nmr-processing 9.0.3 → 9.1.0

package/src/xyz/NMRSignal2D.ts

@@ -8,13 +8,13 @@ export interface Signal2DProjection {
   atoms?: number[];
   diaIDs?: string[];
 }
-export interface NMRSignal2D {
+export interface NMRSignal2D<T extends Peak2D = Peak2D> {
   x: Signal2DProjection;
   y: Signal2DProjection;
   j?: {
     pathLength?: number | FromTo;
   };
   id?: string;
-  peaks?: Peak2D[];
+  peaks?: T[];
   kind?: string;
 }

package/src/xyz/util/formatZone.ts

@@ -1,8 +1,9 @@
-import { NMRSignal2D } from '../NMRSignal2D';
-import { NMRZone } from '../NMRZone';
+import { v4 as generateID } from '@lukeed/uuid';
 
-export function formatZones(signals: NMRSignal2D[]) {
-  let zones: NMRZone[] = [];
+import { NMRSignal2DWithID, NMRZoneWithID } from '../xyzAutoZonesPicking';
+
+export function formatZones(signals: NMRSignal2DWithID[]) {
+  let zones: NMRZoneWithID[] = [];
   for (const signal of signals) {
     let minMax1 = [Number.MAX_VALUE, 0];
     let minMax2 = [Number.MAX_VALUE, 0];
@@ -21,6 +22,7 @@ export function formatZones(signals: NMRSignal2D[]) {
       }
     }
     zones.push({
+      id: generateID(),
       x: {
         from: minMax1[0],
         to: minMax1[1],

package/src/xyz/xyzAutoZonesPicking.ts

@@ -1,15 +1,19 @@
+import { v4 as generateID } from '@lukeed/uuid';
 import { Matrix } from 'ml-matrix';
 import * as convolution from 'ml-matrix-convolution';
 import * as matrixPeakFinders from 'ml-matrix-peaks-finder';
 import type { Peak2D } from 'ml-matrix-peaks-finder';
 import simpleClustering from 'ml-simple-clustering';
 
+import { addMissingIDs } from '../peaks/util/addMissingIDs';
 import { determineRealTop } from '../peaks/util/determineRealTop';
 import { getKernel } from '../peaks/util/getKernel';
 import type { GetKernelOptions } from '../peaks/util/getKernel';
 import * as PeakOptimizer from '../peaks/util/peakOptimizer';
+import { MakeMandatory } from '../utilities/MakeMandatory';
 
 import type { NMRSignal2D } from './NMRSignal2D';
+import { NMRZone } from './NMRZone';
 import { formatZones } from './util/formatZone';
 
 const smallFilter = [
@@ -88,10 +92,16 @@ export interface XYZAutoZonesPickingOptions {
   kernel?: GetKernelOptions;
 }
 
+export type NMRSignal2DWithID<T extends Peak2D = Peak2D> = MakeMandatory<
+  NMRSignal2D<T>,
+  'id'
+>;
+export type NMRZoneWithID = MakeMandatory<NMRZone, 'id'>;
+
 export function xyzAutoZonesPicking(
   spectraData: Data2D,
   options: XYZAutoZonesPickingOptions,
-) {
+): NMRZoneWithID[] {
   let {
     sizeToPad = 14,
     realTopDetection = true,
@@ -161,7 +171,7 @@ export function xyzAutoZonesPicking(
     peaksMC1 = PeakOptimizer.clean(peaksMC1, maxPercentCutOff);
   }
 
-  let signals = createSignals2D(peaksMC1, {
+  let signals = createSignals2D(addMissingIDs(peaksMC1), {
     nRows: nbSubSpectra,
     nCols: nbPoints,
     minX: spectraData.minX,
@@ -203,7 +213,11 @@ export interface CreateSignals2DOptions {
   minX: number;
   maxX: number;
 }
-const createSignals2D = (peaks: Peak2D[], options: CreateSignals2DOptions) => {
+
+function createSignals2D<T extends Peak2D>(
+  peaks: T[],
+  options: CreateSignals2DOptions,
+) {
   let {
     nCols,
     nRows,
@@ -267,10 +281,11 @@ const createSignals2D = (peaks: Peak2D[], options: CreateSignals2DOptions) => {
   }
   let clusters = simpleClustering(connectivity);
 
-  let signals: NMRSignal2D[] = [];
+  let signals: NMRSignal2DWithID<T>[] = [];
   if (clusters) {
     for (const cluster of clusters) {
       let signal: any = {
+        id: generateID(),
         x: {
           delta: 0,
           nucleus: nucleusX,
@@ -282,7 +297,7 @@ const createSignals2D = (peaks: Peak2D[], options: CreateSignals2DOptions) => {
           resolution: dy,
         },
       };
-      let peaks2D: Peak2D[] = [];
+      let peaks2D: T[] = [];
       let sumZ = 0;
 
       for (let jPeak = 0; jPeak < cluster.length; jPeak++) {
@@ -297,13 +312,13 @@ const createSignals2D = (peaks: Peak2D[], options: CreateSignals2DOptions) => {
       signal.x.delta /= sumZ;
       signal.y.delta /= sumZ;
       signal.peaks = peaks2D;
-      signals.push(signal as NMRSignal2D);
+      signals.push(signal as NMRSignal2DWithID<T>);
     }
   }
   return signals;
-};
+}
 
-const padData = (spectraData: Data2D, options: { width: number }) => {
+function padData(spectraData: Data2D, options: { width: number }) {
   let { minX, maxX, minY, maxY } = spectraData;
 
   const width = options.width;
@@ -335,4 +350,4 @@ const padData = (spectraData: Data2D, options: { width: number }) => {
     minY: minY - yOffset * yInterval,
     maxY: maxY + yOffset * yInterval,
   };
-};
+}

package/src/xyz/xyzJResAnalyzer.ts

@@ -1,6 +1,8 @@
+import { v4 as generateID } from '@lukeed/uuid';
 import type { Peak2D } from 'ml-matrix-peaks-finder';
 import simpleClustering from 'ml-simple-clustering';
 
+import { addMissingIDs } from '../peaks/util/addMissingIDs';
 import type { JAxisKeys } from '../signals/utils/jAnalyzer';
 import jAnalyzer from '../signals/utils/jAnalyzer';
 import type { MakeMandatory } from '../utilities/MakeMandatory';
@@ -8,6 +10,8 @@ import type { MakeMandatory } from '../utilities/MakeMandatory';
 import type { NMRSignal2D } from './NMRSignal2D';
 import { formatZones } from './util/formatZone';
 
+const { parse, stringify } = JSON;
+
 interface CompilePatternOptions {
   observedFrequencies?: number[] | Float64Array;
   tolerances?: number[] | Float64Array;
@@ -33,6 +37,18 @@ interface XYZJResAnalyzerOptions extends CompilePatternOptions {
   getZones?: boolean;
 }
 
+interface Peak2DInternalCompiler extends Peak2D {
+  width?: number;
+}
+type Signal2DInternalCompiler = Omit<NMRSignal2D, 'peaks'> & {
+  peaks: Peak2DInternalCompiler[];
+  integralData: { from: number; to: number };
+  nbPeaks: number;
+  multiplicity: string;
+  pattern: string;
+  observe: number;
+};
+
 type CompilePatternOptionsMandatory = MakeMandatory<
   CompilePatternOptions,
   'observedFrequencies' | 'tolerances' | 'nuclei' | 'jAnalyzer'
@@ -53,7 +69,7 @@ export function xyzJResAnalyzer(
       jAxisKey: { jAxis: 'y', intensity: 'z' },
     },
   } = options;
-  let temporalSignals = compilePattern([...signals], {
+  let temporalSignals = compilePattern(signals, {
     observedFrequencies,
     tolerances,
     nuclei,
@@ -66,6 +82,9 @@ export function xyzJResAnalyzer(
     if (Math.abs(delta - reference) > referenceMaxShiftError) continue;
     signals2D.push(tempSignal);
   }
+
+  signals2D = addMissingIDs(signals2D);
+
   return getZones ? formatZones(signals2D) : signals2D;
 }
 
@@ -89,7 +108,7 @@ function compilePattern(
   };
 
   const defaultWidth = 0.02 * observedFrequencies[0];
-  const newSignals = JSON.parse(JSON.stringify(signals));
+  const newSignals = parse(stringify(signals));
   //adapt to 1D jAnalyzer
   for (const signal of newSignals) {
     let peaks = signal.peaks;
@@ -146,22 +165,10 @@ function compilePattern(
   return signals;
 }
 
-interface Peak2DHack extends Peak2D {
-  width?: number;
-}
-type Signal2DHack = Omit<NMRSignal2D, 'peaks'> & {
-  peaks: Peak2DHack[];
-  integralData: { from: number; to: number };
-  nbPeaks: number;
-  multiplicity: string;
-  pattern: string;
-  observe: number;
-};
-
 function createSignals2D(peaksInput: Peak2D[], options: any) {
   let { observedFrequencies, tolerances, nuclei, dx, dy } = options;
 
-  const peaks: Peak2DHack[] = JSON.parse(JSON.stringify(peaksInput));
+  const peaks: Peak2DInternalCompiler[] = parse(stringify(peaksInput));
 
   let [nucleusX, nucleusY] = nuclei;
   let [toleranceX, toleranceY] = tolerances;
@@ -189,6 +196,7 @@ function createSignals2D(peaksInput: Peak2D[], options: any) {
   if (clusters) {
     for (let cluster of clusters) {
       let signal: any = {
+        id: generateID(),
         nucleusX,
         nucleusY,
         integralData: {
@@ -239,7 +247,7 @@ function createSignals2D(peaksInput: Peak2D[], options: any) {
       signal.shiftY /= sumZ;
       signal.delta1 = signal.shiftY;
       signal.peaks = peaks2D;
-      signals.push(signal as Signal2DHack);
+      signals.push(signal as Signal2DInternalCompiler);
     }
   }
   return signals;

package/lib/assignment/utils/generateID.d.ts

@@ -1 +0,0 @@
-export default function generateID(): string;

package/lib/assignment/utils/generateID.js

@@ -1,13 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-const BASE62 = '0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ';
-const LENGTH = 8;
-function generateID() {
-    let id = '';
-    for (let i = 0; i < LENGTH; i++) {
-        id += BASE62.charAt(Math.floor(Math.random() * 62));
-    }
-    return id;
-}
-exports.default = generateID;
-//# sourceMappingURL=generateID.js.map

package/lib/assignment/utils/generateID.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"generateID.js","sourceRoot":"","sources":["../../../src/assignment/utils/generateID.ts"],"names":[],"mappings":";;AAAA,MAAM,MAAM,GAAG,gEAAgE,CAAC;AAEhF,MAAM,MAAM,GAAG,CAAC,CAAC;AAEjB,SAAwB,UAAU;IAChC,IAAI,EAAE,GAAG,EAAE,CAAC;IACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE;QAC/B,EAAE,IAAI,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,EAAE,GAAG,EAAE,CAAC,CAAC,CAAC;KACrD;IACD,OAAO,EAAE,CAAC;AACZ,CAAC;AAND,6BAMC"}

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

@@ -1,10 +0,0 @@
-const BASE62 = '0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ';
-const LENGTH = 8;
-export default function generateID() {
-    let id = '';
-    for (let i = 0; i < LENGTH; i++) {
-        id += BASE62.charAt(Math.floor(Math.random() * 62));
-    }
-    return id;
-}
-//# sourceMappingURL=generateID.js.map

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

@@ -1 +0,0 @@
-{"version":3,"file":"generateID.js","sourceRoot":"","sources":["../../../src/assignment/utils/generateID.ts"],"names":[],"mappings":"AAAA,MAAM,MAAM,GAAG,gEAAgE,CAAC;AAEhF,MAAM,MAAM,GAAG,CAAC,CAAC;AAEjB,MAAM,CAAC,OAAO,UAAU,UAAU;IAChC,IAAI,EAAE,GAAG,EAAE,CAAC;IACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE;QAC/B,EAAE,IAAI,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,MAAM,EAAE,GAAG,EAAE,CAAC,CAAC,CAAC;KACrD;IACD,OAAO,EAAE,CAAC;AACZ,CAAC"}

package/src/assignment/utils/generateID.ts

@@ -1,11 +0,0 @@
-const BASE62 = '0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ';
-
-const LENGTH = 8;
-
-export default function generateID() {
-  let id = '';
-  for (let i = 0; i < LENGTH; i++) {
-    id += BASE62.charAt(Math.floor(Math.random() * 62));
-  }
-  return id;
-}