nmr-processing 7.4.3 → 8.2.0

package/src/xyz/util/formatZone.ts

@@ -0,0 +1,36 @@
+import { NMRSignal2D } from '../NMRSignal2D';
+import { NMRZone } from '../NMRZone';
+
+export function formatZones(signals: NMRSignal2D[]) {
+  let zones: NMRZone[] = [];
+  for (const signal of signals) {
+    let minMax1 = [Number.MAX_VALUE, 0];
+    let minMax2 = [Number.MAX_VALUE, 0];
+    for (const peak of signal.peaks || []) {
+      if (peak.minX < minMax1[0]) {
+        minMax1[0] = peak.minX;
+      }
+      if (peak.maxX > minMax1[1]) {
+        minMax1[1] = peak.maxX;
+      }
+      if (peak.minY < minMax2[0]) {
+        minMax2[0] = peak.minY;
+      }
+      if (peak.maxY > minMax2[1]) {
+        minMax2[1] = peak.maxY;
+      }
+    }
+    zones.push({
+      x: {
+        from: minMax1[0],
+        to: minMax1[1],
+      },
+      y: {
+        from: minMax2[0],
+        to: minMax2[1],
+      },
+      signals: [signal],
+    });
+  }
+  return zones;
+}

package/src/xyz/xyzAutoZonesPicking.ts

@@ -4,13 +4,13 @@ import * as matrixPeakFinders from 'ml-matrix-peaks-finder';
 import type { Peak2D } from 'ml-matrix-peaks-finder';
 import simpleClustering from 'ml-simple-clustering';
 
-import { NMRZone } from '..';
 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 type { NMRSignal2D } from './NMRSignal2D';
+import { formatZones } from './util/formatZone';
 
 const smallFilter = [
   [0, 0, 1, 2, 2, 2, 1, 0, 0],
@@ -183,40 +183,6 @@ export function xyzAutoZonesPicking(
   return formatZones(signals);
 }
 
-function formatZones(signals: NMRSignal2D[]) {
-  let zones: NMRZone[] = [];
-  for (const signal of signals) {
-    let minMax1 = [Number.MAX_VALUE, 0];
-    let minMax2 = [Number.MAX_VALUE, 0];
-    for (const peak of signal.peaks || []) {
-      if (peak.minX < minMax1[0]) {
-        minMax1[0] = peak.minX;
-      }
-      if (peak.maxX > minMax1[1]) {
-        minMax1[1] = peak.maxX;
-      }
-      if (peak.minY < minMax2[0]) {
-        minMax2[0] = peak.minY;
-      }
-      if (peak.maxY > minMax2[1]) {
-        minMax2[1] = peak.maxY;
-      }
-    }
-    zones.push({
-      x: {
-        from: minMax1[0],
-        to: minMax1[1],
-      },
-      y: {
-        from: minMax2[0],
-        to: minMax2[1],
-      },
-      signals: [signal],
-    });
-  }
-  return zones;
-}
-
 /**
  * This function converts a set of 2D-peaks in 2D-signals. Each signal could be composed
  * of many 2D-peaks, and it has some additional information related to the NMR spectrum.

package/src/xyz/xyzJResAnalyzer.ts

@@ -6,6 +6,7 @@ import jAnalyzer from '../peaks/util/jAnalyzer';
 import type { MakeMandatory } from '../utilities/MakeMandatory';
 
 import type { NMRSignal2D } from './NMRSignal2D';
+import { formatZones } from './util/formatZone';
 
 interface CompilePatternOptions {
   observedFrequencies?: number[] | Float64Array;
@@ -25,6 +26,11 @@ interface XYZJResAnalyzerOptions extends CompilePatternOptions {
    * @default 0
    */
   reference?: number;
+  /**
+   * if it is true returns zones instead of signals 2D
+   * @default false
+   */
+  getZones?: boolean;
 }
 
 type CompilePatternOptionsMandatory = MakeMandatory<
@@ -38,6 +44,7 @@ export function xyzJResAnalyzer(
 ) {
   let {
     reference = 0,
+    getZones = false,
     referenceMaxShiftError = 0.08,
     tolerances = [10, 100],
     nuclei = ['1H', '1H'],
@@ -46,20 +53,20 @@ export function xyzJResAnalyzer(
       jAxisKey: { jAxis: 'y', intensity: 'z' },
     },
   } = options;
-  let temporalSignals = compilePattern(signals, {
+  let temporalSignals = compilePattern([...signals], {
     observedFrequencies,
     tolerances,
     nuclei,
     jAnalyzer,
   });
   //check if the signal are symmetric around the reference
-  let result = [];
+  let signals2D = [];
   for (const tempSignal of temporalSignals) {
     let delta = tempSignal.y.delta;
     if (Math.abs(delta - reference) > referenceMaxShiftError) continue;
-    result.push(tempSignal);
+    signals2D.push(tempSignal);
   }
-  return result;
+  return getZones ? formatZones(signals2D) : signals2D;
 }
 
 function compilePattern(
@@ -122,10 +129,10 @@ function compilePattern(
       }
       if (peaksO.length > 0) {
         peaksO.reverse();
-        let ranges = createSignals2D(peaksO, signalOptions);
+        let signals2D = createSignals2D(peaksO, signalOptions);
 
-        for (const range of ranges) {
-          newSignals.push(range);
+        for (const signal of signals2D) {
+          newSignals.push(signal);
         }
       }
     }

package/lib/constants/gyromagneticRatio.d.ts

@@ -1,6 +0,0 @@
-export declare type Nuclei = '1H' | '2H' | '3H' | '3He' | '7Li' | '13C' | '14N' | '15N' | '17O' | '19F' | '23Na' | '27Al' | '29Si' | '31P' | '57Fe' | '63Cu' | '67Zn' | '129Xe';
-declare type GyromagneticRatio = {
-    [key in Nuclei]: number;
-};
-export declare const gyromagneticRatio: GyromagneticRatio;
-export {};

package/lib/constants/gyromagneticRatio.js

@@ -1,26 +0,0 @@
-"use strict";
-// sources:
-// https://en.wikipedia.org/wiki/Gyromagnetic_ratio
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.gyromagneticRatio = void 0;
-exports.gyromagneticRatio = {
-    '1H': 267.52218744e6,
-    '2H': 41.065e6,
-    '3H': 285.3508e6,
-    '3He': -203.789e6,
-    '7Li': 103.962e6,
-    '13C': 67.28284e6,
-    '14N': 19.331e6,
-    '15N': -27.116e6,
-    '17O': -36.264e6,
-    '19F': 251.662e6,
-    '23Na': 70.761e6,
-    '27Al': 69.763e6,
-    '29Si': -53.19e6,
-    '31P': 108.291e6,
-    '57Fe': 8.681e6,
-    '63Cu': 71.118e6,
-    '67Zn': 16.767e6,
-    '129Xe': -73.997e6,
-};
-//# sourceMappingURL=gyromagneticRatio.js.map

package/lib/constants/gyromagneticRatio.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"gyromagneticRatio.js","sourceRoot":"","sources":["../../src/constants/gyromagneticRatio.ts"],"names":[],"mappings":";AAAA,WAAW;AACX,mDAAmD;;;AA4BtC,QAAA,iBAAiB,GAAsB;IAClD,IAAI,EAAE,cAAc;IACpB,IAAI,EAAE,QAAQ;IACd,IAAI,EAAE,UAAU;IAChB,KAAK,EAAE,CAAC,SAAS;IACjB,KAAK,EAAE,SAAS;IAChB,KAAK,EAAE,UAAU;IACjB,KAAK,EAAE,QAAQ;IACf,KAAK,EAAE,CAAC,QAAQ;IAChB,KAAK,EAAE,CAAC,QAAQ;IAChB,KAAK,EAAE,SAAS;IAChB,MAAM,EAAE,QAAQ;IAChB,MAAM,EAAE,QAAQ;IAChB,MAAM,EAAE,CAAC,OAAO;IAChB,KAAK,EAAE,SAAS;IAChB,MAAM,EAAE,OAAO;IACf,MAAM,EAAE,QAAQ;IAChB,MAAM,EAAE,QAAQ;IAChB,OAAO,EAAE,CAAC,QAAQ;CACnB,CAAC"}

package/lib-esm/constants/gyromagneticRatio.js

@@ -1,23 +0,0 @@
-// sources:
-// https://en.wikipedia.org/wiki/Gyromagnetic_ratio
-export const gyromagneticRatio = {
-    '1H': 267.52218744e6,
-    '2H': 41.065e6,
-    '3H': 285.3508e6,
-    '3He': -203.789e6,
-    '7Li': 103.962e6,
-    '13C': 67.28284e6,
-    '14N': 19.331e6,
-    '15N': -27.116e6,
-    '17O': -36.264e6,
-    '19F': 251.662e6,
-    '23Na': 70.761e6,
-    '27Al': 69.763e6,
-    '29Si': -53.19e6,
-    '31P': 108.291e6,
-    '57Fe': 8.681e6,
-    '63Cu': 71.118e6,
-    '67Zn': 16.767e6,
-    '129Xe': -73.997e6,
-};
-//# sourceMappingURL=gyromagneticRatio.js.map

package/lib-esm/constants/gyromagneticRatio.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"gyromagneticRatio.js","sourceRoot":"","sources":["../../src/constants/gyromagneticRatio.ts"],"names":[],"mappings":"AAAA,WAAW;AACX,mDAAmD;AA4BnD,MAAM,CAAC,MAAM,iBAAiB,GAAsB;IAClD,IAAI,EAAE,cAAc;IACpB,IAAI,EAAE,QAAQ;IACd,IAAI,EAAE,UAAU;IAChB,KAAK,EAAE,CAAC,SAAS;IACjB,KAAK,EAAE,SAAS;IAChB,KAAK,EAAE,UAAU;IACjB,KAAK,EAAE,QAAQ;IACf,KAAK,EAAE,CAAC,QAAQ;IAChB,KAAK,EAAE,CAAC,QAAQ;IAChB,KAAK,EAAE,SAAS;IAChB,MAAM,EAAE,QAAQ;IAChB,MAAM,EAAE,QAAQ;IAChB,MAAM,EAAE,CAAC,OAAO;IAChB,KAAK,EAAE,SAAS;IAChB,MAAM,EAAE,OAAO;IACf,MAAM,EAAE,QAAQ;IAChB,MAAM,EAAE,QAAQ;IAChB,OAAO,EAAE,CAAC,QAAQ;CACnB,CAAC"}

package/src/constants/gyromagneticRatio.ts

@@ -1,49 +0,0 @@
-// sources:
-// https://en.wikipedia.org/wiki/Gyromagnetic_ratio
-
-// TODO: #13 can we have a better source and more digits ? @jwist
-
-export type Nuclei =
-  | '1H'
-  | '2H'
-  | '3H'
-  | '3He'
-  | '7Li'
-  | '13C'
-  | '14N'
-  | '15N'
-  | '17O'
-  | '19F'
-  | '23Na'
-  | '27Al'
-  | '29Si'
-  | '31P'
-  | '57Fe'
-  | '63Cu'
-  | '67Zn'
-  | '129Xe';
-
-type GyromagneticRatio = {
-  [key in Nuclei]: number;
-};
-
-export const gyromagneticRatio: GyromagneticRatio = {
-  '1H': 267.52218744e6,
-  '2H': 41.065e6,
-  '3H': 285.3508e6,
-  '3He': -203.789e6,
-  '7Li': 103.962e6,
-  '13C': 67.28284e6,
-  '14N': 19.331e6,
-  '15N': -27.116e6,
-  '17O': -36.264e6,
-  '19F': 251.662e6,
-  '23Na': 70.761e6,
-  '27Al': 69.763e6,
-  '29Si': -53.19e6,
-  '31P': 108.291e6,
-  '57Fe': 8.681e6,
-  '63Cu': 71.118e6,
-  '67Zn': 16.767e6,
-  '129Xe': -73.997e6,
-};