nmr-processing 9.1.0 → 9.2.0-pre.1668170175

package/lib/signals/optimization/getInternalSignals.js

@@ -0,0 +1,150 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getInternalSignals = void 0;
+const ml_peak_shape_generator_1 = require("ml-peak-shape-generator");
+const ml_spectra_processing_1 = require("ml-spectra-processing");
+const defaultParameters_1 = require("./defaultParameters");
+const signalsToPointXY_1 = require("./signalsToPointXY");
+const properties = ['init', 'min', 'max', 'gradientDifference'];
+function getInternalSignals(data, signals, minMaxY, options) {
+    var _a, _b;
+    let index = 0;
+    let internalSignals = [];
+    const { shape: shapeAsOption = { kind: 'gaussian' }, baseline: shiftValue = minMaxY.min, lineWidth = 1, frequency, } = options;
+    const normalizedSignals = normalizeSignals({
+        signals,
+        data,
+        shiftValue,
+        frequency,
+        range: minMaxY.range,
+    });
+    for (const signal of normalizedSignals) {
+        const { shape = { ...shapeAsOption } } = signal;
+        if (!shape.fwhm) {
+            shape.fwhm = lineWidth;
+        }
+        shape.fwhm /= frequency;
+        const shapeFct = (0, ml_peak_shape_generator_1.getShape1D)(shape);
+        const parameters = [
+            'delta',
+            'intensity',
+            ...shapeFct.getParameters(),
+        ];
+        const propertiesValues = {
+            min: [],
+            max: [],
+            init: [],
+            gradientDifference: [],
+        };
+        for (const parameter of parameters) {
+            for (const property of properties) {
+                propertiesValues[property].push(getPropertyValue({
+                    signal,
+                    frequency,
+                    parameter,
+                    property,
+                    minMaxY,
+                    shapeFct,
+                }));
+            }
+        }
+        for (const jCoupling of signal.js || []) {
+            for (const property of properties) {
+                const parameter = 'coupling';
+                let generalParameterValue = (_b = (_a = options === null || options === void 0 ? void 0 : options.parameters) === null || _a === void 0 ? void 0 : _a[parameter]) === null || _b === void 0 ? void 0 : _b[property];
+                if (generalParameterValue) {
+                    if (typeof generalParameterValue === 'number') {
+                        propertiesValues[property].push(getNormalizedValue(generalParameterValue, parameter, property, minMaxY, frequency, options.baseline));
+                    }
+                    else {
+                        let value = generalParameterValue({ jCoupling });
+                        propertiesValues[property].push(getNormalizedValue(value, parameter, property, minMaxY, frequency, options.baseline));
+                    }
+                }
+                if (!defaultParameters_1.defaultParameters[parameter]) {
+                    throw new Error(`No default parameter for ${parameter}`);
+                }
+                const defaultParameterValues = defaultParameters_1.defaultParameters[parameter][property];
+                propertiesValues[property].push(defaultParameterValues({ jCoupling }));
+            }
+        }
+        const fromIndex = index;
+        const toIndex = fromIndex + parameters.length - 1;
+        const fromIndexCoupling = toIndex + 1;
+        const toIndexCoupling = fromIndexCoupling + signal.js.length - 1;
+        index += toIndexCoupling - fromIndex + 1;
+        internalSignals.push({
+            shape: shape,
+            shapeFct,
+            signal,
+            parameters,
+            propertiesValues,
+            fromIndex,
+            toIndex,
+            fromIndexCoupling,
+            toIndexCoupling,
+        });
+    }
+    return internalSignals;
+}
+exports.getInternalSignals = getInternalSignals;
+function normalizeSignals(options) {
+    const { signals, data, frequency, shiftValue, range } = options;
+    const getMaxIntensity = (signal) => {
+        const peaks = (0, signalsToPointXY_1.signalsToPointXY)([signal], { frequency, maxClusterSize: 1 });
+        const biggestPeak = peaks.reduce((biggest, peak) => (peak.y > biggest.y ? peak : biggest), peaks[0]);
+        const { y: maxIntensity } = (0, ml_spectra_processing_1.xyFindClosestPoint)(data, biggestPeak.x);
+        return maxIntensity;
+    };
+    return signals.map((signal) => {
+        const { intensity = getMaxIntensity(signal) } = signal;
+        return {
+            ...signal,
+            js: signal.js || [],
+            intensity: (intensity - shiftValue) / range,
+        };
+    });
+}
+function getPropertyValue(options) {
+    var _a, _b, _c, _d;
+    const { signal, frequency, parameter, property, minMaxY, shapeFct } = options;
+    // check if the property is specified in the signal
+    let propertyValue = (_b = (_a = signal === null || signal === void 0 ? void 0 : signal.parameters) === null || _a === void 0 ? void 0 : _a[parameter]) === null || _b === void 0 ? void 0 : _b[property];
+    if (propertyValue) {
+        return getNormalizedValue(propertyValue, parameter, property, minMaxY, frequency, options.baseline);
+    }
+    // check if there are some global option, it could be a number or a callback
+    let generalParameterValue = (_d = (_c = options === null || options === void 0 ? void 0 : options.parameters) === null || _c === void 0 ? void 0 : _c[parameter]) === null || _d === void 0 ? void 0 : _d[property];
+    if (generalParameterValue) {
+        if (typeof generalParameterValue === 'number') {
+            return getNormalizedValue(generalParameterValue, parameter, property, minMaxY, frequency, options.baseline);
+        }
+        else {
+            let value = generalParameterValue(signal);
+            return getNormalizedValue(value, parameter, property, minMaxY, frequency, options.baseline);
+        }
+    }
+    // we just need to take the default parameters
+    if (!defaultParameters_1.defaultParameters[parameter]) {
+        throw new Error(`No default parameter for ${parameter}`);
+    }
+    const defaultParameterValues = defaultParameters_1.defaultParameters[parameter][property];
+    return defaultParameterValues({ signal, shape: shapeFct });
+}
+function getNormalizedValue(value, parameter, property, minMaxY, frequency, baseline) {
+    if (parameter === 'intensity') {
+        if (property === 'gradientDifference') {
+            return value;
+        }
+        else {
+            return baseline !== undefined
+                ? (value - baseline) / minMaxY.range
+                : (value - minMaxY.min) / minMaxY.range;
+        }
+    }
+    else if (parameter === 'fwhm') {
+        return value / frequency;
+    }
+    return value;
+}
+//# sourceMappingURL=getInternalSignals.js.map

package/lib/signals/optimization/getInternalSignals.js.map

@@ -0,0 +1 @@
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package/lib/signals/optimization/getSumOfShapes.d.ts

@@ -0,0 +1,4 @@
+import { InternalSignal } from './getInternalSignals';
+import { SignalsToPointXYOptions } from './signalsToPointXY';
+export declare type SumOfShapes = (parameters: number[]) => (x: number) => number;
+export declare function getSumOfShapes(internalSignals: InternalSignal[], options: SignalsToPointXYOptions): (parameters: number[]) => (currentX: number) => number;

package/lib/signals/optimization/getSumOfShapes.js

@@ -0,0 +1,46 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getSumOfShapes = void 0;
+const signalsToPointXY_1 = require("./signalsToPointXY");
+const defaultSimulationOptions = {
+    maxClusterSize: 1,
+};
+function getSumOfShapes(internalSignals, options) {
+    const simulationOptions = { ...defaultSimulationOptions, ...options };
+    return function sumOfShapes(parameters) {
+        const peaks = [];
+        for (const internalSignal of internalSignals) {
+            const delta = parameters[internalSignal.fromIndex];
+            const intensity = parameters[internalSignal.fromIndex + 1];
+            for (let i = 2; i < internalSignal.parameters.length; i++) {
+                //@ts-expect-error Not simply to solve the issue
+                internalSignal.shapeFct[internalSignal.parameters[i]] =
+                    parameters[internalSignal.fromIndex + i];
+            }
+            const couplings = internalSignal.signal.js;
+            for (let i = 0; i < couplings.length; i++) {
+                couplings[i].coupling =
+                    parameters[internalSignal.fromIndexCoupling + i];
+            }
+            const currentPeaks = (0, signalsToPointXY_1.signalsToPointXY)([
+                {
+                    delta,
+                    js: couplings,
+                },
+            ], simulationOptions);
+            peaks.push(...currentPeaks.map((peak) => {
+                return { intensity, shape: internalSignal.shapeFct, ...peak };
+            }));
+        }
+        return (currentX) => {
+            let totalY = 0;
+            for (let peak of peaks) {
+                const { x, y, intensity, shape } = peak;
+                totalY += y * intensity * shape.fct(currentX - x);
+            }
+            return totalY;
+        };
+    };
+}
+exports.getSumOfShapes = getSumOfShapes;
+//# sourceMappingURL=getSumOfShapes.js.map

package/lib/signals/optimization/getSumOfShapes.js.map

@@ -0,0 +1 @@
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package/lib/signals/optimization/signalsToPointXY.d.ts

@@ -0,0 +1,9 @@
+import { NMRSignal1D } from '../NMRSignal1D';
+export interface SignalsToPointXYOptions {
+    frequency: number;
+    maxClusterSize?: number;
+}
+export declare function signalsToPointXY(signals: NMRSignal1D[], options: SignalsToPointXYOptions): {
+    x: number;
+    y: number;
+}[];

package/lib/signals/optimization/signalsToPointXY.js

@@ -0,0 +1,24 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.signalsToPointXY = void 0;
+const addDummySignals_1 = require("../addDummySignals");
+const signalsToSpinSystem_1 = require("../simulation/signalsToSpinSystem");
+const simulateXYPeaks_1 = require("../simulation/simulateXYPeaks");
+const splitSpinSystem_1 = require("../simulation/splitSpinSystem");
+function signalsToPointXY(signals, options) {
+    const { frequency, maxClusterSize = 1 } = options;
+    const completeSignalSet = (0, addDummySignals_1.addDummySignals)(signals);
+    const spinSystem = (0, signalsToSpinSystem_1.signalsToSpinSystem)(completeSignalSet);
+    spinSystem.clusters = (0, splitSpinSystem_1.splitSpinSystem)(spinSystem, {
+        frequency,
+        maxClusterSize,
+    });
+    const pointsXY = (0, simulateXYPeaks_1.simulateXYPeaks)(spinSystem, options).filter((point) => point.x < 1000);
+    const maxIntensity = pointsXY.reduce((max, peak) => (peak.y > max ? peak.y : max), Number.MIN_SAFE_INTEGER);
+    for (const point of pointsXY) {
+        point.y /= maxIntensity;
+    }
+    return pointsXY;
+}
+exports.signalsToPointXY = signalsToPointXY;
+//# sourceMappingURL=signalsToPointXY.js.map

package/lib/signals/optimization/signalsToPointXY.js.map

@@ -0,0 +1 @@
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package/lib/signals/optimizeSignals.d.ts

@@ -0,0 +1,40 @@
+import { DataXY } from 'cheminfo-types';
+import { Shape1D } from 'ml-peak-shape-generator';
+import { NMRPeak1D } from '../peaks/NMRPeak1D';
+import { NMRSignal1D } from './NMRSignal1D';
+import { ParametersFromOptions, Shape1DWithFWHM } from './optimization/getInternalSignals';
+import { SignalsToPointXYOptions } from './optimization/signalsToPointXY';
+declare type ParametersFromSignal = Record<string, Record<string, number>>;
+export interface Signal extends NMRSignal1D {
+    intensity?: number;
+    shape?: Shape1D;
+    parameters?: ParametersFromSignal;
+}
+export interface NMRPeak1DFull extends NMRPeak1D {
+    id: string;
+    shape: Shape1DWithFWHM;
+    width: number;
+}
+export interface OptimizeSignalsOptions {
+    /**
+     * Initial line width in Hz
+     * @default 1
+     */
+    lineWidth?: number;
+    baseline?: number;
+    shape?: Shape1D;
+    parameters?: ParametersFromOptions;
+    optimization?: any;
+    simulation: SignalsToPointXYOptions;
+}
+export declare function optimizeSignals(data: DataXY, signals: Signal[], options: OptimizeSignalsOptions): {
+    delta: number;
+    js: import("./Jcoupling").Jcoupling[];
+    shape: {
+        kind: "gaussian" | "lorentzian" | "pseudoVoigt";
+        fwhm: number;
+    };
+    intensity: number;
+    peaks: NMRPeak1DFull[];
+}[];
+export {};

package/lib/signals/optimizeSignals.js

@@ -0,0 +1,108 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.optimizeSignals = void 0;
+const uuid_1 = require("@lukeed/uuid");
+const ml_levenberg_marquardt_1 = require("ml-levenberg-marquardt");
+const ml_peak_shape_generator_1 = require("ml-peak-shape-generator");
+const ml_spectra_processing_1 = require("ml-spectra-processing");
+const directOptimization_1 = require("./optimization/directOptimization");
+const getInternalSignals_1 = require("./optimization/getInternalSignals");
+const getSumOfShapes_1 = require("./optimization/getSumOfShapes");
+const signalsToPointXY_1 = require("./optimization/signalsToPointXY");
+const defaultLMOptimizationOptions = {
+    damping: 1.5,
+    maxIterations: 100,
+    errorTolerance: 1e-8,
+};
+const defaultDirectOptimizationOptions = {
+    iterations: 25,
+};
+function optimizeSignals(data, signals, options) {
+    const { optimization = {}, simulation: simulationOptions, ...restOptions } = options;
+    let temp = (0, ml_spectra_processing_1.xMinMaxValues)(data.y);
+    const minMaxY = { ...temp, range: temp.max - temp.min };
+    const internalSignals = (0, getInternalSignals_1.getInternalSignals)(data, signals, minMaxY, {
+        frequency: simulationOptions.frequency,
+        ...restOptions,
+    });
+    const { baseline: shiftValue = minMaxY.min } = options;
+    let normalizedY = new Float64Array(data.y.length);
+    for (let i = 0; i < data.y.length; i++) {
+        normalizedY[i] = (data.y[i] - shiftValue) / minMaxY.range;
+    }
+    const nbParams = internalSignals[internalSignals.length - 1].toIndexCoupling + 1;
+    const minValues = new Float64Array(nbParams);
+    const maxValues = new Float64Array(nbParams);
+    const initialValues = new Float64Array(nbParams);
+    const gradientDifferences = new Float64Array(nbParams);
+    let index = 0;
+    for (const internalSignal of internalSignals) {
+        for (let i = 0; i < internalSignal.parameters.length; i++) {
+            minValues[index] = internalSignal.propertiesValues.min[i];
+            maxValues[index] = internalSignal.propertiesValues.max[i];
+            initialValues[index] = internalSignal.propertiesValues.init[i];
+            gradientDifferences[index++] =
+                internalSignal.propertiesValues.gradientDifference[i];
+        }
+        for (let i = internalSignal.parameters.length; i < internalSignal.parameters.length + internalSignal.signal.js.length; i++) {
+            minValues[index] = internalSignal.propertiesValues.min[i];
+            maxValues[index] = internalSignal.propertiesValues.max[i];
+            initialValues[index] = internalSignal.propertiesValues.init[i];
+            gradientDifferences[index++] =
+                internalSignal.propertiesValues.gradientDifference[i];
+        }
+    }
+    const sumOfShapes = (0, getSumOfShapes_1.getSumOfShapes)(internalSignals, simulationOptions);
+    const { kind, options: optimizationOptions } = optimization;
+    const [algorithm, defaultOptimizationOptions] = kind === 'direct'
+        ? [directOptimization_1.directOptimization, defaultDirectOptimizationOptions]
+        : [ml_levenberg_marquardt_1.levenbergMarquardt, defaultLMOptimizationOptions];
+    let fitted = algorithm({ x: data.x, y: normalizedY }, sumOfShapes, {
+        minValues,
+        maxValues,
+        initialValues,
+        gradientDifference: gradientDifferences,
+        ...defaultOptimizationOptions,
+        ...optimizationOptions,
+    });
+    const fittedValues = fitted.parameterValues;
+    const newSignals = [];
+    for (const internalSignal of internalSignals) {
+        const { fromIndexCoupling } = internalSignal;
+        const js = internalSignal.signal.js.map((jCoupling, i) => {
+            jCoupling.coupling = fittedValues[fromIndexCoupling + i];
+            return jCoupling;
+        });
+        const delta = fittedValues[internalSignal.fromIndex];
+        const pointXYs = (0, signalsToPointXY_1.signalsToPointXY)([{ delta, js }], simulationOptions);
+        const intensity = fittedValues[internalSignal.fromIndex + 1] * minMaxY.range + shiftValue;
+        const newPeaks = [];
+        for (const { x, y } of pointXYs) {
+            const peak = {
+                id: (0, uuid_1.v4)(),
+                x,
+                y: intensity * y,
+                width: 0,
+                shape: { ...internalSignal.shape },
+            };
+            for (let i = 2; i < internalSignal.parameters.length; i++) {
+                //@ts-expect-error should be fixed once
+                peak.shape[internalSignal.parameters[i]] =
+                    fittedValues[internalSignal.fromIndex + i];
+            }
+            peak.shape.fwhm *= simulationOptions.frequency;
+            peak.width = (0, ml_peak_shape_generator_1.getShape1D)(peak.shape).fwhmToWidth(peak.shape.fwhm);
+            newPeaks.push(peak);
+        }
+        newSignals.push({
+            delta,
+            js,
+            shape: { ...newPeaks[0].shape },
+            intensity,
+            peaks: newPeaks,
+        });
+    }
+    return newSignals;
+}
+exports.optimizeSignals = optimizeSignals;
+//# sourceMappingURL=optimizeSignals.js.map

package/lib/signals/optimizeSignals.js.map

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package/lib/signals/signalsJoin.d.ts

@@ -1,7 +1,7 @@
 import type { SignalJoinCouplingsOptions } from '../signal/signalJoinCouplings';
 import type { MakeMandatory } from '../utilities/MakeMandatory';
+import type { Jcoupling } from './Jcoupling';
 import type { NMRSignal1D } from './NMRSignal1D';
-import type { Jcoupling } from './jcoupling';
 export interface SignalsJoinOptions {
     /**
      * options for signalJoinCouplings

package/lib/signals/signalsToFID.d.ts

@@ -0,0 +1,13 @@
+import { NMRSignal1D } from './NMRSignal1D';
+export interface SignalsToFIDOptions {
+    lb?: number;
+    from?: number;
+    to?: number;
+    nbPoints?: number;
+    frequency?: number;
+    maxClusterSize?: number;
+}
+export declare function signalsToFID(signals: NMRSignal1D[], options: SignalsToFIDOptions): {
+    re: import("cheminfo-types").DoubleArray;
+    im: import("cheminfo-types").DoubleArray;
+};

package/lib/signals/signalsToFID.js

@@ -0,0 +1,56 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.signalsToFID = void 0;
+const ml_spectra_processing_1 = require("ml-spectra-processing");
+const apodization_1 = require("../apodization/apodization");
+const signalsToSpinSystem_1 = require("./simulation/signalsToSpinSystem");
+const simulateXYPeaks_1 = require("./simulation/simulateXYPeaks");
+const splitSpinSystem_1 = require("./simulation/splitSpinSystem");
+const twoPi = Math.PI * 2;
+function signalsToFID(signals, options) {
+    const { lb = 1, from = 0, to = 10, nbPoints = 1024, frequency = 400, maxClusterSize = 8, } = options;
+    let spinSystem = (0, signalsToSpinSystem_1.signalsToSpinSystem)(signals);
+    spinSystem.clusters = (0, splitSpinSystem_1.splitSpinSystem)(spinSystem, {
+        frequency,
+        maxClusterSize,
+    });
+    const peaks = (0, simulateXYPeaks_1.simulateXYPeaks)(spinSystem, { frequency });
+    const re = new Float64Array(nbPoints);
+    const im = new Float64Array(nbPoints);
+    const sw = Math.abs(to - from);
+    const adquisitionTime = nbPoints / (2 * sw * frequency);
+    const time = (0, ml_spectra_processing_1.xSequentialFill)({
+        size: nbPoints,
+        from: 0,
+        to: adquisitionTime,
+    });
+    for (const peak of peaks) {
+        const { x, y } = peak;
+        const cs = x * frequency * twoPi;
+        for (let i = 0; i < nbPoints; i++) {
+            re[i] += y * Math.cos(cs * time[i]);
+            im[i] += y * Math.sin(cs * time[i]);
+        }
+    }
+    const { windowData, ...result } = (0, apodization_1.apodization)({ re, im }, {
+        pointsToShift: 0,
+        compose: {
+            length: nbPoints,
+            shapes: [
+                {
+                    start: 0,
+                    shape: {
+                        kind: 'exponential',
+                        options: {
+                            dw: adquisitionTime / (nbPoints - 1),
+                            lb,
+                        },
+                    },
+                },
+            ],
+        },
+    });
+    return result;
+}
+exports.signalsToFID = signalsToFID;
+//# sourceMappingURL=signalsToFID.js.map

package/lib/signals/signalsToFID.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"signalsToFID.js","sourceRoot":"","sources":["../../src/signals/signalsToFID.ts"],"names":[],"mappings":";;;AAAA,iEAAwD;AAExD,4DAAyD;AAGzD,0EAAuE;AACvE,kEAA+D;AAC/D,kEAA+D;AAW/D,MAAM,KAAK,GAAG,IAAI,CAAC,EAAE,GAAG,CAAC,CAAC;AAE1B,SAAgB,YAAY,CAC1B,OAAsB,EACtB,OAA4B;IAE5B,MAAM,EACJ,EAAE,GAAG,CAAC,EACN,IAAI,GAAG,CAAC,EACR,EAAE,GAAG,EAAE,EACP,QAAQ,GAAG,IAAI,EACf,SAAS,GAAG,GAAG,EACf,cAAc,GAAG,CAAC,GACnB,GAAG,OAAO,CAAC;IAEZ,IAAI,UAAU,GAAG,IAAA,yCAAmB,EAAC,OAAO,CAAC,CAAC;IAE9C,UAAU,CAAC,QAAQ,GAAG,IAAA,iCAAe,EAAC,UAAU,EAAE;QAChD,SAAS;QACT,cAAc;KACf,CAAC,CAAC;IAEH,MAAM,KAAK,GAAG,IAAA,iCAAe,EAAC,UAAU,EAAE,EAAE,SAAS,EAAE,CAAC,CAAC;IACzD,MAAM,EAAE,GAAG,IAAI,YAAY,CAAC,QAAQ,CAAC,CAAC;IACtC,MAAM,EAAE,GAAG,IAAI,YAAY,CAAC,QAAQ,CAAC,CAAC;IAEtC,MAAM,EAAE,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,GAAG,IAAI,CAAC,CAAC;IAC/B,MAAM,eAAe,GAAG,QAAQ,GAAG,CAAC,CAAC,GAAG,EAAE,GAAG,SAAS,CAAC,CAAC;IACxD,MAAM,IAAI,GAAG,IAAA,uCAAe,EAAC;QAC3B,IAAI,EAAE,QAAQ;QACd,IAAI,EAAE,CAAC;QACP,EAAE,EAAE,eAAe;KACpB,CAAC,CAAC;IAEH,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE;QACxB,MAAM,EAAE,CAAC,EAAE,CAAC,EAAE,GAAG,IAAI,CAAC;QACtB,MAAM,EAAE,GAAG,CAAC,GAAG,SAAS,GAAG,KAAK,CAAC;QACjC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE;YACjC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC;YACpC,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,EAAE,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC;SACrC;KACF;IAED,MAAM,EAAE,UAAU,EAAE,GAAG,MAAM,EAAE,GAAG,IAAA,yBAAW,EAC3C,EAAE,EAAE,EAAE,EAAE,EAAE,EACV;QACE,aAAa,EAAE,CAAC;QAChB,OAAO,EAAE;YACP,MAAM,EAAE,QAAQ;YAChB,MAAM,EAAE;gBACN;oBACE,KAAK,EAAE,CAAC;oBACR,KAAK,EAAE;wBACL,IAAI,EAAE,aAAa;wBACnB,OAAO,EAAE;4BACP,EAAE,EAAE,eAAe,GAAG,CAAC,QAAQ,GAAG,CAAC,CAAC;4BACpC,EAAE;yBACH;qBACF;iBACF;aACF;SACF;KACF,CACF,CAAC;IACF,OAAO,MAAM,CAAC;AAChB,CAAC;AA/DD,oCA+DC"}

package/lib/signals/simulation/simulateXYPeaks.js

@@ -168,7 +168,7 @@ spinSystem, options = {}) {
             });
         }
     }
-    return xyPeaks;
+    return xyPeaks.filter((peak) => peak.x < 1000);
 }
 exports.simulateXYPeaks = simulateXYPeaks;
 function triuTimesAbs(A, val) {

package/lib/signals/simulation/simulateXYPeaks.js.map

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

@@ -42,5 +42,5 @@ export interface OptionsXYAutoPeaksPicking extends Partial<GetPeakListOptions> {
      */
     frequency: number;
 }
-export declare type NMRPeak1DWithID = MakeMandatory<NMRPeak1D, 'id'>;
-export declare function xyAutoPeaksPicking(data: DataXY, options: OptionsXYAutoPeaksPicking): NMRPeak1DWithID[];
+export declare type NMRPeak1DWithShapeID = MakeMandatory<NMRPeak1D, 'id' | 'shape'>;
+export declare function xyAutoPeaksPicking(data: DataXY, options: OptionsXYAutoPeaksPicking): NMRPeak1DWithShapeID[];

package/lib/xy/xyAutoPeaksPicking.js

@@ -56,8 +56,7 @@ function getNegativePeaks(data, cutOff, getPeakOptions) {
 }
 function getPeakList(data, options) {
     const { shape, frequency, broadWidth, optimize, maxCriteria, factorLimits, sgOptions, minMaxRatio, broadRatio, noiseLevel, smoothY, optimization, realTopDetection, } = options;
-    let peakList = (0, ml_gsd_1.gsd)(data, {
-        shape,
+    const peaks = (0, ml_gsd_1.gsd)(data, {
         sgOptions,
         maxCriteria,
         minMaxRatio,
@@ -65,6 +64,7 @@ function getPeakList(data, options) {
         smoothY,
         realTopDetection,
     });
+    const peakList = (0, ml_gsd_1.setShape)(peaks, { output: peaks, shape });
     const newPeaks = broadWidth
         ? (0, ml_gsd_1.joinBroadPeaks)(peakList, {
             broadRatio,

package/lib/xy/xyAutoPeaksPicking.js.map

@@ -1 +1 @@
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package/lib/xy/xyPeaksOptimization.js

@@ -8,10 +8,11 @@ function xyPeaksOptimization(data, peaks, options) {
     const { frequency } = options;
     const newPeaks = (0, convertWidthToPPM_1.convertWidthToPPM)(peaks, { frequency });
     const optimizedPeaks = (0, ml_gsd_1.optimizePeaks)(data, newPeaks, options);
-    return (0, convertWidthToHz_1.convertWidthToHz)(optimizedPeaks, {
+    const result = (0, convertWidthToHz_1.convertWidthToHz)(optimizedPeaks, {
         frequency,
         output: optimizedPeaks,
     });
+    return result;
 }
 exports.xyPeaksOptimization = xyPeaksOptimization;
 //# sourceMappingURL=xyPeaksOptimization.js.map

package/lib/xy/xyPeaksOptimization.js.map

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