spectrum-generator - npm Package Compare versions

Comparing version 4.4.2 to 4.5.0

CHANGELOG.md

 # Changelog
 
+## [4.5.0](https://www.github.com/cheminfo/spectrum-generator/compare/v4.4.2...v4.5.0) (2020-12-10)
+
+
+### Features
+
+* Improve speed by calculating point to point the peak shape. ([#24](https://www.github.com/cheminfo/spectrum-generator/issues/24)) ([b987289](https://www.github.com/cheminfo/spectrum-generator/commit/b987289b4b8aa9b44a81366ad68d29c3650e692b))
+
 ### [4.4.2](https://www.github.com/cheminfo/spectrum-generator/compare/v4.4.1...v4.4.2) (2020-12-04)
@@ -4,0 +11,0 @@

lib/index.js

@@ -5,5 +5,3 @@ 'use strict';
 
-var normed = require('ml-array-normed');
 var mlPeakShapeGenerator = require('ml-peak-shape-generator');
-var objectHash = require('object-hash');
 var d3Random = require('d3-random');
@@ -14,4 +12,2 @@ var XSAdd = require('ml-xsadd');
 
-var normed__default = /*#__PURE__*/_interopDefaultLegacy(normed);
-var objectHash__default = /*#__PURE__*/_interopDefaultLegacy(objectHash);
 var XSAdd__default = /*#__PURE__*/_interopDefaultLegacy(XSAdd);
@@ -69,5 +65,2 @@
 
-let shapesCache = {};
-const MAX_CACHE_LENGTH = 20;
-
 class SpectrumGenerator {
@@ -84,6 +77,2 @@ constructor(options = {}) {
           kind: 'gaussian',
-          options: {
-            fwhm: 1000,
-            length: 5001,
-          },
         },
@@ -93,2 +82,3 @@ },
     );
+
     this.from = options.from;
@@ -100,4 +90,6 @@ this.to = options.to;
     this.maxPeakHeight = Number.MIN_SAFE_INTEGER;
-    this.shape = createShape(options.shape.kind, options.shape.options);
 
+    let shapeGenerator = mlPeakShapeGenerator.getShapeGenerator(options.shape);
+    this.shape = shapeGenerator;
+
     assertNumber(this.from, 'from');
@@ -178,4 +170,4 @@ assertNumber(this.to, 'to');
 
-    const shape = shapeOptions
-      ? createShape(shapeOptions.kind, shapeOptions.options)
+    let shapeGenerator = shapeOptions
+      ? mlPeakShapeGenerator.getShapeGenerator(shapeOptions)
       : this.shape;
@@ -186,5 +178,10 @@
 
-    const firstValue = xPosition - (widthLeft / 2) * shape.factor;
-    const lastValue = xPosition + (widthRight / 2) * shape.factor;
+    let factor =
+      options.factor === undefined
+        ? shapeGenerator.getFactor()
+        : options.factor;
 
+    const firstValue = xPosition - (widthLeft / 2) * factor;
+    const lastValue = xPosition + (widthRight / 2) * factor;
+
     const firstPoint = Math.max(
@@ -202,19 +199,10 @@ 0,
 
+    shapeGenerator.setFWHM(widthLeft);
     for (let index = firstPoint; index < Math.max(middlePoint, 0); index++) {
-      let ratio = ((xPosition - this.data.x[index]) / widthLeft) * 2;
+      this.data.y[index] +=
+        intensity * shapeGenerator.fct(this.data.x[index] - xPosition);
+    }
 
-      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
+    shapeGenerator.setFWHM(widthRight);
     for (
@@ -225,16 +213,4 @@ let index = Math.min(middlePoint, lastPoint);
     ) {
-      let ratio = ((this.data.x[index] - xPosition) / widthRight) * 2;
-
-      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;
-      }
+      this.data.y[index] +=
+        intensity * shapeGenerator.fct(this.data.x[index] - xPosition);
     }
@@ -318,30 +294,3 @@
 
-function createShape(kind, options) {
-  const hash = objectHash__default['default']({ kind, options });
-  if (shapesCache[hash]) {
-    return shapesCache[hash];
-  }
-
-  let shape = {};
-
-  let newShape = mlPeakShapeGenerator.getShape(kind, options);
-
-  shape.data = normed__default['default'](newShape.data, {
-    algorithm: 'max',
-  });
-  shape.fwhm = newShape.fwhm;
-  shape.factor = (newShape.data.length - 1) / newShape.fwhm;
-  shape.length = newShape.data.length;
-  shape.halfLength = Math.floor(newShape.data.length / 2);
-
-  if (Object.keys(shapesCache > MAX_CACHE_LENGTH)) {
-    shapesCache = {};
-  }
-
-  shapesCache[hash] = shape;
-
-  return shape;
-}
-
 exports.SpectrumGenerator = SpectrumGenerator;
 exports.generateSpectrum = generateSpectrum;

package.json

 {
   "name": "spectrum-generator",
-  "version": "4.4.2",
+  "version": "4.5.0",
   "description": "generate a spectrum from discrete peaks",
@@ -43,24 +43,22 @@ "main": "lib/index.js",
     "@babel/plugin-transform-modules-commonjs": "^7.12.1",
-    "@types/jest": "^26.0.15",
+    "@types/jest": "^26.0.18",
     "cheminfo-build": "^1.1.8",
     "convert-to-jcamp": "^4.2.0",
-    "eslint": "^7.13.0",
+    "eslint": "^7.15.0",
     "eslint-config-cheminfo": "^5.2.2",
     "eslint-plugin-import": "^2.22.1",
     "eslint-plugin-jest": "^24.1.3",
-    "eslint-plugin-prettier": "^3.1.4",
+    "eslint-plugin-prettier": "^3.2.0",
     "esm": "^3.2.25",
     "jest": "^26.6.3",
-    "ml-spectra-processing": "^4.8.0",
-    "pnpm": "^5.13.1",
-    "prettier": "^2.1.2",
-    "rollup": "^2.33.3"
+    "ml-spectra-processing": "^4.10.0",
+    "pnpm": "^5.13.5",
+    "prettier": "^2.2.1",
+    "rollup": "^2.34.2"
   },
   "dependencies": {
     "d3-random": "^2.2.2",
-    "ml-array-normed": "^1.3.2",
-    "ml-peak-shape-generator": "^0.10.2",
-    "ml-xsadd": "2.0.0",
-    "object-hash": "^2.0.3"
+    "ml-peak-shape-generator": "^0.11.0",
+    "ml-xsadd": "2.0.0"
   }
 }

src/__tests__/generateSpectrum.test.js

@@ -92,3 +92,3 @@ import { xyMaxYPoint } from 'ml-spectra-processing';
     let max = xyMaxYPoint(spectrum);
-    expect(spectrum.y[9]).toBeCloseTo(0.15749, 4);
+    expect(spectrum.y[9]).toBeCloseTo(0.0625, 4);
     expect(max.x).toBe(10);
@@ -95,0 +95,0 @@ expect(max.y).toBe(1);

src/__tests__/SpectrumGenerator.shapes.test.js

@@ -0,1 +1,2 @@
+import { Lorentzian } from 'ml-peak-shape-generator';
 import { xyMaxYPoint } from 'ml-spectra-processing';
@@ -39,4 +40,4 @@
     const ys = spectrum.y;
-    expect(ys[30]).toBe(10);
-    expect(ys[70]).toBe(10);
+    expect(ys[30]).toBeCloseTo(10 + 10 * Lorentzian.fct(3 - 7, 1), 7);
+    expect(ys[70]).toBeCloseTo(10, 7);
 
@@ -88,5 +89,5 @@ expect(ys[31] !== ys[71]).toBe(true);
     let max = xyMaxYPoint(spectrum);
-    expect(spectrum.y[49]).toBeCloseTo(0.5, 10);
+    expect(spectrum.y[49]).toBeCloseTo(0.5, 2);
     expect(max.x).toBe(2.5);
-    expect(max.y).toBe(2);
+    expect(max.y).toBeCloseTo(2, 3);
   });
@@ -140,6 +141,2 @@
           kind: 'lorentzian',
-          options: {
-            length: 13,
-            fwhm: 4,
-          },
         },
@@ -154,6 +151,2 @@ },
           kind: 'gaussian',
-          options: {
-            length: 13,
-            fwhm: 4,
-          },
         },
@@ -164,6 +157,6 @@ },
     let max = xyMaxYPoint(spectrum);
-    expect(spectrum.y[49]).toBeCloseTo(0.5, 10);
+    expect(spectrum.y[49]).toBeCloseTo(0.5, 2);
     expect(max.x).toBe(2.5);
-    expect(max.y).toBe(2);
+    expect(max.y).toBeCloseTo(2, 2);
   });
 });

src/__tests__/SpectrumGenerator.test.js

@@ -0,1 +1,3 @@
+import { Gaussian } from 'ml-peak-shape-generator';
+
 import { SpectrumGenerator } from '..';
@@ -49,9 +51,13 @@
     });
-    generator.addPeak([50, 100], { widthLeft: 10, widthRight: 30 });
+    generator.addPeak([50, 100], { widthLeft: 10, widthRight: 30, factor: 15 });
     const spectrum = generator.getSpectrum();
-
     const sumX = spectrum.x.reduce((previous, value) => previous + value);
     const sumY = spectrum.y.reduce((previous, value) => previous + value);
     expect(sumX).toBe(10050);
-    expect(sumY).toBeCloseTo(4257.612789255516, 4);
+    expect(sumY * generator.interval).toBeCloseTo(
+      (Gaussian.getArea(10, { height: 100 }) +
+        Gaussian.getArea(30, { height: 100 })) /
+        2,
+      0,
+    );
   });
@@ -90,3 +96,3 @@
     for (let i = 0; i < nPoints / 2; i++) {
-      expect(spectrum.y[i]).toBe(spectrum.y[nPoints - 1 - i]);
+      expect(spectrum.y[i]).toBeCloseTo(spectrum.y[nPoints - 1 - i], 7);
       expect(spectrum.y[i]).toBeLessThan(2);
@@ -108,6 +114,6 @@ }
 
-    expect(spectrum.y[0]).toBe(1);
-    expect(spectrum.y[50 * 10]).toBe(12);
-    expect(spectrum.y[100 * 10]).toBe(10);
-    expect(spectrum.y[14 * 10]).toBe(2);
+    expect(spectrum.y[0]).toBeCloseTo(1, 3);
+    expect(spectrum.y[50 * 10]).toBeCloseTo(12, 3);
+    expect(spectrum.y[100 * 10]).toBeCloseTo(10, 3);
+    expect(spectrum.y[14 * 10]).toBeCloseTo(2, 3);
   });
@@ -127,6 +133,6 @@
 
-    expect(spectrum.y[0]).toBe(1);
-    expect(spectrum.y[50 * 10]).toBe(12);
-    expect(spectrum.y[100 * 10]).toBe(10);
-    expect(spectrum.y[14 * 10]).toBe(2);
+    expect(spectrum.y[0]).toBeCloseTo(1, 3);
+    expect(spectrum.y[50 * 10]).toBeCloseTo(12, 3);
+    expect(spectrum.y[100 * 10]).toBeCloseTo(10, 3);
+    expect(spectrum.y[14 * 10]).toBeCloseTo(2, 3);
   });
@@ -142,7 +148,7 @@
     const spectrum = generator.getSpectrum();
-
-    expect(spectrum.y[0]).toBe(1);
-    expect(spectrum.y[50 * 10]).toBe(12);
-    expect(spectrum.y[100 * 10]).toBe(10);
-    expect(spectrum.y[14 * 10]).toBe(2);
+    // console.log(spectrum)
+    expect(spectrum.y[0]).toBeCloseTo(1, 3);
+    expect(spectrum.y[50 * 10]).toBeCloseTo(12, 3);
+    expect(spectrum.y[100 * 10]).toBeCloseTo(10, 3);
+    expect(spectrum.y[14 * 10]).toBeCloseTo(2, 3);
   });
@@ -149,0 +155,0 @@

src/index.js

@@ -1,4 +0,2 @@
-import normed from 'ml-array-normed';
-import { getShape } from 'ml-peak-shape-generator';
-import objectHash from 'object-hash';
+import { getShapeGenerator } from 'ml-peak-shape-generator';
 
@@ -8,5 +6,2 @@ import addBaseline from './util/addBaseline.js';
 
-let shapesCache = {};
-const MAX_CACHE_LENGTH = 20;
-
 export class SpectrumGenerator {
@@ -23,6 +18,2 @@ constructor(options = {}) {
           kind: 'gaussian',
-          options: {
-            fwhm: 1000,
-            length: 5001,
-          },
         },
@@ -32,2 +23,3 @@ },
     );
+
     this.from = options.from;
@@ -39,4 +31,6 @@ this.to = options.to;
     this.maxPeakHeight = Number.MIN_SAFE_INTEGER;
-    this.shape = createShape(options.shape.kind, options.shape.options);
 
+    let shapeGenerator = getShapeGenerator(options.shape);
+    this.shape = shapeGenerator;
+
     assertNumber(this.from, 'from');
@@ -117,4 +111,4 @@ assertNumber(this.to, 'to');
 
-    const shape = shapeOptions
-      ? createShape(shapeOptions.kind, shapeOptions.options)
+    let shapeGenerator = shapeOptions
+      ? getShapeGenerator(shapeOptions)
       : this.shape;
@@ -125,5 +119,10 @@
 
-    const firstValue = xPosition - (widthLeft / 2) * shape.factor;
-    const lastValue = xPosition + (widthRight / 2) * shape.factor;
+    let factor =
+      options.factor === undefined
+        ? shapeGenerator.getFactor()
+        : options.factor;
 
+    const firstValue = xPosition - (widthLeft / 2) * factor;
+    const lastValue = xPosition + (widthRight / 2) * factor;
+
     const firstPoint = Math.max(
@@ -141,19 +140,10 @@ 0,
 
+    shapeGenerator.setFWHM(widthLeft);
     for (let index = firstPoint; index < Math.max(middlePoint, 0); index++) {
-      let ratio = ((xPosition - this.data.x[index]) / widthLeft) * 2;
+      this.data.y[index] +=
+        intensity * shapeGenerator.fct(this.data.x[index] - xPosition);
+    }
 
-      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
+    shapeGenerator.setFWHM(widthRight);
     for (
@@ -164,16 +154,4 @@ let index = Math.min(middlePoint, lastPoint);
     ) {
-      let ratio = ((this.data.x[index] - xPosition) / widthRight) * 2;
-
-      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;
-      }
+      this.data.y[index] +=
+        intensity * shapeGenerator.fct(this.data.x[index] - xPosition);
     }
@@ -256,28 +234,1 @@
 }
-
-function createShape(kind, options) {
-  const hash = objectHash({ kind, options });
-  if (shapesCache[hash]) {
-    return shapesCache[hash];
-  }
-
-  let shape = {};
-
-  let newShape = getShape(kind, options);
-
-  shape.data = normed(newShape.data, {
-    algorithm: 'max',
-  });
-  shape.fwhm = newShape.fwhm;
-  shape.factor = (newShape.data.length - 1) / newShape.fwhm;
-  shape.length = newShape.data.length;
-  shape.halfLength = Math.floor(newShape.data.length / 2);
-
-  if (Object.keys(shapesCache > MAX_CACHE_LENGTH)) {
-    shapesCache = {};
-  }
-
-  shapesCache[hash] = shape;
-
-  return shape;
-}

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Improved metrics

Dependency count

3

decreased by-40%

Worsened metrics

Total package byte prevSize

48046

decreased by-5.52%

Lines of code

1231

decreased by-6.67%

Dependency changes

• + Addedcompute-array-constructors@1.0.1(transitive)

• + Addedcompute-array-dtype@1.0.1(transitive)

• + Addedcompute-dtype@1.0.0(transitive)

• + Addedcompute-erfinv@3.0.1(transitive)

• + Addedcompute-indexspace@1.0.1(transitive)

• + Addedcompute-polynomial@1.1.0(transitive)

• + Addedconst-max-uint32@1.0.2(transitive)

• + Addedconst-pinf-float64@1.0.0(transitive)

• + Addeddstructs-array-constructors@1.0.2(transitive)

• + Addeddstructs-array-dtype@1.0.2(transitive)

• + Addeddstructs-cast-arrays@1.0.3(transitive)

• + Addeddstructs-matrix@2.1.2(transitive)

• + Addedml-peak-shape-generator@0.11.0(transitive)

• + Addedobject-keys@1.1.1(transitive)

• + Addedregex-regex@1.0.0(transitive)

• + Addedtype-name@1.1.02.0.2(transitive)

• + Addedutils-copy@1.1.1(transitive)

• + Addedutils-copy-error@1.0.1(transitive)

• + Addedutils-deep-get@1.0.0(transitive)

• + Addedutils-deep-set@1.0.1(transitive)

• + Addedutils-indexof@1.0.0(transitive)

• + Addedutils-regex-from-string@1.0.0(transitive)

• + Addedvalidate.io-array@1.0.6(transitive)

• + Addedvalidate.io-array-like@1.0.2(transitive)

• + Addedvalidate.io-boolean-primitive@1.0.0(transitive)

• + Addedvalidate.io-buffer@1.0.2(transitive)

• + Addedvalidate.io-contains@1.0.0(transitive)

• + Addedvalidate.io-function@1.0.2(transitive)

• + Addedvalidate.io-integer@1.0.5(transitive)

• + Addedvalidate.io-integer-primitive@1.0.0(transitive)

• + Addedvalidate.io-matrix-like@1.0.2(transitive)

• + Addedvalidate.io-nan@1.0.3(transitive)

• + Addedvalidate.io-nan-primitive@1.0.0(transitive)

• + Addedvalidate.io-nonnegative-integer@1.0.0(transitive)

• + Addedvalidate.io-nonnegative-integer-array@1.0.1(transitive)

• + Addedvalidate.io-number@1.0.3(transitive)

• + Addedvalidate.io-number-primitive@1.0.0(transitive)

• + Addedvalidate.io-number-primitive-array@1.0.0(transitive)

• + Addedvalidate.io-object@1.0.4(transitive)

• + Addedvalidate.io-string-primitive@1.0.1(transitive)

• + Addedvalidate.io-typed-array-like@1.0.1(transitive)

• - Removedml-array-normed@^1.3.2

• - Removedobject-hash@^2.0.3

• - Removedis-any-array@2.0.1(transitive)

• - Removedml-array-max@1.2.4(transitive)

• - Removedml-array-normed@1.3.7(transitive)

• - Removedml-array-sum@1.1.6(transitive)

• - Removedml-peak-shape-generator@0.10.2(transitive)

• - Removedobject-hash@2.2.0(transitive)

• Updatedml-peak-shape-generator@^0.11.0