feat: update ml-peak-shape-generator (#44)

Author: jobo322

package.json

@@ -35,7 +35,8 @@
   ],
   "author": "Andres Castillo",
   "contributors": [
-    "Miguel Asencio <[email protected]> (https://github.com/maasencioh)"
+    "Miguel Asencio <[email protected]> (https://github.com/maasencioh)",
+    "Alejandro Bolaños <[email protected]> (https://github.com/jobo322)" 
   ],
   "license": "MIT",
   "bugs": {
@@ -74,7 +75,7 @@
     "xy-parser": "^3.0.0"
   },
   "dependencies": {
-    "ml-peak-shape-generator": "^0.10.2",
+    "ml-peak-shape-generator": "^0.12.0",
     "ml-savitzky-golay-generalized": "2.0.3",
     "ml-spectra-fitting": "0.9.0",
     "ml-spectra-processing": "^4.9.4"

src/__tests__/simulated.js

@@ -5,11 +5,16 @@ const { generateSpectrum } = require('spectrum-generator');
 describe('Global spectra deconvolution with simulated spectra', () => {
   it('Overlapping peaks', () => {
     const peaks = [
-      { x: -0.1, y: 0.2, width: 0.3 },
-      { x: 0.1, y: 0.2, width: 0.1 },
+      { x: -0.1, y: 0.2, width: 0.03 },
+      { x: 0.1, y: 0.2, width: 0.01 },
     ];
 
-    const data = generateSpectrum(peaks, { from: -1, to: 1, nbPoints: 101 });
+    const data = generateSpectrum(peaks, {
+      from: -1,
+      to: 1,
+      nbPoints: 1001,
+      factor: 6,
+    });
 
     let peakList = gsd(data, {
       minMaxRatio: 0,
@@ -23,18 +28,18 @@ describe('Global spectra deconvolution with simulated spectra', () => {
 
     expect(peakList[0].x).toBeCloseTo(-0.1, 2);
     expect(peakList[0].y).toBeCloseTo(0.2, 2);
-    expect(peakList[0].width).toBeCloseTo(0.3, 2);
+    expect(peakList[0].width).toBeCloseTo(0.03, 2);
     expect(peakList[1].x).toBeCloseTo(0.1, 2);
     expect(peakList[1].y).toBeCloseTo(0.2, 2);
-    expect(peakList[1].width).toBeCloseTo(0.1, 2);
+    expect(peakList[1].width).toBeCloseTo(0.01, 2);
 
     expect(optimizedPeaks[0].x).toBeCloseTo(-0.1, 2);
     expect(optimizedPeaks[0].y).toBeCloseTo(0.2, 2);
-    expect(optimizedPeaks[0].width).toBeCloseTo(0.3, 2);
+    expect(optimizedPeaks[0].width).toBeCloseTo(0.03, 2);
     expect(optimizedPeaks[0].group).toBe(0);
     expect(optimizedPeaks[1].x).toBeCloseTo(0.1, 2);
     expect(optimizedPeaks[1].y).toBeCloseTo(0.2, 2);
-    expect(optimizedPeaks[1].width).toBeCloseTo(0.1, 2);
+    expect(optimizedPeaks[1].width).toBeCloseTo(0.01, 2);
     expect(optimizedPeaks[1].group).toBe(1);
   });
 
@@ -116,9 +121,6 @@ describe('Global spectra deconvolution with simulated spectra', () => {
       nbPoints: 10001,
       shape: {
         kind: 'gaussian',
-        options: {
-          fwhm: 10000,
-        },
       },
     });
 

src/gsd.js

@@ -1,4 +1,4 @@
-import { inflectionPointsWidthToFWHM } from 'ml-peak-shape-generator';
+import { getShapeGenerator } from 'ml-peak-shape-generator';
 import SG from 'ml-savitzky-golay-generalized';
 
 /**
@@ -167,12 +167,15 @@ export function gsd(data, options = {}) {
 
     // Minimum in second derivative
     if (ddY[i] < ddY[i - 1] && ddY[i] < ddY[i + 1]) {
-      // TODO should we change this to have 3 arrays ? Huge overhead creating arrays
-      minddY.push(i); // ( [xData[i], yData[i], i] );
+      minddY.push(i);
       broadMask.push(Math.abs(ddY[i]) <= broadRatio * maxDdy);
     }
   }
 
+  let widthProcessor = shape.kind
+    ? getShapeGenerator(shape.kind, shape.options).widthToFWHM
+    : (x) => x;
+
   let signals = [];
   let lastK = -1;
   let possible, frequency, distanceJ, minDistance, gettingCloser;
@@ -206,9 +209,7 @@ export function gsd(data, options = {}) {
           index: minddY[j],
           x: frequency,
           y: (yData[minddY[j]] + yCorrection.b) / yCorrection.m,
-          width: shape.kind
-            ? inflectionPointsWidthToFWHM(width, shape.kind, shape.options)
-            : width, // widthCorrection
+          width: widthProcessor(width),
           soft: broadMask[j],
         });
 

src/post/__tests__/groupPeaks.test.js

@@ -7,7 +7,7 @@ describe('groupPeaks', () => {
       { x: 10, y: 10, width: 5 },
       { x: 30, y: 10, width: 5 },
     ]);
-    expect(result).toEqual([
+    expect(result).toStrictEqual([
       [
         { x: 5, y: 10, width: 5, group: 0 },
         { x: 10, y: 10, width: 5, group: 0 },
@@ -25,7 +25,7 @@ describe('groupPeaks', () => {
       ],
       0.1,
     );
-    expect(result).toEqual([
+    expect(result).toStrictEqual([
       [{ x: 5, y: 10, width: 5, group: 0 }],
       [{ x: 10, y: 10, width: 5, group: 1 }],
       [{ x: 30, y: 10, width: 5, group: 2 }],
@@ -41,7 +41,7 @@ describe('groupPeaks', () => {
       ],
       3,
     );
-    expect(result).toEqual([
+    expect(result).toStrictEqual([
       [
         { x: 5, y: 10, width: 5, group: 0 },
         { x: 10, y: 10, width: 5, group: 0 },
@@ -59,7 +59,7 @@ describe('groupPeaks', () => {
       ],
       5,
     );
-    expect(result).toEqual([
+    expect(result).toStrictEqual([
       [
         { x: 5, y: 10, width: 5, group: 0 },
         { x: 10, y: 10, width: 5, group: 0 },