feat!: homogenize and generalize output (#63)

* feat!: refactor gsd

homogenize output
rename base to noiseLevel
by default width is FWHM of a gaussian
remove properties 'left' and 'right'

* feat!: refactor broadenPeaks

homogenize output
remove properties 'from' and 'to'

* chore: refactor groupPeaks

make a copy

* feat!: refactor joinBroadPeaks

make a copy
homogenize output

* feat!: homogenize input/output optimizePeaks

* chore: adaptation of test cases

* chore: remove nodejs 10.x 15.x n add 16.x

* feat!: update ml-spectra-fitting to 2.0.0

* chore: use toBeClose instead of toStrictEqual

Author: jobo322

.github/workflows/nodejs.yml

@@ -24,7 +24,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        node-version: [10.x, 12.x, 14.x, 15.x]
+        node-version: [12.x, 14.x, 16.x]
       fail-fast: false
     steps:
       - uses: actions/checkout@v2

package.json

@@ -20,6 +20,8 @@
     "eslint-fix": "npm run eslint -- --fix",
     "compile": "rollup -c",
     "prepack": "npm run compile",
+    "prettier": "prettier --check src",
+    "prettier-write": "prettier --write src",
     "test": "npm run test-coverage && npm run eslint",
     "test-only": "jest",
     "test-coverage": "jest --coverage"
@@ -77,7 +79,7 @@
     "cheminfo-types": "^0.5.0",
     "ml-peak-shape-generator": "^2.0.2",
     "ml-savitzky-golay-generalized": "2.0.3",
-    "ml-spectra-fitting": "^1.0.0",
+    "ml-spectra-fitting": "^2.0.0",
     "ml-spectra-processing": "^6.8.0"
   }
 }

src/__tests__/bigLowS2NSpectrum.js renamed to src/__tests__/bigLowS2NSpectrum.test.js

@@ -23,7 +23,7 @@ describe('Global spectra deconvolution NMR spectra', () => {
       },
     );
 
-    joinBroadPeaks(pp, { width: 0.25 });
+    pp = joinBroadPeaks(pp, { width: 0.25 });
 
     expect(pp).toHaveLength(91);
   });

src/__tests__/broadNMR.js renamed to src/__tests__/broadNMR.test.js

@@ -21,11 +21,11 @@ describe('Global spectra deconvolution NMR spectra', () => {
         },
       },
     );
-    joinBroadPeaks(result, { width: 0.25, shape: { kind: 'lorentzian' } });
-    expect(result).toHaveLength(14);
-    result.forEach((peak) => {
+    const newResult = joinBroadPeaks(result, { width: 0.25, shape: { kind: 'lorentzian' } });
+    expect(newResult).toHaveLength(14);
+    newResult.forEach((peak) => {
       if (Math.abs(peak.x - 4.31) < 0.01) {
-        expect(peak.width).toBeCloseTo(0.39, 2);
+        expect(peak.shape.width).toBeCloseTo(0.39, 2);
       }
     });
   });

src/__tests__/ethylvinylether.js renamed to src/__tests__/ethylvinylether.test.js

@@ -43,26 +43,26 @@ describe('Check the peak picking of a simulated mass spectrum', () => {
     });
     expect(result[0].x).toBeCloseTo(69.938, 1);
     expect(result[0].y).toBeCloseTo(max, 2);
-    expect(result[0].width).toBeCloseTo(0.01, 4);
+    expect(result[0].shape.width).toBeCloseTo(0.01, 4);
 
     expect(result[1].x).toBeCloseTo(71.935, 2);
     expect(result[1].y).toBeCloseTo((63.99155 * max) / 100, 3);
-    expect(result[1].width).toBeCloseTo(0.01, 4);
+    expect(result[1].shape.width).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].width).toBeCloseTo(0.01, 4);
+    expect(result[2].shape.width).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].width).toBeCloseTo(0.01, 4);
+    expect(result[3].shape.width).toBeCloseTo(0.01, 4);
 
     expect(result[4].x).toBeCloseTo(159.835, 1);
     expect(result[4].y).toBeCloseTo(max, 2);
-    expect(result[4].width).toBeCloseTo(0.01, 4);
+    expect(result[4].shape.width).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].width).toBeCloseTo(0.01, 4);
+    expect(result[5].shape.width).toBeCloseTo(0.01, 4);
   });
 });

src/__tests__/test.js renamed to src/__tests__/general.test.js

@@ -1,4 +1,5 @@
 import { toMatchCloseTo } from 'jest-matcher-deep-close-to';
+import { getShape1D } from 'ml-peak-shape-generator';
 
 import { gsd } from '..';
 
@@ -25,6 +26,8 @@ describe('Simple test cases', () => {
     negY.push(0);
   }
 
+  let widthToFWHM = getShape1D('gaussian').widthToFWHM;
+
   it('gsd not realtop', () => {
     let peaks = gsd(
       { x, y },
@@ -39,8 +42,8 @@ describe('Simple test cases', () => {
     );
 
     expect(peaks[0].y).toBeCloseTo(4.657, 3);
-    expect(peaks[0].base).toBeCloseTo(1.1956, 3);
-    expect(peaks[0].x).toStrictEqual(15);
+    expect(peaks[0].shape.noiseLevel).toBeCloseTo(1.1956, 3);
+    expect(peaks[0].x).toBeCloseTo(15, 2);
   });
 
   it('gsd negative peak', () => {
@@ -57,8 +60,8 @@ describe('Simple test cases', () => {
       },
     );
     expect(peaks[0].y).toBeCloseTo(-4.657, 3);
-    expect(peaks[0].base).toBeCloseTo(1.1956, 3);
-    expect(peaks[0].x).toStrictEqual(15);
+    expect(peaks[0].shape.noiseLevel).toBeCloseTo(1.1956, 3);
+    expect(peaks[0].x).toBeCloseTo(15,2);
   });
 
   it('gsd not realtop asymetric', () => {
@@ -79,18 +82,11 @@ describe('Simple test cases', () => {
     expect(peaks).toMatchCloseTo(
       [
         {
-          base: 1.2434539324230613,
-          index: 15,
-          left: {
-            index: 13,
-            x: 13,
-          },
-          right: {
-            index: 16,
-            x: 16,
+          shape: {
+            noiseLevel: 1.2434539324230613,
+            soft: false,
+            width: widthToFWHM(3),
           },
-          soft: false,
-          width: 3,
           x: 15,
           y: 5,
         },
@@ -116,18 +112,7 @@ describe('Simple test cases', () => {
     expect(peaks).toMatchCloseTo(
       [
         {
-          base: 1.2434539324230613,
-          index: 15,
-          left: {
-            index: 13,
-            x: 13,
-          },
-          right: {
-            index: 16,
-            x: 16,
-          },
-          soft: false,
-          width: 3,
+          shape: { noiseLevel: 1.2434539324230613, soft: false, width: widthToFWHM(3) },
           x: 14.5,
           y: 4.006546067576939,
         },

src/__tests__/infraRed.js renamed to src/__tests__/infraRed.test.js

@@ -1,4 +1,5 @@
 import { toMatchCloseTo } from 'jest-matcher-deep-close-to';
+import { getShape1D } from 'ml-peak-shape-generator';
 
 import { gsd } from '..';
 
@@ -37,16 +38,16 @@ describe('Simple shifted baseline test cases', () => {
         },
       },
     );
+    let widthToFWHM = getShape1D('gaussian').widthToFWHM;
     expect(peaks).toHaveLength(1);
     expect(peaks[0]).toMatchCloseTo({
-      index: 15,
       x: 15,
       y: 4.657142857142857,
-      width: 2,
-      soft: false,
-      left: { x: 14, index: 14 },
-      right: { x: 16, index: 16 },
-      base: 0.6695521174585716,
+      shape: {
+        width: widthToFWHM(2),
+        soft: false,
+        noiseLevel: 0.6695521174585716,
+      },
     });
   });
 
@@ -63,16 +64,16 @@ describe('Simple shifted baseline test cases', () => {
         },
       },
     );
+    let widthToFWHM = getShape1D('gaussian').widthToFWHM;
     expect(peaks).toHaveLength(1);
     expect(peaks[0]).toMatchCloseTo({
-      index: 15,
       x: 15,
       y: -4.657142857142857,
-      width: 2,
-      soft: false,
-      left: { x: 14, index: 14 },
-      right: { x: 16, index: 16 },
-      base: 0.6695521174585716,
+      shape: {
+        width: widthToFWHM(2),
+        soft: false,
+        noiseLevel: 0.6695521174585716,
+      },
     });
   });
 });