nmr-processing 9.1.0 → 9.2.0-pre.1668170175

package/src/signals/simulation/signalsToSpinSystem.ts

@@ -2,8 +2,8 @@ import { Matrix } from 'ml-matrix';
 import simpleClustering from 'ml-simple-clustering';
 
 import type { MakeMandatory } from '../../utilities/MakeMandatory';
+import type { Jcoupling } from '../Jcoupling';
 import type { NMRSignal1D } from '../NMRSignal1D';
-import type { Jcoupling } from '../jcoupling';
 import type { SpinSystem } from '../spinSystem';
 
 interface Ids {

package/src/signals/simulation/simulateXYPeaks.ts

@@ -207,7 +207,6 @@ export function simulateXYPeaks(
     }
 
     const numFreq = frequencies.length;
-
     if (numFreq > 0) {
       weight /= sumI;
       const diff = lineWidth / 64;
@@ -237,7 +236,7 @@ export function simulateXYPeaks(
     }
   }
 
-  return xyPeaks;
+  return xyPeaks.filter((peak) => peak.x < 1000);
 }
 
 function triuTimesAbs(A: SparseMatrix, val: number) {

package/src/xy/xyAutoPeaksPicking.ts

@@ -8,7 +8,9 @@ import {
   OptimizePeaksOptions,
   JoinBroadPeaksOptions,
   GSDPeakOptimizedID,
+  setShape,
 } from 'ml-gsd';
+import { Shape1D } from 'ml-peak-shape-generator';
 import {
   xyExtract,
   xNoiseSanPlot,
@@ -77,12 +79,13 @@ export interface OptionsXYAutoPeaksPicking extends Partial<GetPeakListOptions> {
   frequency: number;
 }
 
-export type NMRPeak1DWithID = MakeMandatory<NMRPeak1D, 'id'>;
+type GSDPeakShapeID = GSDPeakID & { shape: Shape1D };
+export type NMRPeak1DWithShapeID = MakeMandatory<NMRPeak1D, 'id' | 'shape'>;
 
 export function xyAutoPeaksPicking(
   data: DataXY,
   options: OptionsXYAutoPeaksPicking,
-): NMRPeak1DWithID[] {
+): NMRPeak1DWithShapeID[] {
   const {
     from,
     to,
@@ -177,8 +180,7 @@ function getPeakList(data: DataXY, options: GetPeakListOptions) {
     realTopDetection,
   } = options;
 
-  let peakList = gsd(data, {
-    shape,
+  const peaks = gsd(data, {
     sgOptions,
     maxCriteria,
     minMaxRatio,
@@ -187,6 +189,8 @@ function getPeakList(data: DataXY, options: GetPeakListOptions) {
     realTopDetection,
   });
 
+  const peakList = setShape(peaks, { output: peaks, shape });
+
   const newPeaks = broadWidth
     ? joinBroadPeaks(peakList, {
         broadRatio,
@@ -226,8 +230,8 @@ function getCutOff(data: number[] | Float64Array, options: OptionsGetCutOff) {
 }
 
 function toNMRPeak1DStructure(
-  peak: GSDPeakID | GSDPeakOptimizedID,
-): NMRPeak1DWithID {
+  peak: GSDPeakShapeID | GSDPeakOptimizedID,
+): NMRPeak1DWithShapeID {
   const { id, shape, x, y, width } = peak;
   return {
     id,

package/src/xy/xyPeaksOptimization.ts

@@ -10,6 +10,7 @@ export interface XYPeaksOptimizationOptions extends OptimizePeaksOptions {
    */
   frequency: number;
 }
+
 export function xyPeaksOptimization<T extends PeakXYWidth>(
   data: DataXY,
   peaks: T[],
@@ -18,8 +19,9 @@ export function xyPeaksOptimization<T extends PeakXYWidth>(
   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;
 }

package/lib/prediction/prediction1D.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"prediction1D.js","sourceRoot":"","sources":["../../src/prediction/prediction1D.ts"],"names":[],"mappings":""}

package/lib/signals/jcoupling.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"jcoupling.js","sourceRoot":"","sources":["../../src/signals/jcoupling.ts"],"names":[],"mappings":""}

package/lib-esm/prediction/prediction1D.js

@@ -1,2 +0,0 @@
-export {};
-//# sourceMappingURL=prediction1D.js.map

package/lib-esm/prediction/prediction1D.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"prediction1D.js","sourceRoot":"","sources":["../../src/prediction/prediction1D.ts"],"names":[],"mappings":""}

package/lib-esm/signals/jcoupling.js

@@ -1,2 +0,0 @@
-export {};
-//# sourceMappingURL=jcoupling.js.map

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

@@ -1 +0,0 @@
-{"version":3,"file":"jcoupling.js","sourceRoot":"","sources":["../../src/signals/jcoupling.ts"],"names":[],"mappings":""}