feat!: change peak shape structure (#68)

* feat!: change peak shape structure

* use Peak1D interface and Shape1D in the peak structure

* remove properties from output soft, noiseLevel, fromTo

* check the peak list to homogenize fwhm n width in optimizePeaks

* generate the soft mask in joinBroadPeaks

* change input of joinBroadPeaks

* use types from cheminfo-types

* update ml-peak-shape-generator to 3.0.1

* fix: avoid unnecessary assertion

* fix: update ml-peak-shape-generator to 3.0.2

Author: jobo322

examples/example.ts

@@ -9,8 +9,7 @@ import { writeFileSync } from 'fs';
 import { join } from 'path';
 
 import { generateSpectrum } from 'spectrum-generator';
-
-import { DataType, gsd, optimizePeaks } from '../src';
+import { gsd, optimizePeaks } from '../src';
 
 const peaks = [
   { x: -0.1, y: 0.2, width: 0.3 },
@@ -31,7 +30,7 @@ let peakList = gsd(original, {
   realTopDetection: false,
   smoothY: false,
   heightFactor: 1,
-  shape: { kind: 'gaussian', width: 0 },
+  shape: { kind: 'gaussian' },
 });
 
 let optimizedPeaks = optimizePeaks(original, peakList);

package.json

@@ -63,6 +63,7 @@
     "cheminfo-build": "^1.1.11",
     "eslint": "^8.1.0",
     "eslint-config-cheminfo-typescript": "^10.2.2",
+    "eslint-plugin-jest": "^25.2.4",
     "esm": "^3.2.25",
     "jest": "^27.3.1",
     "jest-matcher-deep-close-to": "^3.0.2",
@@ -71,16 +72,16 @@
     "nodemon": "^2.0.14",
     "prettier": "^2.4.1",
     "rimraf": "^3.0.2",
-    "spectrum-generator": "^5.4.1",
+    "spectrum-generator": "^6.0.0",
     "ts-jest": "^27.0.7",
     "typescript": "^4.4.4",
     "xy-parser": "^3.2.0"
   },
   "dependencies": {
-    "cheminfo-types": "^0.7.0",
-    "ml-peak-shape-generator": "^2.0.2",
+    "cheminfo-types": "^0.8.0",
+    "ml-peak-shape-generator": "^3.0.2",
     "ml-savitzky-golay-generalized": "2.0.3",
-    "ml-spectra-fitting": "^2.0.0",
+    "ml-spectra-fitting": "^3.0.0",
     "ml-spectra-processing": "^6.8.0"
   }
 }

src/__tests__/bigLowS2NSpectrum.test.ts

@@ -1,7 +1,3 @@
-/**
- * Created by acastillo on 2/2/16.
- */
-
 import { readFileSync } from 'fs';
 import { join } from 'path';
 
@@ -18,11 +14,14 @@ describe('Global spectra deconvolution NMR spectra', () => {
       {
         noiseLevel: 57000.21889405926, // 1049200.537996172/2,
         minMaxRatio: 0.01,
-        broadRatio: 0.0025,
         sgOptions: { windowSize: 13, polynomial: 3 },
       },
     );
-    pp = joinBroadPeaks(pp, { width: 0.25 });
+
+    pp = joinBroadPeaks({ x: spectrum[0], y: spectrum[1] }, pp, {
+      broadRatio: 0.0025,
+      sgOptions: { windowSize: 13, polynomial: 3 },
+    });
 
     expect(pp).toHaveLength(91);
   });

src/__tests__/broadNMR.test.ts

@@ -14,21 +14,30 @@ describe('Global spectra deconvolution NMR spectra', () => {
       {
         noiseLevel: 1049200.537996172 / 2,
         minMaxRatio: 0.01,
+        sgOptions: {
+          windowSize: 9,
+          polynomial: 3,
+        },
+      },
+    );
+
+    const newResult = joinBroadPeaks(
+      { x: spectrum[0], y: spectrum[1] },
+      result,
+      {
+        width: 0.25,
         broadRatio: 0.0025,
+        shape: { kind: 'lorentzian' },
         sgOptions: {
           windowSize: 9,
           polynomial: 3,
         },
       },
     );
-    const newResult = joinBroadPeaks(result, {
-      width: 0.25,
-      shape: { kind: 'lorentzian', width: 0 },
-    });
     expect(newResult).toHaveLength(14);
     newResult.forEach((peak) => {
       if (Math.abs(peak.x - 4.31) < 0.01) {
-        expect(peak.shape.width).toBeCloseTo(0.39, 2);
+        expect(peak.width).toBeCloseTo(0.39, 2);
       }
     });
   });

src/__tests__/infraRed.test.ts

@@ -1,11 +1,13 @@
 import { readFileSync } from 'fs';
 
-import { DataType, gsd } from '../gsd';
+import type { DataXY } from 'cheminfo-types';
+
+import { gsd } from '../gsd';
 
 describe('Global spectra deconvolution Infrared spectra', () => {
   // Test case obtained from Pag 443, Chap 8.
   it('Should get the correct result', () => {
-    let spectrum: DataType = JSON.parse(
+    let spectrum: DataXY = JSON.parse(
       readFileSync(`${__dirname}/data/infraRed.json`, 'utf-8'),
     );
     gsd(spectrum, {

src/__tests__/massPeakPicking.test.ts

@@ -1,14 +1,16 @@
 import CC from 'chemcalc';
+import type { DataXY } from 'cheminfo-types';
+import { Gaussian } from 'ml-peak-shape-generator';
 import Stat from 'ml-stat';
 
-import { DataType, gsd, optimizePeaks } from '..';
+import { gsd, optimizePeaks } from '..';
 
 let spectrum = CC.analyseMF('Cl2.Br2', {
   isotopomers: 'arrayXXYY',
   fwhm: 0.01,
   gaussianWidth: 11,
 });
-let xy: DataType = spectrum.arrayXXYY;
+let xy: DataXY = spectrum.arrayXXYY;
 let x: number[] = xy[0];
 let y: number[] = xy[1];
 let max = Stat.array.max(y);
@@ -30,7 +32,6 @@ describe('Check the peak picking of a simulated mass spectrum', () => {
       {
         noiseLevel: noiseLevel,
         minMaxRatio: 0,
-        broadRatio: 0,
         smoothY: false,
         realTopDetection: true,
       },
@@ -39,31 +40,31 @@ describe('Check the peak picking of a simulated mass spectrum', () => {
       factorWidth: 4,
       shape: {
         kind: 'gaussian',
-        width: 0,
       },
     });
     expect(result[0].x).toBeCloseTo(69.938, 1);
     expect(result[0].y).toBeCloseTo(max, 2);
-    expect(result[0].shape.width).toBeCloseTo(0.01, 4);
+    expect(result[0].fwhm).toBeCloseTo(0.01, 4);
+    expect(result[0].width).toBeCloseTo(Gaussian.fwhmToWidth(0.01), 4);
 
     expect(result[1].x).toBeCloseTo(71.935, 2);
     expect(result[1].y).toBeCloseTo((63.99155 * max) / 100, 3);
-    expect(result[1].shape.width).toBeCloseTo(0.01, 4);
+    expect(result[1].fwhm).toBeCloseTo(0.01, 4);
 
     expect(result[2].x).toBeCloseTo(73.932, 1);
     expect(result[2].y).toBeCloseTo((10.2373 * max) / 100, 2);
-    expect(result[2].shape.width).toBeCloseTo(0.01, 4);
+    expect(result[2].fwhm).toBeCloseTo(0.01, 4);
 
     expect(result[3].x).toBeCloseTo(157.837, 1);
     expect(result[3].y).toBeCloseTo((51.39931 * max) / 100, 2);
-    expect(result[3].shape.width).toBeCloseTo(0.01, 4);
+    expect(result[3].fwhm).toBeCloseTo(0.01, 4);
 
     expect(result[4].x).toBeCloseTo(159.835, 1);
     expect(result[4].y).toBeCloseTo(max, 2);
-    expect(result[4].shape.width).toBeCloseTo(0.01, 4);
+    expect(result[4].fwhm).toBeCloseTo(0.01, 4);
 
     expect(result[5].x).toBeCloseTo(161.833, 1);
     expect(result[5].y).toBeCloseTo((48.63878 * max) / 100, 2);
-    expect(result[5].shape.width).toBeCloseTo(0.01, 4);
+    expect(result[5].fwhm).toBeCloseTo(0.01, 4);
   });
 });

src/__tests__/simple.test.ts

@@ -26,7 +26,7 @@ describe('Simple test cases', () => {
     negY.push(0);
   }
 
-  let widthToFWHM = getShape1D('gaussian').widthToFWHM;
+  let widthToFWHM = getShape1D({ kind: 'gaussian' }).widthToFWHM;
 
   it('gsd not realtop', () => {
     let peaks = gsd(
@@ -42,7 +42,6 @@ describe('Simple test cases', () => {
     );
 
     expect(peaks[0].y).toBeCloseTo(4.657, 3);
-    expect(peaks[0].shape.noiseLevel).toBeCloseTo(1.1956, 3);
     expect(peaks[0].x).toBeCloseTo(15, 2);
   });
 
@@ -60,7 +59,6 @@ describe('Simple test cases', () => {
       },
     );
     expect(peaks[0].y).toBeCloseTo(-4.657, 3);
-    expect(peaks[0].shape.noiseLevel).toBeCloseTo(1.1956, 3);
     expect(peaks[0].x).toBeCloseTo(15, 2);
   });
 
@@ -82,13 +80,11 @@ describe('Simple test cases', () => {
     expect(peaks).toMatchCloseTo(
       [
         {
-          shape: {
-            noiseLevel: 1.2434539324230613,
-            soft: false,
-            width: widthToFWHM(3),
-          },
+          width: 3,
+          fwhm: widthToFWHM(3),
           x: 15,
           y: 5,
+          shape: { kind: 'gaussian' },
         },
       ],
       2,
@@ -112,13 +108,11 @@ describe('Simple test cases', () => {
     expect(peaks).toMatchCloseTo(
       [
         {
-          shape: {
-            noiseLevel: 1.2434539324230613,
-            soft: false,
-            width: widthToFWHM(3),
-          },
+          width: 3,
+          fwhm: widthToFWHM(3),
           x: 14.5,
           y: 4.006546067576939,
+          shape: { kind: 'gaussian' },
         },
       ],
       2,

src/__tests__/simpleShifted.test.ts

@@ -38,16 +38,14 @@ describe('Simple shifted baseline test cases', () => {
         },
       },
     );
-    let widthToFWHM = getShape1D('gaussian').widthToFWHM;
+    let widthToFWHM = getShape1D({ kind: 'gaussian' }).widthToFWHM;
     expect(peaks).toHaveLength(1);
     expect(peaks[0]).toMatchCloseTo({
       x: 15,
       y: 4.657142857142857,
-      shape: {
-        width: widthToFWHM(2),
-        soft: false,
-        noiseLevel: 0.6695521174585716,
-      },
+      width: 2,
+      fwhm: widthToFWHM(2),
+      shape: { kind: 'gaussian' },
     });
   });
 
@@ -64,16 +62,14 @@ describe('Simple shifted baseline test cases', () => {
         },
       },
     );
-    let widthToFWHM = getShape1D('gaussian').widthToFWHM;
+    let widthToFWHM = getShape1D({ kind: 'gaussian' }).widthToFWHM;
     expect(peaks).toHaveLength(1);
     expect(peaks[0]).toMatchCloseTo({
       x: 15,
       y: -4.657142857142857,
-      shape: {
-        width: widthToFWHM(2),
-        soft: false,
-        noiseLevel: 0.6695521174585716,
-      },
+      width: 2,
+      fwhm: widthToFWHM(2),
+      shape: { kind: 'gaussian' },
     });
   });
 });