nmr-processing 8.7.1 → 8.7.2

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

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

@@ -4,7 +4,7 @@ import { xyAutoPeaksPicking } from './xyAutoPeaksPicking';
 /**
  * Detect peaks, optimize parameters and compile multiplicity if required.
  */
-export function xyAutoRangesPicking(data, options) {
+export function xyAutoRangesPicking(data, options = {}) {
     let peaks = xyAutoPeaksPicking(data, options.peakPicking);
     peaks = peaksFilterImpurities(peaks, options.impurities);
     return peaksToRanges(data, peaks, options.ranges);

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

@@ -1 +1 @@
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+{"version":3,"file":"xyAutoRangesPicking.js","sourceRoot":"","sources":["../../src/xy/xyAutoRangesPicking.ts"],"names":[],"mappings":"AAEA,OAAO,EAAE,qBAAqB,EAAE,MAAM,gCAAgC,CAAC;AAEvE,OAAO,EAAwB,aAAa,EAAE,MAAM,wBAAwB,CAAC;AAE7E,OAAO,EAAE,kBAAkB,EAAE,MAAM,sBAAsB,CAAC;AAS1D;;GAEG;AACH,MAAM,UAAU,mBAAmB,CACjC,IAAY,EACZ,UAAsC,EAAE;IAExC,IAAI,KAAK,GAAG,kBAAkB,CAAC,IAAI,EAAE,OAAO,CAAC,WAAW,CAAC,CAAC;IAC1D,KAAK,GAAG,qBAAqB,CAAC,KAAK,EAAE,OAAO,CAAC,UAAU,CAAC,CAAC;IACzD,OAAO,aAAa,CAAC,IAAI,EAAE,KAAK,EAAE,OAAO,CAAC,MAAM,CAAC,CAAC;AACpD,CAAC"}

package/lib-esm/xyz/xyzJResAnalyzer.js

@@ -1,5 +1,5 @@
 import simpleClustering from 'ml-simple-clustering';
-import jAnalyzer from '../signals/utils/jAnalyzer';
+import jAnalyzer from '../peaks/util/jAnalyzer';
 import { formatZones } from './util/formatZone';
 export function xyzJResAnalyzer(signals, options = {}) {
     let { reference = 0, getZones = false, referenceMaxShiftError = 0.08, tolerances = [10, 100], nuclei = ['1H', '1H'], observedFrequencies = [400, 400], jAnalyzer = {

package/lib-esm/xyz/xyzJResAnalyzer.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "nmr-processing",
-  "version": "8.7.1",
+  "version": "8.7.2",
   "description": "Pure functions allowing to process NMR spectra.",
   "main": "./lib/index.js",
   "module": "./lib-esm/index.js",

package/src/peaks/peakToXY.ts

@@ -1,6 +1,8 @@
-import { NMRPeak1D } from './NMRPeak1D';
-import { peaksToXY, PeaksToXYOptions } from './peaksToXY';
+import { PeakXYWidth } from 'cheminfo-types';
+import { OptionsSG1D } from 'spectrum-generator';
 
-export function peakToXY(peak: NMRPeak1D, options: PeaksToXYOptions) {
+import { peaksToXY } from './peaksToXY';
+
+export function peakToXY(peak: PeakXYWidth, options: OptionsSG1D = {}) {
   return peaksToXY([peak], options);
 }

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 {
   /**

package/src/peaks/peaksToXY.ts

@@ -1,23 +1,9 @@
+import { PeakXYWidth } from 'cheminfo-types';
 import { generateSpectrum, OptionsSG1D } from 'spectrum-generator';
 
-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 {
-  /**
-   * frequency of the spectrum
-   */
-  frequency: number;
-}
-
-export function peaksToXY(peaks: NMRPeak1D[], options: PeaksToXYOptions) {
-  const { from, to, nbPoints = 1024, shape, frequency } = options;
-
-  return generateSpectrum(convertWidthToPPM(peaks, frequency), {
+export function peaksToXY(peaks: PeakXYWidth[], options: OptionsSG1D = {}) {
+  const { from, to, nbPoints = 1024, shape } = options;
+  return generateSpectrum(peaks, {
     generator: {
       from,
       to,

package/src/{signals/utils → peaks/util}/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:

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/xy/xyAutoPeaksPicking.ts

@@ -12,7 +12,6 @@ import {
 } from 'ml-spectra-processing';
 
 import { NMRPeak1D } from '..';
-import { convertWidthToHz } from '../peaks/util/convertWidthToHz';
 
 /**
  * Implementation of the peak picking method described by Cobas in:
@@ -36,10 +35,6 @@ export interface GetPeakListOptions
    * @default false
    */
   optimize: boolean;
-  /**
-   * frequency used to convert width and fwhm to Hz
-   */
-  frequency: number;
 }
 
 export interface OptionsXYAutoPeaksPicking extends Partial<GetPeakListOptions> {
@@ -66,20 +61,15 @@ 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,
@@ -108,7 +98,6 @@ export function xyAutoPeaksPicking(
 
   let getPeakOptions: GetPeakListOptions = {
     shape,
-    frequency,
     broadWidth,
     optimize,
     factorLimits,
@@ -156,7 +145,6 @@ function getNegativePeaks(
 function getPeakList(data: DataXY, options: GetPeakListOptions) {
   const {
     shape,
-    frequency,
     broadWidth,
     optimize,
     maxCriteria,
@@ -197,7 +185,7 @@ function getPeakList(data: DataXY, options: GetPeakListOptions) {
     });
   }
 
-  return convertWidthToHz(peakList, frequency);
+  return peakList;
 }
 
 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/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 '../signals/utils/jAnalyzer';
-import jAnalyzer from '../signals/utils/jAnalyzer';
+import type { JAxisKeys } from '../peaks/util/jAnalyzer';
+import jAnalyzer from '../peaks/util/jAnalyzer';
 import type { MakeMandatory } from '../utilities/MakeMandatory';
 
 import type { NMRSignal2D } from './NMRSignal2D';

package/lib/peaks/util/convertWidth.d.ts

@@ -1,13 +0,0 @@
-import { MakeMandatory } from '../../utilities/MakeMandatory';
-import { NMRPeak1D } from '../NMRPeak1D';
-export declare type NMRPeak1DWithShape = MakeMandatory<NMRPeak1D, 'shape'>;
-export interface ConvertWidthOptions {
-    convertTo: string & {
-        _kind?: 'hz' | 'ppm';
-    };
-    frequency: number;
-}
-/**
- * convert width and fwhm to ppm
- */
-export declare function convertWidth(peaks: NMRPeak1D[], options: ConvertWidthOptions): NMRPeak1D[];

package/lib/peaks/util/convertWidth.js

@@ -1,34 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.convertWidth = void 0;
-/**
- * convert width and fwhm to ppm
- */
-function convertWidth(peaks, options) {
-    const { frequency, convertTo } = options;
-    const convert = getConverter(convertTo, frequency);
-    return peaks.map((peak) => {
-        peak.width = convert(peak.width);
-        if (hasShape(peak)) {
-            if (peak.shape.fwhm) {
-                peak.shape.fwhm = convert(peak.shape.fwhm);
-            }
-        }
-        return peak;
-    });
-}
-exports.convertWidth = convertWidth;
-function hasShape(peak) {
-    return 'shape' in peak;
-}
-function getConverter(convertTo, frequency) {
-    switch (convertTo) {
-        case 'ppm':
-            return (x) => x / frequency;
-        case 'hz':
-            return (x) => x * frequency;
-        default:
-            throw new Error(`Does not support convert to ${convertTo}`);
-    }
-}
-//# sourceMappingURL=convertWidth.js.map

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

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package/lib/peaks/util/convertWidthToHz.d.ts

@@ -1,2 +0,0 @@
-import { NMRPeak1D } from '../NMRPeak1D';
-export declare function convertWidthToHz(peaks: NMRPeak1D[], frequency: number): NMRPeak1D[];

package/lib/peaks/util/convertWidthToHz.js

@@ -1,9 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.convertWidthToHz = void 0;
-const convertWidth_1 = require("./convertWidth");
-function convertWidthToHz(peaks, frequency) {
-    return (0, convertWidth_1.convertWidth)(peaks, { frequency, convertTo: 'hz' });
-}
-exports.convertWidthToHz = convertWidthToHz;
-//# sourceMappingURL=convertWidthToHz.js.map

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

@@ -1 +0,0 @@
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package/lib/peaks/util/convertWidthToPPM.d.ts

@@ -1,2 +0,0 @@
-import { NMRPeak1D } from '../NMRPeak1D';
-export declare function convertWidthToPPM(peaks: NMRPeak1D[], frequency: number): NMRPeak1D[];

package/lib/peaks/util/convertWidthToPPM.js

@@ -1,9 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.convertWidthToPPM = void 0;
-const convertWidth_1 = require("./convertWidth");
-function convertWidthToPPM(peaks, frequency) {
-    return (0, convertWidth_1.convertWidth)(peaks, { frequency, convertTo: 'ppm' });
-}
-exports.convertWidthToPPM = convertWidthToPPM;
-//# sourceMappingURL=convertWidthToPPM.js.map

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

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package/lib/ranges/utils/joinRanges.js.map

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package/lib/signals/utils/jAnalyzer.js.map

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package/lib-esm/peaks/util/convertWidth.js

@@ -1,30 +0,0 @@
-/**
- * convert width and fwhm to ppm
- */
-export function convertWidth(peaks, options) {
-    const { frequency, convertTo } = options;
-    const convert = getConverter(convertTo, frequency);
-    return peaks.map((peak) => {
-        peak.width = convert(peak.width);
-        if (hasShape(peak)) {
-            if (peak.shape.fwhm) {
-                peak.shape.fwhm = convert(peak.shape.fwhm);
-            }
-        }
-        return peak;
-    });
-}
-function hasShape(peak) {
-    return 'shape' in peak;
-}
-function getConverter(convertTo, frequency) {
-    switch (convertTo) {
-        case 'ppm':
-            return (x) => x / frequency;
-        case 'hz':
-            return (x) => x * frequency;
-        default:
-            throw new Error(`Does not support convert to ${convertTo}`);
-    }
-}
-//# sourceMappingURL=convertWidth.js.map

package/lib-esm/peaks/util/convertWidth.js.map

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

@@ -1,5 +0,0 @@
-import { convertWidth } from './convertWidth';
-export function convertWidthToHz(peaks, frequency) {
-    return convertWidth(peaks, { frequency, convertTo: 'hz' });
-}
-//# sourceMappingURL=convertWidthToHz.js.map

package/lib-esm/peaks/util/convertWidthToHz.js.map

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package/lib-esm/peaks/util/convertWidthToPPM.js

@@ -1,5 +0,0 @@
-import { convertWidth } from './convertWidth';
-export function convertWidthToPPM(peaks, frequency) {
-    return convertWidth(peaks, { frequency, convertTo: 'ppm' });
-}
-//# sourceMappingURL=convertWidthToPPM.js.map

package/lib-esm/peaks/util/convertWidthToPPM.js.map

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package/lib-esm/ranges/utils/joinRanges.js.map

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package/src/peaks/util/convertWidth.ts

@@ -1,40 +0,0 @@
-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;
-}
-/**
- * convert width and fwhm to ppm
- */
-export function convertWidth(peaks: NMRPeak1D[], options: ConvertWidthOptions) {
-  const { frequency, convertTo } = options;
-  const convert = getConverter(convertTo, frequency);
-  return peaks.map((peak) => {
-    peak.width = convert(peak.width);
-    if (hasShape(peak)) {
-      if (peak.shape.fwhm) {
-        peak.shape.fwhm = convert(peak.shape.fwhm);
-      }
-    }
-    return peak;
-  });
-}
-
-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

@@ -1,7 +0,0 @@
-import { NMRPeak1D } from '../NMRPeak1D';
-
-import { convertWidth } from './convertWidth';
-
-export function convertWidthToHz(peaks: NMRPeak1D[], frequency: number) {
-  return convertWidth(peaks, { frequency, convertTo: 'hz' });
-}

package/src/peaks/util/convertWidthToPPM.ts

@@ -1,7 +0,0 @@
-import { NMRPeak1D } from '../NMRPeak1D';
-
-import { convertWidth } from './convertWidth';
-
-export function convertWidthToPPM(peaks: NMRPeak1D[], frequency: number) {
-  return convertWidth(peaks, { frequency, convertTo: 'ppm' });
-}