
                 if (Math.abs(diffL - diffR) < maxError) {
                     avg = Math.min(peaks[left].intensity, peaks[right].intensity);
                     avgWidth = Math.min(peaks[left].width, peaks[right].width);
-                    peaks[left].intensity = peaks[right].intensity = avg;
-                    peaks[left].width = peaks[right].width = avgWidth;
+                    peaks[left].intensity = avg;
+                    peaks[right].intensity = avg;
+                    peaks[left].width = avgWidth;
+                    peaks[right].width = avgWidth;
                     middle = [
                         middle[0] + (peaks[right].x + peaks[left].x) / 2,
                         middle[1] + 1,
                     ];
                 }
+                else if (Math.max(diffL, diffR) === diffR) {
+                    mask[right] = false;
+                    left--;
+                }
                 else {
-                    if (Math.max(diffL, diffR) === diffR) {
-                        mask[right] = false;
-                        left--;
-                    }
-                    else {
-                        mask[left] = false;
-                        right++;
-                    }
+                    mask[left] = false;
+                    right++;
                 }
             }
         }
@@ -497,10 +495,8 @@ function symmetrize(signalInput, maxError, iteration, key) {
         }
         symFactor /= weight;
     }
-    else {
-        if (peaks.length === 1) {
-            symFactor = 1;
-        }
+    else if (peaks.length === 1) {
+        symFactor = 1;
     }
     let newSumHeights = 0;
     for (const peak of peaks) {
@@ -511,15 +507,13 @@ function symmetrize(signalInput, maxError, iteration, key) {
     if (symFactor > 0.8 && symFactor < 0.97 && iteration < 2) {
         return symmetrize(newSignal, maxErrorIter2, 2, key);
     }
-    else {
+    else if (peaks.length > 1) {
         // Center the given pattern at cs and symmetrize x
-        if (peaks.length > 1) {
-            let dxi;
-            for (let i = Math.ceil(peaks.length / 2) - 1; i >= 0; i--) {
-                dxi = (peaks[i].x - peaks[peaks.length - 1 - i].x) / 2.0;
-                peaks[i].x = cs + dxi;
-                peaks[peaks.length - 1 - i].x = cs - dxi;
-            }
+        let dxi;
+        for (let i = Math.ceil(peaks.length / 2) - 1; i >= 0; i--) {
+            dxi = (peaks[i].x - peaks[peaks.length - 1 - i].x) / 2.0;
+            peaks[i].x = cs + dxi;
+            peaks[peaks.length - 1 - i].x = cs - dxi;
         }
     }
     newSignal.symRank = symFactor;
@@ -562,7 +556,7 @@ function normalize(signal, n) {
     let index = signal.mask2.length - 1;
     for (let i = peaks.length - 1; i >= 0; i--) {
         peaks[i].intensity *= norm;
-        while (index >= 0 && signal.mask2[index] === false) {
+        while (index >= 0 && !signal.mask2[index]) {
             index--;
         }
         if (peaks[i].intensity < 0.75) {
@@ -593,7 +587,7 @@ function chemicalShift(peaks, mask = []) {
     let area;
     if (mask.length > 0) {
         for (let i = 0; i < peaks.length; i++) {
-            if (mask[i] === true) {
+            if (mask[i]) {
                 area = getArea(peaks[i]);
                 sum += area;
                 cs += area * peaks[i].x;