nmr-processing 9.1.0 → 9.2.0-pre.1668170175

package/lib-esm/signals/optimizeSignals.js

@@ -0,0 +1,104 @@
+import { v4 } from '@lukeed/uuid';
+import { levenbergMarquardt } from 'ml-levenberg-marquardt';
+import { getShape1D } from 'ml-peak-shape-generator';
+import { xMinMaxValues } from 'ml-spectra-processing';
+import { directOptimization } from './optimization/directOptimization';
+import { getInternalSignals, } from './optimization/getInternalSignals';
+import { getSumOfShapes } from './optimization/getSumOfShapes';
+import { signalsToPointXY, } from './optimization/signalsToPointXY';
+const defaultLMOptimizationOptions = {
+    damping: 1.5,
+    maxIterations: 100,
+    errorTolerance: 1e-8,
+};
+const defaultDirectOptimizationOptions = {
+    iterations: 25,
+};
+export function optimizeSignals(data, signals, options) {
+    const { optimization = {}, simulation: simulationOptions, ...restOptions } = options;
+    let temp = xMinMaxValues(data.y);
+    const minMaxY = { ...temp, range: temp.max - temp.min };
+    const internalSignals = 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 = getSumOfShapes(internalSignals, simulationOptions);
+    const { kind, options: optimizationOptions } = optimization;
+    const [algorithm, defaultOptimizationOptions] = kind === 'direct'
+        ? [directOptimization, defaultDirectOptimizationOptions]
+        : [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 = signalsToPointXY([{ delta, js }], simulationOptions);
+        const intensity = fittedValues[internalSignal.fromIndex + 1] * minMaxY.range + shiftValue;
+        const newPeaks = [];
+        for (const { x, y } of pointXYs) {
+            const peak = {
+                id: 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 = getShape1D(peak.shape).fwhmToWidth(peak.shape.fwhm);
+            newPeaks.push(peak);
+        }
+        newSignals.push({
+            delta,
+            js,
+            shape: { ...newPeaks[0].shape },
+            intensity,
+            peaks: newPeaks,
+        });
+    }
+    return newSignals;
+}
+//# sourceMappingURL=optimizeSignals.js.map

package/lib-esm/signals/optimizeSignals.js.map

@@ -0,0 +1 @@
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package/lib-esm/signals/signalsToFID.js

@@ -0,0 +1,52 @@
+import { xSequentialFill } from 'ml-spectra-processing';
+import { apodization } from '../apodization/apodization';
+import { signalsToSpinSystem } from './simulation/signalsToSpinSystem';
+import { simulateXYPeaks } from './simulation/simulateXYPeaks';
+import { splitSpinSystem } from './simulation/splitSpinSystem';
+const twoPi = Math.PI * 2;
+export function signalsToFID(signals, options) {
+    const { lb = 1, from = 0, to = 10, nbPoints = 1024, frequency = 400, maxClusterSize = 8, } = options;
+    let spinSystem = signalsToSpinSystem(signals);
+    spinSystem.clusters = splitSpinSystem(spinSystem, {
+        frequency,
+        maxClusterSize,
+    });
+    const peaks = 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 = 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 } = apodization({ re, im }, {
+        pointsToShift: 0,
+        compose: {
+            length: nbPoints,
+            shapes: [
+                {
+                    start: 0,
+                    shape: {
+                        kind: 'exponential',
+                        options: {
+                            dw: adquisitionTime / (nbPoints - 1),
+                            lb,
+                        },
+                    },
+                },
+            ],
+        },
+    });
+    return result;
+}
+//# sourceMappingURL=signalsToFID.js.map

package/lib-esm/signals/signalsToFID.js.map

@@ -0,0 +1 @@
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package/lib-esm/signals/simulation/simulateXYPeaks.js

@@ -162,7 +162,7 @@ spinSystem, options = {}) {
             });
         }
     }
-    return xyPeaks;
+    return xyPeaks.filter((peak) => peak.x < 1000);
 }
 function triuTimesAbs(A, val) {
     A.forEachNonZero((i, j, v) => {

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

@@ -1 +1 @@
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package/lib-esm/xy/xyAutoPeaksPicking.js

@@ -1,4 +1,4 @@
-import { gsd, optimizePeaks, joinBroadPeaks, } from 'ml-gsd';
+import { gsd, optimizePeaks, joinBroadPeaks, setShape, } from 'ml-gsd';
 import { xyExtract, xNoiseSanPlot, xAbsoluteMedian, } from 'ml-spectra-processing';
 import { convertWidthToHz } from '../peaks/util/convertWidthToHz';
 export function xyAutoPeaksPicking(data, options) {
@@ -52,8 +52,7 @@ 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 = gsd(data, {
-        shape,
+    const peaks = gsd(data, {
         sgOptions,
         maxCriteria,
         minMaxRatio,
@@ -61,6 +60,7 @@ function getPeakList(data, options) {
         smoothY,
         realTopDetection,
     });
+    const peakList = setShape(peaks, { output: peaks, shape });
     const newPeaks = broadWidth
         ? joinBroadPeaks(peakList, {
             broadRatio,

package/lib-esm/xy/xyAutoPeaksPicking.js.map

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

@@ -5,9 +5,10 @@ export function xyPeaksOptimization(data, peaks, options) {
     const { frequency } = options;
     const newPeaks = convertWidthToPPM(peaks, { frequency });
     const optimizedPeaks = optimizePeaks(data, newPeaks, options);
-    return convertWidthToHz(optimizedPeaks, {
+    const result = convertWidthToHz(optimizedPeaks, {
         frequency,
         output: optimizedPeaks,
     });
+    return result;
 }
 //# sourceMappingURL=xyPeaksOptimization.js.map

package/lib-esm/xy/xyPeaksOptimization.js.map

@@ -1 +1 @@
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+{"version":3,"file":"xyPeaksOptimization.js","sourceRoot":"","sources":["../../src/xy/xyPeaksOptimization.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,aAAa,EAAwB,MAAM,QAAQ,CAAC;AAE7D,OAAO,EAAE,gBAAgB,EAAE,MAAM,gCAAgC,CAAC;AAClE,OAAO,EAAE,iBAAiB,EAAE,MAAM,iCAAiC,CAAC;AASpE,MAAM,UAAU,mBAAmB,CACjC,IAAY,EACZ,KAAU,EACV,OAAmC;IAEnC,MAAM,EAAE,SAAS,EAAE,GAAG,OAAO,CAAC;IAC9B,MAAM,QAAQ,GAAG,iBAAiB,CAAC,KAAK,EAAE,EAAE,SAAS,EAAE,CAAC,CAAC;IACzD,MAAM,cAAc,GAAG,aAAa,CAAC,IAAI,EAAE,QAAQ,EAAE,OAAO,CAAC,CAAC;IAC9D,MAAM,MAAM,GAAG,gBAAgB,CAAC,cAAc,EAAE;QAC9C,SAAS;QACT,MAAM,EAAE,cAAc;KACvB,CAAC,CAAC;IACH,OAAO,MAAM,CAAC;AAChB,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "nmr-processing",
-  "version": "9.1.0",
+  "version": "9.2.0-pre.1668170175",
   "description": "Pure functions allowing to process NMR spectra.",
   "main": "./lib/index.js",
   "module": "./lib-esm/index.js",
@@ -64,7 +64,8 @@
     "ml-array-mean": "^1.1.6",
     "ml-array-rescale": "^1.3.7",
     "ml-array-sum": "^1.1.6",
-    "ml-gsd": "^12.1.0",
+    "ml-direct": "^0.1.1",
+    "ml-gsd": "^12.1.2",
     "ml-hclust": "^3.1.0",
     "ml-levenberg-marquardt": "^4.1.0",
     "ml-matrix": "^6.10.2",

package/src/assignment/utils/getAssignment/buildAssignments.ts

@@ -337,7 +337,7 @@ function initializePartials(
 }
 
 function fillPartial(nSources: number, value: string | null = null) {
-  const partial: Array<string | null> = new Array(nSources);
+  const partial = new Array<string | null>(nSources);
   for (let i = 0; i < nSources; i++) {
     partial[i] = value;
   }

package/src/index.ts

@@ -24,6 +24,8 @@ export * from './ranges/rangesToXY';
 export * from './signals/signalsToRanges';
 export * from './signals/signalsToXY';
 export * from './signals/signals2DToZ';
+export * from './signals/optimizeSignals';
+export * from './signals/signalsToFID';
 
 export * from './utilities/resurrect';
 export * from './utilities/rangeFromSignal';
@@ -50,8 +52,8 @@ export type { NMRSignal2D, Signal2DProjection } from './xyz/NMRSignal2D';
 export type { NMRRange } from './xy/NMRRange';
 export type { NMRZone } from './xyz/NMRZone';
 export type { NMRPeak1D } from './peaks/NMRPeak1D';
-export type { Prediction1D } from './prediction/prediction1D';
-export type { Jcoupling } from './signals/jcoupling';
+export type { Prediction1D } from './prediction/Prediction1D';
+export type { Jcoupling } from './signals/Jcoupling';
 export type { DatabaseNMREntry } from './databases/DatabaseNMREntry';
 export type {
   DataBaseLevelStructure,

package/src/prediction/predictAll.ts

@@ -1,11 +1,11 @@
 import type { Molecule } from 'openchemlib';
 
+import type { Prediction1D } from './Prediction1D';
 import { predictCOSY } from './predictCOSY';
 import { predictCarbon, PredictCarbonOptions } from './predictCarbon';
 import { predictHMBC } from './predictHMBC';
 import { predictHSQC } from './predictHSQC';
 import { predictProton, PredictProtonOptions } from './predictProton';
-import type { Prediction1D } from './prediction1D';
 import { getPredictions } from './utils/getPredictions';
 import type { Predictor } from './utils/predict2D';
 

package/src/prediction/predictAllSpectra.ts

@@ -52,8 +52,8 @@ export async function predictAllSpectra(
     ...{
       proton: { from: 0, to: 14 },
       carbon: { from: 0, to: 200 },
-      nbPoints: 4098,
-      lineWidth: 0.03,
+      nbPoints: 65536,
+      lineWidth: 1,
     },
     ...(simulationOptions.oneD || {}),
   };

package/src/prediction/predictCOSY.ts

@@ -1,7 +1,7 @@
 import { Molecule } from 'openchemlib';
 
+import type { Prediction1D } from './Prediction1D';
 import { predictProton, PredictProtonOptions } from './predictProton';
-import type { Prediction1D } from './prediction1D';
 import { predict2D, Predictor } from './utils/predict2D';
 
 export interface PredictCOSYOptions {

package/src/prediction/predictCarbon.ts

@@ -7,8 +7,8 @@ import type { NMRSignal1D } from '../signals/NMRSignal1D';
 import { signalsToRanges } from '../signals/signalsToRanges';
 import type { MakeMandatory } from '../utilities/MakeMandatory';
 
+import type { Prediction1D } from './Prediction1D';
 import type { DataBaseStructure } from './dataStructure';
-import type { Prediction1D } from './prediction1D';
 import { fetchPrediction } from './utils/fetchPrediction';
 import { flatGroupedDiaIDs } from './utils/flatGroupedDiaIDs';
 import { getFilteredIDiaIDs } from './utils/getFilteredIDiaIDs';

package/src/prediction/predictHMBC.ts

@@ -1,10 +1,10 @@
 import { Molecule } from 'openchemlib';
 
+import type { Prediction1D } from './Prediction1D';
 import { predictCarbon } from './predictCarbon';
 import type { PredictCarbonOptions } from './predictCarbon';
 import { predictProton } from './predictProton';
 import type { PredictProtonOptions } from './predictProton';
-import type { Prediction1D } from './prediction1D';
 import { predict2D } from './utils/predict2D';
 import type { Predictor } from './utils/predict2D';
 

package/src/prediction/predictHSQC.ts

@@ -1,8 +1,8 @@
 import { Molecule } from 'openchemlib';
 
+import type { Prediction1D } from './Prediction1D';
 import { predictCarbon, PredictCarbonOptions } from './predictCarbon';
 import { predictProton, PredictProtonOptions } from './predictProton';
-import type { Prediction1D } from './prediction1D';
 import { predict2D, Predictor } from './utils/predict2D';
 
 export interface PredictHSQCOptions {

package/src/prediction/predictProton.ts

@@ -12,7 +12,7 @@ import type { NMRSignal1D } from '../signals/NMRSignal1D';
 import { signalsJoin } from '../signals/signalsJoin';
 import { signalsToRanges } from '../signals/signalsToRanges';
 
-import type { Prediction1D } from './prediction1D';
+import type { Prediction1D } from './Prediction1D';
 
 /**
  * Makes a prediction using proton.

package/src/prediction/utils/fetchPrediction.ts

@@ -1,7 +1,7 @@
 import { fetch } from 'cross-fetch';
 import { Molecule } from 'openchemlib';
 
-import type { Prediction1D } from '../prediction1D';
+import type { Prediction1D } from '../Prediction1D';
 
 interface FetchPredictionOptions {
   webserviceURL: string;

package/src/prediction/utils/getPredictions.ts

@@ -1,6 +1,6 @@
 import type { Molecule } from 'openchemlib';
 
-import type { Prediction1D } from '../prediction1D';
+import type { Prediction1D } from '../Prediction1D';
 
 import type { Predictions, PredictOptions, Predictors } from './predict2D';
 

package/src/prediction/utils/predict2D.ts

@@ -12,16 +12,16 @@ import type {
   PathInfo,
 } from 'openchemlib-utils';
 
+import { setIDs } from '../../peaks/util/setIDs';
 import type { NMRSignal1D } from '../../signals/NMRSignal1D';
 import type { MakeMandatory } from '../../utilities/MakeMandatory';
 import type { NMRSignal2D } from '../../xyz/NMRSignal2D';
+import type { Prediction1D } from '../Prediction1D';
 import type { PredictCarbon, PredictCarbonOptions } from '../predictCarbon';
 import type { PredictProton, PredictProtonOptions } from '../predictProton';
-import type { Prediction1D } from '../prediction1D';
 
 import { getNuclei } from './getNuclei';
 import { getPredictions } from './getPredictions';
-import { setIDs } from '../../peaks/util/setIDs';
 
 /**
  * Generate the correlation bidimensional nmr peaks based on the number of bonds between a pair of atoms

package/src/signal/signalJoinCouplings.ts

@@ -1,7 +1,7 @@
 import sum from 'ml-array-sum';
 
+import type { Jcoupling } from '../signals/Jcoupling';
 import type { NMRSignal1D } from '../signals/NMRSignal1D';
-import type { Jcoupling } from '../signals/jcoupling';
 import type { MakeMandatory } from '../utilities/MakeMandatory';
 import { joinPatterns } from '../utilities/joinPatterns';
 

package/src/signals/NMRSignal1D.ts

@@ -1,6 +1,6 @@
 import type { NMRPeak1D } from '../peaks/NMRPeak1D';
 
-import type { Jcoupling } from './jcoupling';
+import type { Jcoupling } from './Jcoupling';
 
 export interface NMRSignal1D {
   delta: number;

package/src/signals/addDummySignals.ts

@@ -1,18 +1,28 @@
 import { couplingPatterns } from '../constants/couplingPatterns';
 
+import type { Jcoupling } from './Jcoupling';
 import { NMRSignal1D } from './NMRSignal1D';
-import type { Jcoupling } from './jcoupling';
 
 export function addDummySignals(signals: NMRSignal1D[]) {
   let newSignals: NMRSignal1D[] = JSON.parse(JSON.stringify(signals));
 
+  let nextAtomToAssign =
+    signals.reduce((nextAtomToAssign, signal) => {
+      const { atoms = [] } = signal;
+      return Math.max(...atoms) > nextAtomToAssign
+        ? Math.max(...atoms)
+        : nextAtomToAssign;
+    }, 0) + 1;
   signals.forEach((signal, s) => {
-    const { js: jCouplings = [], atoms: signalAssignment = [s] } = signal;
-
+    const {
+      js: jCouplings = [],
+      atoms: signalAssignment = [nextAtomToAssign++],
+    } = signal;
     let { newCouplings, tempSignals } = checkCouplings(
       jCouplings,
       newSignals,
       signalAssignment,
+      nextAtomToAssign + signals.length,
     );
 
     if (tempSignals.length > 0) newSignals.push(...tempSignals);
@@ -28,8 +38,8 @@ function checkCouplings(
   jCouplings: Jcoupling[],
   signals: NMRSignal1D[],
   signalAssignment: number[],
+  nextAtomToAssign: number,
 ) {
-  let newSignalAssignment = signals.length - 1;
   let tempSignals: NMRSignal1D[] = [];
   const newCouplings = jCouplings.reduce<Jcoupling[]>(
     (newCouplings, jCoupling) => {
@@ -39,13 +49,13 @@ function checkCouplings(
           let tempCouplings: Jcoupling[] = [];
           const nbLinks = couplingPatterns.indexOf(multiplicity);
           for (let i = 0; i < nbLinks; i++) {
-            newSignalAssignment++;
+            nextAtomToAssign++;
             tempCouplings.push({
               coupling,
-              atoms: [newSignalAssignment],
+              atoms: [nextAtomToAssign],
             });
             tempSignals.push(
-              formatSignal(coupling, [newSignalAssignment], signalAssignment),
+              formatSignal(coupling, [nextAtomToAssign], signalAssignment),
             );
           }
         } else {

package/src/signals/optimization/defaultParameters.ts

@@ -0,0 +1,45 @@
+import { PseudoVoigtShape1D, Shape1D } from 'ml-peak-shape-generator';
+
+import { Jcoupling } from '../Jcoupling';
+import { Signal } from '../optimizeSignals';
+
+type Shape1DWithFWHM = Omit<Shape1D, 'fwhm'> & { fwhm: number };
+
+export const defaultParameters: Record<
+  string,
+  Record<string, (...args: any) => number>
+> = {
+  delta: {
+    init: (data: { signal: Signal }) => data.signal.delta,
+    min: (data: { signal: Signal; shape: Shape1DWithFWHM }) =>
+      data.signal.delta - data.shape.fwhm * 2,
+    max: (data: { signal: Signal; shape: Shape1DWithFWHM }) =>
+      data.signal.delta + data.shape.fwhm * 2,
+    gradientDifference: () => 2e-3,
+  },
+  intensity: {
+    init: (data: { signal: Signal }) => data.signal.intensity || 1,
+    min: () => 0,
+    max: () => 1.5,
+    gradientDifference: () => 1e-3,
+  },
+  fwhm: {
+    init: (data: { shape: Shape1DWithFWHM }) => data.shape.fwhm,
+    min: (data: { shape: Shape1DWithFWHM }) => data.shape.fwhm * 0.25,
+    max: (data: { shape: Shape1DWithFWHM }) => data.shape.fwhm * 4,
+    gradientDifference: (data: { shape: Shape1DWithFWHM }) =>
+      data.shape.fwhm * 2e-3,
+  },
+  mu: {
+    init: (data: { shape: PseudoVoigtShape1D }) => data.shape.mu || 0.5,
+    min: () => 0,
+    max: () => 1,
+    gradientDifference: () => 0.01,
+  },
+  coupling: {
+    init: (data: { jCoupling: Jcoupling }) => data.jCoupling.coupling,
+    min: (data: { jCoupling: Jcoupling }) => data.jCoupling.coupling * 0.8,
+    max: (data: { jCoupling: Jcoupling }) => data.jCoupling.coupling * 1.2,
+    gradientDifference: () => 0.01,
+  },
+};