nmr-processing 8.7.2 → 9.0.2

package/src/peaks/peaksToRanges.ts

@@ -1,14 +1,14 @@
 import type { DataXY } from 'cheminfo-types';
 import { xyIntegration } from 'ml-spectra-processing';
 
+import { joinRanges } from '../ranges/utils/joinRanges';
 import type { NMRSignal1D } from '../signals/NMRSignal1D';
+import jAnalyzer from '../signals/utils/jAnalyzer';
+import type { SignalIntern, Peak1DIntern } from '../signals/utils/jAnalyzer';
 import type { MakeMandatory } from '../utilities/MakeMandatory';
 import type { NMRRange } from '../xy/NMRRange';
 
 import type { NMRPeak1D } from './NMRPeak1D';
-import jAnalyzer from './util/jAnalyzer';
-import type { SignalIntern, Peak1DIntern } from './util/jAnalyzer';
-import { joinRanges } from './util/joinRanges';
 
 export interface OptionsPeaksToRanges {
   /**
@@ -93,13 +93,13 @@ const assignSignal = (
     delta: NaN,
     nbPeaks: 1,
     kind: 'signal',
-    startX: peak.x - peak.width,
-    stopX: peak.x + peak.width,
+    startX: peak.x - peak.width / frequency,
+    stopX: peak.x + peak.width / frequency,
     observe: frequency,
     nucleus,
     integralData: {
-      from: peak.x - peak.width * 3,
-      to: peak.x + peak.width * 3,
+      from: peak.x - (peak.width * 3) / frequency,
+      to: peak.x + (peak.width * 3) / frequency,
       value: 0,
     },
     peaks: [
@@ -148,7 +148,6 @@ export function peaksToRanges(
   }
 
   let signals = detectSignals(data, peakList, signalOptions);
-
   if (clean) {
     for (let i = 0; i < signals.length; i++) {
       if (Math.abs(signals[i].integralData.value) < clean) {
@@ -173,7 +172,7 @@ export function peaksToRanges(
         sum = 0;
         let peaksO = [];
         for (let j = signal.maskPattern.length - 1; j >= 0; j--) {
-          sum += computeArea(signal.peaks[j]);
+          sum += computeArea(signal.peaks[j], frequency);
           if (!signal.maskPattern[j]) {
             let peakR = signal.peaks.splice(j, 1)[0];
             peaksO.push({
@@ -185,7 +184,7 @@ export function peaksToRanges(
             signal.mask2.splice(j, 1);
             signal.maskPattern.splice(j, 1);
             signal.nbPeaks--;
-            nHi += computeArea(peakR);
+            nHi += computeArea(peakR, frequency);
           }
         }
         if (peaksO.length > 0) {
@@ -229,7 +228,6 @@ export function peaksToRanges(
       }
     }
   }
-
   let ranges: NMRRange[] = [];
   for (let i = 0; i < signals.length; i++) {
     let signal = signals[i];
@@ -306,7 +304,7 @@ export function detectSignals(
       if (peak.kind) signal1D.kind = peak.kind;
       signals.push(signal1D);
     } else {
-      let tmp = peak.x + peak.width;
+      let tmp = peak.x + peak.width / frequency;
       signal1D.stopX = Math.max(signal1D.stopX, tmp);
       signal1D.startX = Math.min(signal1D.startX, tmp);
       signal1D.nbPeaks++;
@@ -317,11 +315,11 @@ export function detectSignals(
       });
       signal1D.integralData.from = Math.min(
         signal1D.integralData.from,
-        peak.x - peak.width * 3,
+        peak.x - (peak.width * 3) / frequency,
       );
       signal1D.integralData.to = Math.max(
         signal1D.integralData.to,
-        peak.x + peak.width * 3,
+        peak.x + (peak.width * 3) / frequency,
       );
       if (peak.kind) signal1D.kind = peak.kind;
     }
@@ -334,7 +332,7 @@ export function detectSignals(
     let integralPeaks = 0;
 
     for (const peak of peaks) {
-      let area = computeArea(peak);
+      let area = computeArea(peak, frequency);
       chemicalShift += peak.x * area;
       integralPeaks += area;
     }
@@ -364,10 +362,8 @@ export function detectSignals(
 
 /**
  * Return the area of a Lorentzian function
- * @param {object} peak - object with peak information
- * @return {Number}
  * @private
  */
-function computeArea(peak: Peak1DIntern) {
-  return Math.abs(peak.intensity * peak.width * 1.57); // todo add an option with this value: 1.772453851
+function computeArea(peak: Peak1DIntern, frequency: number) {
+  return Math.abs(((peak.intensity * peak.width) / frequency) * 1.57); // todo add an option with this value: 1.772453851
 }

package/src/peaks/peaksToXY.ts

@@ -1,14 +1,61 @@
-import { PeakXYWidth } from 'cheminfo-types';
 import { generateSpectrum, OptionsSG1D } from 'spectrum-generator';
 
-export function peaksToXY(peaks: PeakXYWidth[], options: OptionsSG1D = {}) {
-  const { from, to, nbPoints = 1024, shape } = options;
-  return generateSpectrum(peaks, {
+import { NMRPeak1D } from './NMRPeak1D';
+import { convertWidthToPPM } from './util/convertWidthToPPM';
+
+/**
+ * Convert an array of peaks assuming that width/fwhm is in Hz
+ */
+
+export interface PeaksToXYOptions extends OptionsSG1D {
+  /**
+   * First x value (inclusive).
+   * @default `firstPeak.x + firstPeak.width * 3`
+   */
+  from?: number;
+  /**
+   * Last x value (inclusive).
+   * @default `lastPeak.x + lastPeak.width * 3`
+   */
+  to?: number;
+  /**
+   * frequency of the spectrum
+   */
+  frequency: number;
+}
+
+export function peaksToXY(peaks: NMRPeak1D[], options: PeaksToXYOptions) {
+  const { frequency, nbPoints = 1024, shape } = options;
+  const newPeaks = convertWidthToPPM(peaks, { frequency });
+
+  return generateSpectrum(newPeaks, {
     generator: {
-      from,
-      to,
+      ...getFromTo(newPeaks, options),
       nbPoints,
       shape,
     },
   });
 }
+
+function getFromTo(newPeaks: NMRPeak1D[], options: PeaksToXYOptions) {
+  if ('to' in options && 'from' in options) {
+    return {
+      from: options.from,
+      to: options.to,
+    };
+  }
+
+  newPeaks.sort((a, b) => a.x - b.x);
+  const firstPeak = newPeaks[0];
+  const lastPeak = newPeaks[newPeaks.length - 1];
+
+  const {
+    from = firstPeak.x - firstPeak.width * 2,
+    to = lastPeak.x + lastPeak.width * 2,
+  } = options;
+
+  return {
+    from,
+    to,
+  };
+}

package/src/peaks/util/convertWidth.ts

@@ -0,0 +1,47 @@
+import { MakeMandatory } from '../../utilities/MakeMandatory';
+import { NMRPeak1D } from '../NMRPeak1D';
+
+export type NMRPeak1DWithShape = MakeMandatory<NMRPeak1D, 'shape'>;
+
+export interface ConvertWidthOptions {
+  convertTo: string & { _kind?: 'hz' | 'ppm' };
+  frequency: number;
+  output?: NMRPeak1D[];
+}
+/**
+ * convert width and fwhm to ppm
+ */
+export function convertWidth(peaks: NMRPeak1D[], options: ConvertWidthOptions) {
+  const {
+    frequency,
+    convertTo,
+    output = JSON.parse(JSON.stringify(peaks)),
+  } = options;
+
+  const convert = getConverter(convertTo, frequency);
+
+  for (const peak of output) {
+    peak.width = convert(peak.width);
+    if (hasShape(peak)) {
+      if (peak.shape.fwhm) {
+        peak.shape.fwhm = convert(peak.shape.fwhm);
+      }
+    }
+  }
+  return output;
+}
+
+function hasShape(peak: NMRPeak1D): peak is NMRPeak1DWithShape {
+  return 'shape' in peak;
+}
+
+function getConverter(convertTo: string, frequency: number) {
+  switch (convertTo) {
+    case 'ppm':
+      return (x: number) => x / frequency;
+    case 'hz':
+      return (x: number) => x * frequency;
+    default:
+      throw new Error(`Does not support convert to ${convertTo}`);
+  }
+}

package/src/peaks/util/convertWidthToHz.ts

@@ -0,0 +1,9 @@
+import { NMRPeak1D } from '../NMRPeak1D';
+
+import { convertWidth, ConvertWidthOptions } from './convertWidth';
+
+export type ConvertWidthTo = Omit<ConvertWidthOptions, 'convertTo'>;
+
+export function convertWidthToHz(peaks: NMRPeak1D[], options: ConvertWidthTo) {
+  return convertWidth(peaks, { ...options, convertTo: 'hz' });
+}

package/src/peaks/util/convertWidthToPPM.ts

@@ -0,0 +1,8 @@
+import { NMRPeak1D } from '../NMRPeak1D';
+
+import { convertWidth } from './convertWidth';
+import { ConvertWidthTo } from './convertWidthToHz';
+
+export function convertWidthToPPM(peaks: NMRPeak1D[], options: ConvertWidthTo) {
+  return convertWidth(peaks, { ...options, convertTo: 'ppm' });
+}

package/src/ranges/markSolventSignal.ts

@@ -4,8 +4,8 @@ import { addIDs } from '../assignment/utils/getAssignment/checkIDs';
 import { NMRPeak1D } from '../peaks/NMRPeak1D';
 import { detectSignals } from '../peaks/peaksToRanges';
 import { solventSuppression } from '../peaks/solventSuppression';
-import { SignalIntern } from '../peaks/util/jAnalyzer';
 import { NMRSignal1D } from '../signals/NMRSignal1D';
+import { SignalIntern } from '../signals/utils/jAnalyzer';
 import { NMRRange } from '../xy/NMRRange';
 
 interface NMRPeak1DWithSignalID extends NMRPeak1D {

package/src/{peaks/util → signals/utils}/jAnalyzer.ts

@@ -1,5 +1,5 @@
+import type { NMRPeak1D } from '../../peaks/NMRPeak1D';
 import type { MakeMandatory } from '../../utilities/MakeMandatory';
-import type { NMRPeak1D } from '../NMRPeak1D';
 
 /*
  * This library implements the J analyser described by Cobas et al in the paper:
@@ -210,6 +210,7 @@ export default {
     // Before to return, change the units of peaksComp from Hz to PPM again
     for (let peakComp of signal.peaksComp) {
       peakComp.x /= signal.observe;
+      peakComp.width *= signal.observe;
     }
     return signal;
   },
@@ -471,7 +472,7 @@ function symmetrize(
     peaks[i] = {
       x: peak[jAxis] * newSignal.observe,
       intensity: peak[intensity],
-      width: peak.width,
+      width: peak.width / newSignal.observe,
     };
   }
   // Join the peaks that are closer than 0.25 Hz

package/src/xy/xyAutoPeaksPicking.ts

@@ -12,6 +12,7 @@ import {
 } from 'ml-spectra-processing';
 
 import { NMRPeak1D } from '..';
+import { convertWidthToHz } from '../peaks/util/convertWidthToHz';
 
 /**
  * Implementation of the peak picking method described by Cobas in:
@@ -35,6 +36,10 @@ export interface GetPeakListOptions
    * @default false
    */
   optimize: boolean;
+  /**
+   * frequency used to convert width and fwhm to Hz
+   */
+  frequency: number;
 }
 
 export interface OptionsXYAutoPeaksPicking extends Partial<GetPeakListOptions> {
@@ -61,15 +66,20 @@ export interface OptionsXYAutoPeaksPicking extends Partial<GetPeakListOptions> {
    * @default false
    */
   useSanPlot?: boolean;
+  /**
+   * frequency used to convert width and fwhm to Hz
+   */
+  frequency: number;
 }
 
 export function xyAutoPeaksPicking(
   data: DataXY,
-  options: OptionsXYAutoPeaksPicking = {},
+  options: OptionsXYAutoPeaksPicking,
 ): NMRPeak1D[] {
   const {
     from,
     to,
+    frequency,
     noiseLevel,
     thresholdFactor = 3,
     minMaxRatio = 0.05,
@@ -98,6 +108,7 @@ export function xyAutoPeaksPicking(
 
   let getPeakOptions: GetPeakListOptions = {
     shape,
+    frequency,
     broadWidth,
     optimize,
     factorLimits,
@@ -145,6 +156,7 @@ function getNegativePeaks(
 function getPeakList(data: DataXY, options: GetPeakListOptions) {
   const {
     shape,
+    frequency,
     broadWidth,
     optimize,
     maxCriteria,
@@ -177,15 +189,16 @@ function getPeakList(data: DataXY, options: GetPeakListOptions) {
     });
   }
 
-  if (optimize) {
-    return optimizePeaks(data, peakList, {
-      shape,
-      factorLimits,
-      optimization,
-    });
-  }
-
-  return peakList;
+  return convertWidthToHz(
+    optimize
+      ? optimizePeaks(data, peakList, {
+          shape,
+          factorLimits,
+          optimization,
+        })
+      : peakList,
+    { frequency },
+  );
 }
 
 function getCutOff(data: number[] | Float64Array, options: OptionsGetCutOff) {

package/src/xy/xyAutoRangesPicking.ts

@@ -8,7 +8,7 @@ import { xyAutoPeaksPicking } from './xyAutoPeaksPicking';
 import type { OptionsXYAutoPeaksPicking } from './xyAutoPeaksPicking';
 
 interface OptionsXYAutoRangesPicking {
-  peakPicking?: OptionsXYAutoPeaksPicking;
+  peakPicking: OptionsXYAutoPeaksPicking;
   impurities?: OptionsPeaksFilterImpurities;
   ranges?: OptionsPeaksToRanges;
 }
@@ -18,7 +18,7 @@ interface OptionsXYAutoRangesPicking {
  */
 export function xyAutoRangesPicking(
   data: DataXY,
-  options: OptionsXYAutoRangesPicking = {},
+  options: OptionsXYAutoRangesPicking,
 ) {
   let peaks = xyAutoPeaksPicking(data, options.peakPicking);
   peaks = peaksFilterImpurities(peaks, options.impurities);

package/src/xy/xyPeaksOptimization.ts

@@ -1,10 +1,25 @@
 import { DataXY, PeakXYWidth } from 'cheminfo-types';
 import { optimizePeaks, OptimizePeaksOptions } from 'ml-gsd';
 
+import { convertWidthToHz } from '../peaks/util/convertWidthToHz';
+import { convertWidthToPPM } from '../peaks/util/convertWidthToPPM';
+
+export interface XYPeaksOptimizationOptions extends OptimizePeaksOptions {
+  /**
+   * frequency to convert width and fwhm to ppm.
+   */
+  frequency: number;
+}
 export function xyPeaksOptimization(
   data: DataXY,
   peaks: PeakXYWidth[],
-  options: OptimizePeaksOptions,
+  options: XYPeaksOptimizationOptions,
 ) {
-  return optimizePeaks(data, peaks, options);
+  const { frequency } = options;
+  const newPeaks = convertWidthToPPM(peaks, { frequency });
+  const optimizedPeaks = optimizePeaks(data, newPeaks, options);
+  return convertWidthToHz(optimizedPeaks, {
+    frequency,
+    output: optimizedPeaks,
+  });
 }

package/src/xyz/xyzJResAnalyzer.ts

@@ -1,8 +1,8 @@
 import type { Peak2D } from 'ml-matrix-peaks-finder';
 import simpleClustering from 'ml-simple-clustering';
 
-import type { JAxisKeys } from '../peaks/util/jAnalyzer';
-import jAnalyzer from '../peaks/util/jAnalyzer';
+import type { JAxisKeys } from '../signals/utils/jAnalyzer';
+import jAnalyzer from '../signals/utils/jAnalyzer';
 import type { MakeMandatory } from '../utilities/MakeMandatory';
 
 import type { NMRSignal2D } from './NMRSignal2D';
@@ -88,6 +88,7 @@ function compilePattern(
     dy: signals[0].y.resolution,
   };
 
+  const defaultWidth = 0.02 * observedFrequencies[0];
   const newSignals = JSON.parse(JSON.stringify(signals));
   //adapt to 1D jAnalyzer
   for (const signal of newSignals) {
@@ -102,7 +103,7 @@ function compilePattern(
       to: Number.MIN_SAFE_INTEGER,
     };
     for (const peak of peaks) {
-      if (!peak.width) peak.width = 0.02;
+      if (!peak.width) peak.width = defaultWidth;
     }
     peaks.sort((a: Peak2D, b: Peak2D) => a.y - b.y);
   }

package/lib/peaks/util/jAnalyzer.js.map

@@ -1 +0,0 @@
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package/lib/peaks/util/joinRanges.js.map

@@ -1 +0,0 @@
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package/lib-esm/peaks/util/jAnalyzer.js.map

@@ -1 +0,0 @@
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package/lib-esm/peaks/util/joinRanges.js.map

@@ -1 +0,0 @@
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