spectrum-generator - npm Package Compare versions

Comparing version 4.4.1 to 4.4.2

CHANGELOG.md

 # Changelog
 
+### [4.4.2](https://www.github.com/cheminfo/spectrum-generator/compare/v4.4.1...v4.4.2) (2020-12-04)
+
+
+### Bug Fixes
+
+* correct some shapes imperfections ([eacf462](https://www.github.com/cheminfo/spectrum-generator/commit/eacf4628077939f7fec6894eb5e8966443feb76f))
+* NaN bug ([17a5fc9](https://www.github.com/cheminfo/spectrum-generator/commit/17a5fc936be41339048898f6d13c2ef4c487f92b))
+
 ### [4.4.1](https://www.github.com/cheminfo/spectrum-generator/compare/v4.4.0...v4.4.1) (2020-11-18)
@@ -4,0 +12,0 @@

lib/index.js

@@ -7,5 +7,5 @@ 'use strict';
 var mlPeakShapeGenerator = require('ml-peak-shape-generator');
+var objectHash = require('object-hash');
 var d3Random = require('d3-random');
 var XSAdd = require('ml-xsadd');
-var objectHash = require('object-hash');
 
@@ -15,4 +15,4 @@ function _interopDefaultLegacy (e) { return e && typeof e === 'object' && 'default' in e ? e : { 'default': e }; }
 var normed__default = /*#__PURE__*/_interopDefaultLegacy(normed);
+var objectHash__default = /*#__PURE__*/_interopDefaultLegacy(objectHash);
 var XSAdd__default = /*#__PURE__*/_interopDefaultLegacy(XSAdd);
-var objectHash__default = /*#__PURE__*/_interopDefaultLegacy(objectHash);
 
@@ -195,16 +195,38 @@ function addBaseline(data, baselineFct) {
     // we calculate the left part of the shape
-    for (let index = firstPoint; index < middlePoint; index++) {
+
+    for (let index = firstPoint; index < Math.max(middlePoint, 0); index++) {
       let ratio = ((xPosition - this.data.x[index]) / widthLeft) * 2;
-      let shapeIndex = Math.round(shape.halfLength - (ratio * shape.fwhm) / 2);
-      if (shapeIndex >= 0 && shapeIndex < shape.data.length) {
-        this.data.y[index] += shape.data[shapeIndex] * intensity;
+
+      let shapeIndex = shape.halfLength - (ratio * shape.fwhm) / 2;
+      let floorIndex = Math.floor(shapeIndex);
+      let ceilIndex = Math.ceil(shapeIndex);
+      let value =
+        floorIndex === shapeIndex
+          ? shape.data[shapeIndex]
+          : shape.data[floorIndex] * (ceilIndex - shapeIndex) +
+            shape.data[ceilIndex] * (shapeIndex - floorIndex);
+      shapeIndex = Math.round(shapeIndex);
+      if (floorIndex >= 0 && ceilIndex < shape.data.length) {
+        this.data.y[index] += value * intensity;
       }
     }
     // we calculate the right part of the gaussian
-    for (let index = middlePoint; index <= lastPoint; index++) {
+    for (
+      let index = Math.min(middlePoint, lastPoint);
+      index <= lastPoint;
+      index++
+    ) {
       let ratio = ((this.data.x[index] - xPosition) / widthRight) * 2;
 
-      let shapeIndex = Math.round(shape.halfLength - (ratio * shape.fwhm) / 2);
-      if (shapeIndex >= 0 && shapeIndex <= shape.data.length) {
-        this.data.y[index] += shape.data[shapeIndex] * intensity;
+      let shapeIndex = shape.halfLength - (ratio * shape.fwhm) / 2;
+      let floorIndex = Math.floor(shapeIndex);
+      let ceilIndex = Math.ceil(shapeIndex);
+      let value =
+        floorIndex === shapeIndex
+          ? shape.data[shapeIndex]
+          : shape.data[floorIndex] * (ceilIndex - shapeIndex) +
+            shape.data[ceilIndex] * (shapeIndex - floorIndex);
+      shapeIndex = Math.round(shapeIndex);
+      if (floorIndex >= 0 && ceilIndex <= shape.data.length) {
+        this.data.y[index] += value * intensity;
       }
@@ -211,0 +233,0 @@ }

package.json

 {
   "name": "spectrum-generator",
-  "version": "4.4.1",
+  "version": "4.4.2",
   "description": "generate a spectrum from discrete peaks",
@@ -5,0 +5,0 @@ "main": "lib/index.js",

src/__tests__/generateSpectrum.test.js

@@ -69,3 +69,3 @@ import { xyMaxYPoint } from 'ml-spectra-processing';
     });
-    expect(spectrum.y[8]).toBe(0.5);
+    expect(spectrum.y[8]).toBeCloseTo(0.5, 10);
 
@@ -113,3 +113,3 @@ checkSymmetry(spectrum);
     let max = xyMaxYPoint(spectrum);
-    expect(spectrum.y[49]).toBe(0.5);
+    expect(spectrum.y[49]).toBeCloseTo(0.5, 10);
     expect(max.x).toBe(5);
@@ -195,4 +195,6 @@ expect(max.y).toBe(1);
   for (let i = 0; i <= Math.floor(spectrum.y.length / 2); i++) {
-    expect(spectrum.y[i]).toStrictEqual(spectrum.y[spectrum.y.length - i - 1]);
+    expect(spectrum.y[i] - spectrum.y[spectrum.y.length - i - 1]).toBeCloseTo(
+      0,
+    );
   }
 }

src/__tests__/SpectrumGenerator.shapes.test.js

 import { xyMaxYPoint } from 'ml-spectra-processing';
+
 import { SpectrumGenerator } from '..';
@@ -86,3 +87,3 @@
     let max = xyMaxYPoint(spectrum);
-    expect(spectrum.y[49]).toBe(0.5);
+    expect(spectrum.y[49]).toBeCloseTo(0.5, 10);
     expect(max.x).toBe(2.5);
@@ -115,3 +116,3 @@ expect(max.y).toBe(2);
 
-    expect(ys[31] === ys[71]).toBe(true);
+    expect(ys[31] - ys[71]).toBeCloseTo(0, 10);
   });
@@ -161,3 +162,3 @@
     let max = xyMaxYPoint(spectrum);
-    expect(spectrum.y[49]).toBe(0.5);
+    expect(spectrum.y[49]).toBeCloseTo(0.5, 10);
     expect(max.x).toBe(2.5);
@@ -164,0 +165,0 @@ expect(max.y).toBe(2);

src/__tests__/SpectrumGenerator.test.js

@@ -55,3 +55,3 @@ import { SpectrumGenerator } from '..';
     expect(sumX).toBe(10050);
-    expect(sumY).toBeCloseTo(4257.612704089137, 4);
+    expect(sumY).toBeCloseTo(4257.612789255516, 4);
   });
@@ -58,0 +58,0 @@

src/index.js

 import normed from 'ml-array-normed';
 import { getShape } from 'ml-peak-shape-generator';
+import objectHash from 'object-hash';
 
 import addBaseline from './util/addBaseline.js';
 import addNoise from './util/addNoise.js';
-import objectHash from 'object-hash';
 
@@ -134,16 +134,38 @@ let shapesCache = {};
     // we calculate the left part of the shape
-    for (let index = firstPoint; index < middlePoint; index++) {
+
+    for (let index = firstPoint; index < Math.max(middlePoint, 0); index++) {
       let ratio = ((xPosition - this.data.x[index]) / widthLeft) * 2;
-      let shapeIndex = Math.round(shape.halfLength - (ratio * shape.fwhm) / 2);
-      if (shapeIndex >= 0 && shapeIndex < shape.data.length) {
-        this.data.y[index] += shape.data[shapeIndex] * intensity;
+
+      let shapeIndex = shape.halfLength - (ratio * shape.fwhm) / 2;
+      let floorIndex = Math.floor(shapeIndex);
+      let ceilIndex = Math.ceil(shapeIndex);
+      let value =
+        floorIndex === shapeIndex
+          ? shape.data[shapeIndex]
+          : shape.data[floorIndex] * (ceilIndex - shapeIndex) +
+            shape.data[ceilIndex] * (shapeIndex - floorIndex);
+      shapeIndex = Math.round(shapeIndex);
+      if (floorIndex >= 0 && ceilIndex < shape.data.length) {
+        this.data.y[index] += value * intensity;
       }
     }
     // we calculate the right part of the gaussian
-    for (let index = middlePoint; index <= lastPoint; index++) {
+    for (
+      let index = Math.min(middlePoint, lastPoint);
+      index <= lastPoint;
+      index++
+    ) {
       let ratio = ((this.data.x[index] - xPosition) / widthRight) * 2;
 
-      let shapeIndex = Math.round(shape.halfLength - (ratio * shape.fwhm) / 2);
-      if (shapeIndex >= 0 && shapeIndex <= shape.data.length) {
-        this.data.y[index] += shape.data[shapeIndex] * intensity;
+      let shapeIndex = shape.halfLength - (ratio * shape.fwhm) / 2;
+      let floorIndex = Math.floor(shapeIndex);
+      let ceilIndex = Math.ceil(shapeIndex);
+      let value =
+        floorIndex === shapeIndex
+          ? shape.data[shapeIndex]
+          : shape.data[floorIndex] * (ceilIndex - shapeIndex) +
+            shape.data[ceilIndex] * (shapeIndex - floorIndex);
+      shapeIndex = Math.round(shapeIndex);
+      if (floorIndex >= 0 && ceilIndex <= shape.data.length) {
+        this.data.y[index] += value * intensity;
       }
@@ -150,0 +172,0 @@ }

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Improved metrics

Total package byte prevSize

50855

increased by5.46%

Number of package files

19

increased by5.56%

Lines of code

1319

increased by5.77%

No dependency changes