chromatography - npm Package Compare versions

Comparing version 2.0.6 to 2.1.0

lib/index.js

@@ -8,2 +8,3 @@ 'use strict';
 var mlGsd = require('ml-gsd');
+var max = _interopDefault(require('ml-array-max'));
 var binarySearch = _interopDefault(require('binary-search'));
@@ -237,2 +238,21 @@ var chemcalc = require('chemcalc');
 
+/**
+ * Calculate bpc
+ * @param {Chromatogram} chrom - GC/MS chromatogram where make the peak picking
+ * @return {Array} - Calculated bpc
+ */
+function calculateBpc(chrom) {
+    let ms = chrom.getSerie('ms');
+    if (!ms) {
+        throw new Error('The mass serie must be defined');
+    }
+    var massSpectra = ms.data;
+    var bpc = [];
+    for (var massSpectrum of massSpectra) {
+        bpc.push(max(massSpectrum[1]));
+    }
+
+    return bpc;
+}
+
 const ascValue = (a, b) => (a - b);
@@ -286,3 +306,29 @@
 
-function integrate1D(time, serie, from, to, fromIndex, toIndex) {
+function baselineCorrection(total, base, kind) {
+    switch (kind) {
+        case 'trapezoid':
+            return {
+                integral: total - ((base.end.time - base.start.time) * (base.end.height + base.start.height) / 2),
+                base
+            };
+        case 'min':
+            if (base.end.height > base.start.height) {
+                base.end.height = base.start.height;
+                return {
+                    integral: total - ((base.end.time - base.start.time) * base.start.height),
+                    base
+                };
+            } else {
+                base.start.height = base.end.height;
+                return {
+                    integral: total - ((base.end.time - base.start.time) * base.end.height),
+                    base
+                };
+            }
+        default:
+            throw new Error(`Unknown baseline method "${kind}"`);
+    }
+}
+
+function integrate1D(time, serie, from, to, fromIndex, toIndex, baseline) {
     if (serie.dimension !== 1) throw new Error('The serie name is not of dimension 1');
@@ -292,2 +338,3 @@ if (!serie.data) return 0;
     let total = 0;
+    let base = {};
     for (let i = fromIndex; i < toIndex; i++) {
@@ -299,2 +346,3 @@ let timeStart = time[i];
             heightStart = serie.data[i] + (serie.data[i + 1] - serie.data[i]) * (from - timeStart) / (timeEnd - timeStart);
+            base.start = {height: heightStart, time: from};
             timeStart = from;
@@ -305,3 +353,4 @@ }
         if (i === toIndex - 1) {
-            heightEnd = serie.data[i] + (serie.data[i + 1] - serie.data[i]) * (timeEnd - to) / (timeEnd - timeStart);
+            heightEnd = serie.data[i] + (serie.data[i + 1] - serie.data[i]) * (to - timeStart) / (timeEnd - timeStart);
+            base.end = {height: heightEnd, time: to};
             timeEnd = to;
@@ -311,3 +360,14 @@ }
     }
-    return total;
+
+    if (baseline) {
+        return baselineCorrection(total, base, baseline);
+    } else {
+        return {
+            integral: total,
+            base: {
+                start: {height: 0, time: from},
+                end: {height: 0, time: to}
+            }
+        };
+    }
 }
@@ -342,6 +402,2 @@
 
-const defaultOptions = {
-    slot: 1
-};
-
 /**
@@ -358,6 +414,12 @@ * Returns a mass spectrum that is the integration of all the spectra in a specific range of time
  * @param {number} [options.slot = 2] - Define when 2 peaks will be combined
+ * @param {string} [options.name] - Name of the serie to integrate, by default all the series are integrated
+ * @param {string|boolean} [options.baseline] - Applies baseline correction
  * @return {{serieName: []}}
  */
-function integrate(chromatogram, ranges, options) {
-    options = Object.assign({}, defaultOptions, options);
+function integrate(chromatogram, ranges, options = {}) {
+    const {
+        slot = 1,
+        name = false,
+        baseline = false
+    } = options;
 
@@ -370,3 +432,8 @@ if (!Array.isArray(ranges)) throw new Error('fromTo must be an array of type [from,to]');
     // by default we integrate all the series
-    var serieNames = chromatogram.getSerieNames();
+    let serieNames;
+    if (name) {
+        serieNames = [name];
+    } else {
+        serieNames = chromatogram.getSerieNames();
+    }
     let results = {};
@@ -381,3 +448,2 @@ serieNames.forEach(name => results[name] = []);
 
-
         for (let serieName of serieNames) {
@@ -387,6 +453,6 @@ let serie = chromatogram.series[serieName];
                 case 1:
-                    results[serieName].push(integrate1D(time, serie, from, to, fromIndex, toIndex, options));
+                    results[serieName].push(integrate1D(time, serie, from, to, fromIndex, toIndex, baseline));
                     break;
                 case 2:
-                    results[serieName].push(integrate2D(time, serie, from, to, fromIndex, toIndex, options));
+                    results[serieName].push(integrate2D(time, serie, from, to, fromIndex, toIndex, {slot}));
                     break;
@@ -483,3 +549,3 @@ default:
 
-    let max = -1;
+    let max$$1 = -1;
     let massList = new Array(massXYObject.x.length);
@@ -492,4 +558,4 @@ for (let i = 0; i < massXYObject.x.length; ++i) {
 
-        if (massXYObject.y[i] > max) {
-            max = massXYObject.y[i];
+        if (massXYObject.y[i] > max$$1) {
+            max$$1 = massXYObject.y[i];
         }
@@ -499,4 +565,4 @@ }
     // filters based in thresholdFactor
-    max *= thresholdFactor;
-    let filteredList = massList.filter((val) => val.y > max);
+    max$$1 *= thresholdFactor;
+    let filteredList = massList.filter((val) => val.y > max$$1);
 
@@ -539,3 +605,3 @@ // filters based in maxNumberPeaks
         let massDictionary = {};
-        let max = -1;
+        let max$$1 = -1;
         for (let j = peakList[i].left.index; j <= peakList[i].right.index; ++j) {
@@ -553,4 +619,4 @@ for (let k = 0; k < sampleMS[j][0].length; ++k) {
 
-                if (massDictionary[mass] > max) {
-                    max = massDictionary[mass];
+                if (massDictionary[mass] > max$$1) {
+                    max$$1 = massDictionary[mass];
                 }
@@ -702,3 +768,3 @@ }
 
-const defaultOptions$1 = {
+const defaultOptions = {
     oddReference: true
@@ -715,3 +781,3 @@ };
 function applyLockMass(mf, options) {
-    options = Object.assign({}, defaultOptions$1, options);
+    options = Object.assign({}, defaultOptions, options);
 
@@ -974,2 +1040,14 @@ // allows mf as string or array
     /**
+     * Calculate bpc
+     * @param {object} [options = {}] - Options object
+     * @param {boolean} [options.force = false] - Force the calculation it it exists
+     */
+    calculateBpc(options = {}) {
+        if (!this.getSerie('bpc') || options.force) {
+            let bpc = calculateBpc(this);
+            this.addSerie('bpc', bpc);
+        }
+    }
+
+    /**
      * Calculates the table of Kovats indexes for the reference spectra
@@ -1184,3 +1262,3 @@ * @param {object} [options = {}] - Options object
     for (let i = 0; i < sample.peaks.length; ++i) {
-        let max = {similarity: -3};
+        let max$$1 = {similarity: -3};
         let biggerCounter = 0;
@@ -1190,4 +1268,4 @@ for (let j = 0; j < reference.peaks.length; ++j) {
 
-            if (sim > options.similarityThreshold && sim > max.similarity) {
-                max = {
+            if (sim > options.similarityThreshold && sim > max$$1.similarity) {
+                max$$1 = {
                     similarity: sim,
@@ -1203,5 +1281,5 @@ chrom1: reference.peaks[j],
         if (biggerCounter === 1) {
-            similarityPeaks.chrom1[similarLen] = max.chrom1;
-            similarityPeaks.chrom2[similarLen] = max.chrom2;
-            similarityPeaks.similarity[similarLen++] = max.similarity;
+            similarityPeaks.chrom1[similarLen] = max$$1.chrom1;
+            similarityPeaks.chrom2[similarLen] = max$$1.chrom2;
+            similarityPeaks.similarity[similarLen++] = max$$1.similarity;
         }
@@ -1208,0 +1286,0 @@ }

package.json

 {
   "name": "chromatography",
-  "version": "2.0.6",
+  "version": "2.1.0",
   "description": "Tools for storing, search and analize GC/MS spectra",
@@ -12,3 +12,3 @@ "main": "lib/index.js",
   "scripts": {
-    "build": "cheminfo build --root Chromatography",
+    "build": "rollup -c && cheminfo build --root Chromatography",
     "build-doc": "cheminfo doc",
@@ -44,2 +44,3 @@ "publish-doc": "cheminfo doc --publish",
     "babel-preset-env": "^1.5.2",
+    "cheminfo-tools": "^1.16.2",
     "codecov": "^2.2.0",
@@ -58,2 +59,3 @@ "documentation": "^4.0.0-rc.1",
     "jcampconverter": "^2.3.0",
+    "ml-array-max": "^1.0.0",
     "ml-gsd": "^2.0.1",
@@ -60,0 +62,0 @@ "ml-regression-polynomial": "^1.0.2",

src/__tests__/chromatogram.js

@@ -59,3 +59,9 @@ import {Chromatogram} from '..';
     var result = chromato.getIntegrations([1.5, 5.5]);
-    expect(result).toEqual({tic: [125]});
+    expect(result).toEqual({tic: [{
+        integral: 125,
+        base: {
+            start: {height: 0, time: 1.5},
+            end: {height: 0, time: 5.5}
+        }
+    }]});
 });

src/__tests__/from/jcamp.js

@@ -5,3 +5,3 @@ import {readFileSync} from 'fs';
 
-test('load JCAMP', async () => {
+test('load JCAMP', () => {
     const path = join(__dirname, '../data/jcamp/MixC8-C40_140630.JDX');
@@ -8,0 +8,0 @@ const jcamp = readFileSync(path, 'utf8');

src/__tests__/from/text.js

@@ -17,1 +17,17 @@ const {fromText} = require('../..');
 
+test('Parse a text with options', () => {
+    const text = `
+        1,2,3
+        2,3,4
+        3,4,5
+    `;
+
+    let newChromatogram = fromText(text, {
+        xColumn: 1,
+        yColumn: 2
+    });
+    expect(newChromatogram.getSerie('intensity').data.length).toEqual(3);
+    expect(newChromatogram.times.length).toEqual(3);
+    expect(newChromatogram.times).toEqual([2, 3, 4]);
+    expect(newChromatogram.getSerieNames()).toEqual(['intensity']);
+});

src/__tests__/massInPeaks.js

@@ -6,3 +6,3 @@ import {readFileSync} from 'fs';
 
-test('from a Diesel chromatogram', async () => {
+test('from a Diesel chromatogram', () => {
     const path = join(__dirname, 'data/jcamp/P064.JDX');
@@ -9,0 +9,0 @@ const jcamp = readFileSync(path, 'utf8');

src/__tests__/rescaleTime.js

@@ -28,3 +28,3 @@ import {readFileSync} from 'fs';
 
-test('Non-in place', async () => {
+test('Non-in place', () => {
     const path = join(__dirname, 'data/jcamp/P064.JDX');
@@ -68,3 +68,3 @@ const jcamp = readFileSync(path, 'utf8');
 
-test('In place', async () => {
+test('In place', () => {
     const path = join(__dirname, 'data/jcamp/P064.JDX');
@@ -71,0 +71,0 @@ const jcamp = readFileSync(path, 'utf8');

src/__tests__/scaleAlignment.js

 import {Chromatogram, spectraComparison, scaleAlignment} from '..';
 import {lorentzian} from './data/examples';
 
-test('Simple case', async () => {
+test('Simple case', () => {
     const size = 70;
@@ -41,3 +41,3 @@ const peakX = 10;
 
-test('Quality and string', async () => {
+test('Quality and string', () => {
     const size = 70;
@@ -44,0 +44,0 @@ const peakX = 10;

src/__tests__/util/integrate.js

@@ -1,4 +0,6 @@
-import {integrate} from '../..';
+import {integrate, Chromatogram} from '../..';
 import {chromato} from '../data/examples';
 
+var chrom = new Chromatogram([1, 2, 3, 4], {tic: [2, 4, 6, 8]});
+
 test('Integrate a tic', () => {
@@ -15,3 +17,9 @@
     var result = integrate(chromato, [1.8, 5.5]);
-    expect(result).toEqual({tic: [120.05]});
+    expect(result).toEqual({tic: [{
+        integral: 120.05,
+        base: {
+            start: {height: 0, time: 1.8},
+            end: {height: 0, time: 5.5}
+        }
+    }]});
 
@@ -39,1 +47,50 @@ //
 });
+
+describe('Applies baseline correction', () => {
+    it('without baseline', () => {
+        var result = integrate(chrom, [1, 3], {name: 'tic', baseline: false});
+        expect(result).toEqual({tic: [{
+            integral: 8,
+            base: {
+                start: {height: 0, time: 1},
+                end: {height: 0, time: 3}
+            }
+        }]});
+    });
+
+    it('trapezoid baseline', () => {
+        var result = integrate(chrom, [1, 3], {name: 'tic', baseline: 'trapezoid'});
+        expect(result).toEqual({tic: [{
+            integral: 0,
+            base: {
+                start: {height: 2, time: 1},
+                end: {height: 6, time: 3}
+            }
+        }]});
+    });
+
+    it('min baseline', () => {
+        var result = integrate(chrom, [1, 3], {name: 'tic', baseline: 'min'});
+        expect(result).toEqual({tic: [{
+            integral: 4,
+            base: {
+                start: {height: 2, time: 1},
+                end: {height: 2, time: 3}
+            }
+        }]});
+
+        var other = new Chromatogram([1, 2, 3], {tic: [6, 4, 2]});
+        result = integrate(other, [1, 3], {name: 'tic', baseline: 'min'});
+        expect(result).toEqual({tic: [{
+            integral: 4,
+            base: {
+                start: {height: 2, time: 1},
+                end: {height: 2, time: 3}
+            }
+        }]});
+    });
+
+    it('error', () => {
+        expect(() => integrate(chrom, [1, 3], {name: 'tic', baseline: 'bla'})).toThrow('Unknown baseline method "bla"');
+    });
+});

src/__tests__/vectorify.js

@@ -6,3 +6,3 @@ import {readFileSync} from 'fs';
 
-test('from a Diesel chromatogram', async () => {
+test('from a Diesel chromatogram', () => {
     const path = join(__dirname, 'data/jcamp/P064.JDX');
@@ -9,0 +9,0 @@ const jcamp = readFileSync(path, 'utf8');

src/Chromatogram.js

@@ -7,2 +7,3 @@ import {rescaleTime} from './rescaleTime';
 import {calculateTic} from './ms/calculateTic';
+import {calculateBpc} from './ms/calculateBpc';
 import {integrate} from './util/integrate';
@@ -196,2 +197,14 @@ import {getKovatsRescale} from './getKovatsRescale';
     /**
+     * Calculate bpc
+     * @param {object} [options = {}] - Options object
+     * @param {boolean} [options.force = false] - Force the calculation it it exists
+     */
+    calculateBpc(options = {}) {
+        if (!this.getSerie('bpc') || options.force) {
+            let bpc = calculateBpc(this);
+            this.addSerie('bpc', bpc);
+        }
+    }
+
+    /**
      * Calculates the table of Kovats indexes for the reference spectra
@@ -198,0 +211,0 @@ * @param {object} [options = {}] - Options object

src/util/integrate.js

@@ -5,6 +5,2 @@ import {getClosestTime} from './getClosestTime';
 
-const defaultOptions = {
-    slot: 1
-};
-
 /**
@@ -21,6 +17,12 @@ * Returns a mass spectrum that is the integration of all the spectra in a specific range of time
  * @param {number} [options.slot = 2] - Define when 2 peaks will be combined
+ * @param {string} [options.name] - Name of the serie to integrate, by default all the series are integrated
+ * @param {string|boolean} [options.baseline] - Applies baseline correction
  * @return {{serieName: []}}
  */
-export function integrate(chromatogram, ranges, options) {
-    options = Object.assign({}, defaultOptions, options);
+export function integrate(chromatogram, ranges, options = {}) {
+    const {
+        slot = 1,
+        name = false,
+        baseline = false
+    } = options;
 
@@ -33,3 +35,8 @@ if (!Array.isArray(ranges)) throw new Error('fromTo must be an array of type [from,to]');
     // by default we integrate all the series
-    var serieNames = chromatogram.getSerieNames();
+    let serieNames;
+    if (name) {
+        serieNames = [name];
+    } else {
+        serieNames = chromatogram.getSerieNames();
+    }
     let results = {};
@@ -44,3 +51,2 @@ serieNames.forEach(name => results[name] = []);
 
-
         for (let serieName of serieNames) {
@@ -50,6 +56,6 @@ let serie = chromatogram.series[serieName];
                 case 1:
-                    results[serieName].push(integrate1D(time, serie, from, to, fromIndex, toIndex, options));
+                    results[serieName].push(integrate1D(time, serie, from, to, fromIndex, toIndex, baseline));
                     break;
                 case 2:
-                    results[serieName].push(integrate2D(time, serie, from, to, fromIndex, toIndex, options));
+                    results[serieName].push(integrate2D(time, serie, from, to, fromIndex, toIndex, {slot}));
                     break;
@@ -56,0 +62,0 @@ default:

src/util/integrate1D.js

@@ -1,2 +0,4 @@
-export function integrate1D(time, serie, from, to, fromIndex, toIndex) {
+import {baselineCorrection} from './baselineCorrection';
+
+export function integrate1D(time, serie, from, to, fromIndex, toIndex, baseline) {
     if (serie.dimension !== 1) throw new Error('The serie name is not of dimension 1');
@@ -6,2 +8,3 @@ if (!serie.data) return 0;
     let total = 0;
+    let base = {};
     for (let i = fromIndex; i < toIndex; i++) {
@@ -13,2 +16,3 @@ let timeStart = time[i];
             heightStart = serie.data[i] + (serie.data[i + 1] - serie.data[i]) * (from - timeStart) / (timeEnd - timeStart);
+            base.start = {height: heightStart, time: from};
             timeStart = from;
@@ -19,3 +23,4 @@ }
         if (i === toIndex - 1) {
-            heightEnd = serie.data[i] + (serie.data[i + 1] - serie.data[i]) * (timeEnd - to) / (timeEnd - timeStart);
+            heightEnd = serie.data[i] + (serie.data[i + 1] - serie.data[i]) * (to - timeStart) / (timeEnd - timeStart);
+            base.end = {height: heightEnd, time: to};
             timeEnd = to;
@@ -25,3 +30,14 @@ }
     }
-    return total;
+
+    if (baseline) {
+        return baselineCorrection(total, base, baseline);
+    } else {
+        return {
+            integral: total,
+            base: {
+                start: {height: 0, time: from},
+                end: {height: 0, time: to}
+            }
+        };
+    }
 }

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Improved metrics

Total package byte prevSize

23647131

increased by0.03%

Number of package files

65

increased by4.84%

Lines of code

5555

increased by4.46%

Number of medium supply chain risk alerts

0

decreased by-100%

Worsened metrics

Dependency count

7

increased by16.67%

Dev dependency count

13

increased by8.33%

Dependency changes

• + Addedml-array-max@^1.0.0