feat: add toJSON and fromJSON methods

src/Chromatogram.js

@@ -99,6 +99,38 @@ class Chromatogram {
     rescaleTime(conversionFunction) {
         this.times = rescaleTime(this.times, conversionFunction);
     }
+
+    /**
+     * Parse the content to an JSON Array
+     * @return {Array<object>} - Returns a list with the following fields:
+     *  * `time`: Number for the retention time
+     *  * `tic`: Number for the total ion chromatogram
+     *  * `mass`: List of mass values and their respective intensities
+     */
+    toJSON() {
+        var ans = new Array(this.times.length);
+        const tic = this.findSerieByName('tic').data;
+        const mass = this.findSerieByName('ms').data.map((ms) => {
+            var ansMS = new Array(ms[0].length);
+            for (var i = 0; i < ansMS.length; i++) {
+                ansMS[i] = {
+                    mass: ms[0][i],
+                    intensity: ms[1][i]
+                };
+            }
+            return ansMS;
+        });
+
+        for (var i = 0; i < ans.length; i++) {
+            ans[i] = {
+                time: this.times[i],
+                tic: tic[i],
+                mass: mass[i]
+            };
+        }
+
+        return ans;
+    }
 }
 
 module.exports = Chromatogram;

src/fromJSON.js

@@ -0,0 +1,40 @@
+'use strict';
+
+const Chromatogram = require('./Chromatogram');
+
+/**
+ * Parse from a JSON element to a new Chromatogram
+ * @param {Array<object>} json - Result from the toJSON
+ * @return {Chromatogram} - New parsed Chromatogram
+ */
+function fromJSON(json) {
+    let time = new Array(json.length);
+    let tic = new Array(json.length);
+    let ms = new Array(json.length);
+
+    for (var i = 0; i < json.length; i++) {
+        time[i] = json[i].time;
+        tic[i] = json[i].tic;
+        ms[i] = [new Array(json[i].mass.length), new Array(json[i].mass.length)];
+        for (var j = 0; j < json[i].mass.length; j++) {
+            ms[i][0][j] = json[i].mass[j].mass;
+            ms[i][1][j] = json[i].mass[j].intensity;
+        }
+    }
+
+    let chrom = new Chromatogram(time);
+    chrom.addSerie({
+        dimension: 1,
+        name: 'tic',
+        data: tic
+    });
+    chrom.addSerie({
+        dimension: 2,
+        name: 'ms',
+        data: ms
+    });
+
+    return chrom;
+}
+
+module.exports = fromJSON;

src/fromJcamp.js

@@ -13,4 +13,4 @@ function fromJcamp(jcamp) {
     return new Chromatogram(data);
 }
 
-module.exports = fromJcamp;
+module.exports = fromJcamp;

src/index.js

@@ -15,3 +15,4 @@ exports.getKovatsTable = require('./getKovatsTable');
 exports.kovatsConversionFunction = require('./kovatsConversionFunction');
 exports.rescaleTime = require('./rescaleTime');
 exports.fromJcamp = require('./fromJcamp');
+exports.fromJSON = require('./fromJSON');

src/spectraComparison.js

@@ -1,6 +1,6 @@
 'use strict';
 
-const peakPicking = require('./getPeaks');
+const getPeaks = require('./getPeaks');
 const massInPeaks = require('./massInPeaks');
 const vectorify = require('./vectorify');
 const cosine = require('./cosine');
@@ -14,7 +14,7 @@ const cosine = require('./cosine');
  */
 function preprocessing(chromatography, options) {
     // peak picking
-    let peaks = peakPicking(chromatography, options);
+    let peaks = getPeaks(chromatography, options);
     peaks = peaks.sort((a, b) => a.index - b.index);
 
     // integrate mass in the peaks

test/JSONparser.js

@@ -0,0 +1,40 @@
+import test from 'ava';
+import {Chromatogram, fromJSON} from '..';
+
+// https://en.wikipedia.org/wiki/Cauchy_distribution
+function lorentzian(x, x0 = 0, gamma = 1) {
+    return (gamma * gamma) / (Math.PI * gamma * (gamma * gamma + (x - x0) * (x - x0)));
+}
+
+test('toJSON - fromJSON', t => {
+    const size = 30;
+    const fourth = size / 4;
+    let times = new Array(size);
+    let tic = new Array(size);
+    let ms = new Array(size);
+    for (let i = 0; i < size; ++i) {
+        times[i] = i;
+        tic[i] = lorentzian(i, fourth) + 2 * lorentzian(i, 2 * fourth) + lorentzian(i, 3 * fourth);
+        ms[i] = [[1, 2, 3], [1, 1, 1]];
+    }
+    let chrom = new Chromatogram(times);
+    chrom.addSerie({
+        dimension: 1,
+        name: 'tic',
+        data: tic
+    });
+    chrom.addSerie({
+        dimension: 2,
+        name: 'ms',
+        data: ms
+    });
+
+    let json = chrom.toJSON();
+    t.is(json.length, chrom.getTimes().length);
+    t.is(json.length, 30);
+
+    let newChrom = fromJSON(json);
+    t.deepEqual(newChrom.getTimes(), chrom.getTimes());
+    t.deepEqual(newChrom.findSerieByName('tic'), chrom.findSerieByName('tic'));
+    t.deepEqual(newChrom.findSerieByName('ms'), chrom.findSerieByName('ms'));
+});

test/loadJcamp.js

@@ -1,9 +1,8 @@
 import test from 'ava';
-import {convert} from 'jcampconverter';
 import fs from 'fs';
 import Promise from 'bluebird';
 import {join} from 'path';
-import {Chromatogram, fromJcamp} from '..';
+import {fromJcamp} from '..';
 
 const readFileAsync = Promise.promisify(fs.readFile);