nmr-processing 6.0.8 → 7.1.0

package/src/xy/xyAutoPeaksPicking.ts

@@ -1,7 +1,6 @@
 import { DataXY } from 'cheminfo-types';
-import { gsd, joinBroadPeaks, optimizePeaks } from 'ml-gsd';
+import { gsd, optimizePeaks, joinBroadPeaks, appendShapeAndFWHM } from 'ml-gsd';
 import type {
-  Peak1D,
   GSDOptions,
   OptimizePeaksOptions,
   JoinBroadPeaksOptions,
@@ -12,6 +11,8 @@ import {
   xAbsoluteMedian,
 } from 'ml-spectra-processing';
 
+import { NMRPeak1D } from '..';
+
 /**
  * Implementation of the peak picking method described by Cobas in:
  * A new approach to improving automated analysis of proton NMR spectra
@@ -25,7 +26,7 @@ interface OptionsGetCutOff {
   thresholdFactor: number;
 }
 
-export interface IGetPeakListOptions
+export interface GetPeakListOptions
   extends GSDOptions,
     OptimizePeaksOptions,
     JoinBroadPeaksOptions {
@@ -35,9 +36,7 @@ export interface IGetPeakListOptions
    */
   optimize: boolean;
 }
-
-export interface OptionsXYAutoPeaksPicking
-  extends Partial<IGetPeakListOptions> {
+export interface OptionsXYAutoPeaksPicking extends Partial<GetPeakListOptions> {
   /**
    * Low limit value in the x axis to extract a sub set of points from the input data.
    */
@@ -66,7 +65,7 @@ export interface OptionsXYAutoPeaksPicking
 export function xyAutoPeaksPicking(
   data: DataXY,
   options: OptionsXYAutoPeaksPicking = {},
-): Peak1D[] {
+): NMRPeak1D[] {
   const {
     from,
     to,
@@ -77,28 +76,31 @@ export function xyAutoPeaksPicking(
     useSanPlot = false,
     smoothY = true,
     optimize = false,
-    factorWidth = 4,
+    factorLimits = 4,
     realTopDetection = true,
     shape = { kind: 'gaussian' },
     optimization = { kind: 'lm' },
     broadWidth = 0.25,
+    sgOptions = {},
     lookNegative = false,
-    sgOptions = { windowSize: 9, polynomial: 3 },
   } = options;
 
+  const { windowSize = 9, polynomial = 3 } = sgOptions;
+
   if (from !== undefined && to !== undefined) {
     data = xyExtract(data, { zones: [{ from, to }] });
   }
-  if (data.x.length < sgOptions.windowSize) return [];
+  if (data.x.length < windowSize) return [];
 
   const cutOff = getCutOff(data.y, { noiseLevel, useSanPlot, thresholdFactor });
 
-  let getPeakOptions: IGetPeakListOptions = {
+  let getPeakOptions: GetPeakListOptions = {
     shape,
     broadWidth,
     optimize,
-    factorWidth,
-    sgOptions,
+    factorLimits,
+    maxCriteria: true,
+    sgOptions: { windowSize, polynomial },
     minMaxRatio,
     broadRatio,
     noiseLevel: cutOff.positive,
@@ -111,17 +113,19 @@ export function xyAutoPeaksPicking(
 
   if (lookNegative) {
     getPeakOptions.noiseLevel = cutOff.negative;
-    peaks.push(...getNegativePeaks(data, getPeakOptions));
+    getPeakOptions.maxCriteria = false;
+    peaks.push(...getPeakList(data, getPeakOptions));
   }
   return peaks;
 }
 
-function getPeakList(data: DataXY, options: IGetPeakListOptions) {
+function getPeakList(data: DataXY, options: GetPeakListOptions) {
   const {
     shape,
     broadWidth,
     optimize,
-    factorWidth,
+    maxCriteria,
+    factorLimits,
     sgOptions,
     minMaxRatio,
     broadRatio,
@@ -132,8 +136,8 @@ function getPeakList(data: DataXY, options: IGetPeakListOptions) {
   } = options;
 
   let peakList = gsd(data, {
-    shape,
     sgOptions,
+    maxCriteria,
     minMaxRatio,
     noiseLevel,
     smoothY,
@@ -141,7 +145,7 @@ function getPeakList(data: DataXY, options: IGetPeakListOptions) {
   });
 
   if (broadWidth) {
-    peakList = joinBroadPeaks(data, peakList, {
+    peakList = joinBroadPeaks(peakList, {
       broadRatio,
       broadWidth,
       shape,
@@ -150,29 +154,14 @@ function getPeakList(data: DataXY, options: IGetPeakListOptions) {
   }
 
   if (optimize) {
-    peakList = optimizePeaks(data, peakList, {
+    return optimizePeaks(data, peakList, {
       shape,
-      factorWidth,
+      factorLimits,
       optimization,
     });
   }
 
-  return peakList;
-}
-
-function getNegativePeaks(data: DataXY, options: IGetPeakListOptions) {
-  let { x, y } = data;
-  let negativeDataY = new Float64Array(data.y.length);
-  for (let i = 0; i < negativeDataY.length; i++) {
-    negativeDataY[i] = -1 * y[i];
-  }
-
-  let peakList = getPeakList({ x, y: negativeDataY }, options);
-
-  for (const peak of peakList) {
-    peak.y *= -1;
-  }
-  return peakList;
+  return appendShapeAndFWHM(peakList, { shape });
 }
 
 function getCutOff(data: number[] | Float64Array, options: OptionsGetCutOff) {