feat: change parameters

BREAKING CHANGES

The function now use the `DataXY` input (an object with x:[] and y:[] properties).
The width of the peaks after gsd is the width between the 2 inflection points.
The width of the peaks after optimizePeaks is always FWHM

Author: lpatiny

README.md

@@ -1,12 +1,15 @@
 # global-spectral-deconvolution
 
 [![NPM version][npm-image]][npm-url]
-[![build status][travis-image]][travis-url]
 [![David deps][david-image]][david-url]
 [![npm download][download-image]][download-url]
 
 Global Spectra Deconvolution + Peak optimizer
 
+`gsd`is using an algorithm that is searching for inflection points to determine the position of peaks and the width of the peaks are between the 2 inflection points. The result of GSD yield to an array of object containing {x, y and width}. However this width is based on the inflection point and may be different from the 'fwhm' (Full Width Half Maximum).
+
+The second algorithm (`optimize`) will optimize the width as a FWHM to match the original peak. After optimization the width with therefore be always FWHM whichever is the function used. 
+
 ## [API documentation](http://mljs.github.io/global-spectral-deconvolution/)
 
 ## Parameters
@@ -61,39 +64,28 @@ By default we enlarge of a factor 2 and we don't allow overlap.
 ## Example
 
 ```js
-var CC = require('chemcalc');
-var Stat = require('ml-stat');
-var peakPicking = require('ml-gsd');
-
-var spectrum = CC.analyseMF('Cl2.Br2', {
-  isotopomers: 'arrayXXYY',
-  fwhm: 0.01,
-  gaussianWidth: 11,
-});
-var xy = spectrum.arrayXXYY;
-var x = xy[0];
-var y = xy[1];
-//Just a fake noiseLevel
-var noiseLevel =
-  Stat.array.median(
-    y.filter(function (a) {
-      return a > 0;
-    }),
-  ) * 3;
-
-var options = {
-  noiseLevel: noiseLevel,
-  minMaxRatio: 0,
-  broadRatio: 0,
-  smoothY: false,
-  realTopDetection: true,
-};
-var result = peakPicking.gsd(x, y, options);
+import { IsotopicDistribution } from 'mf-global';
+import { gsd, optimizePeaks } from '../src';
+
+// generate a sample spectrum of the form {x:[], y:[]}
+const data = new IsotopicDistribution('C').getGaussian();
 
-result = peakPicking.optimizePeaks(result, x, y, {
-  factorWidth: 1,
-  functionName: 'gaussian',
+let peaks = gsd(data, {
+  noiseLevel: 0,
+  minMaxRatio: 0.00025, // Threshold to determine if a given peak should be considered as a noise
+  realTopDetection: true,
+  maxCriteria: true, // inverted:false
+  smoothY: false,
+  sgOptions: { windowSize: 7, polynomial: 3 },
 });
+console.log(peaks); // array of peaks {x,y,width}, width = distance between inflection points
+// GSD
+
+let optimized = optimizePeaks(data, peaks);
+console.log(optimized); // array of peaks {x,y,width}, width = FWHM
+
+
+
 ```
 
 ## License
@@ -102,8 +94,6 @@ result = peakPicking.optimizePeaks(result, x, y, {
 
 [npm-image]: https://img.shields.io/npm/v/ml-gsd.svg?style=flat-square
 [npm-url]: https://npmjs.org/package/ml-gsd
-[travis-image]: https://img.shields.io/travis/mljs/global-spectral-deconvolution/master.svg?style=flat-square
-[travis-url]: https://travis-ci.org/mljs/global-spectral-deconvolution
 [david-image]: https://img.shields.io/david/mljs/global-spectral-deconvolution.svg?style=flat-square
 [david-url]: https://david-dm.org/mljs/global-spectral-deconvolution
 [download-image]: https://img.shields.io/npm/dm/ml-gsd.svg?style=flat-square

examples/example.js

@@ -1,4 +1,4 @@
-var gsd = require('../src/gsd');
+const gsd = require('../src/gsd');
 
 let X = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15];
 let Y = [0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 0, 0, 0, 0, 0];
@@ -8,6 +8,6 @@ let peaks = gsd(X, Y, {
   realTopDetection: true,
   maxCriteria: true, // inverted:false
   smoothY: false,
-  sgOptions: { windowSize: 7, polynomial: 3 }
+  sgOptions: { windowSize: 7, polynomial: 3 },
 });
 console.log(peaks);

examples/mf.js

@@ -0,0 +1,19 @@
+// to execute with `node -r esm ./mf.js`
+
+import { IsotopicDistribution } from 'mf-global';
+import { gsd, optimizePeaks } from '../src';
+
+// generate a sample spectrum of the form {x:[], y:[]}
+const data = new IsotopicDistribution('C').getGaussian();
+
+let peaks = gsd(data, {
+  noiseLevel: 0,
+  minMaxRatio: 0.00025, // Threshold to determine if a given peak should be considered as a noise
+  realTopDetection: true,
+  maxCriteria: true, // inverted:false
+  smoothY: false,
+  sgOptions: { windowSize: 7, polynomial: 3 },
+});
+
+let optimized = optimizePeaks(data, peaks);
+console.log(optimized);

package.json

@@ -59,7 +59,9 @@
     "eslint-plugin-import": "^2.22.1",
     "eslint-plugin-jest": "^24.1.0",
     "eslint-plugin-prettier": "^3.1.4",
+    "esm": "^3.2.25",
     "jest": "^26.6.3",
+    "mf-global": "^1.3.0",
     "ml-stat": "^1.3.3",
     "prettier": "^2.1.2",
     "rollup": "^2.33.1",