ml-peak-shape-generator - npm Package Compare versions

Comparing version 0.12.0 to 0.13.0

CHANGELOG.md

 # Changelog
 
+## [0.13.0](https://www.github.com/mljs/peak-shape-generator/compare/v0.12.0...v0.13.0) (2021-01-29)
+
+
+### Features
+
+* add gaussian2D class ([#37](https://www.github.com/mljs/peak-shape-generator/issues/37)) ([39ba7d9](https://www.github.com/mljs/peak-shape-generator/commit/39ba7d967690a51b4fb9482bf0338b652ec8bd2b))
+
 ## [0.12.0](https://www.github.com/mljs/peak-shape-generator/compare/v0.11.0...v0.12.0) (2020-12-11)
@@ -4,0 +11,0 @@

lib/index.js

@@ -29,3 +29,3 @@ 'use strict';
    * @param {object} [options = {}]
-   * @param {number} [options.height=x] Define the height of the peak, by default area=1 (normalized)
+   * @param {number} [options.height=4*LN2/(PI*FWHM)] Define the height of the peak, by default area=1 (normalized)
    * @param {number} [options.fwhm = 500] - Full Width at Half Maximum in the number of points in FWHM.
@@ -191,3 +191,3 @@ * @param {number} [options.sd] - Standard deviation, if it's defined options.fwhm will be ignored and the value will be computed sd * Math.sqrt(8 * Math.LN2);
    * @param {object} [options = {}]
-   * @param {number} [options.height=x] Define the height of the peak, by default area=1 (normalized)
+   * @param {number} [options.height=2/(PI*FWHM)] Define the height of the peak, by default area=1 (normalized)
    * @param {number} [options.fwhm = 500] - Full Width at Half Maximum in the number of points in FWHM.
@@ -344,3 +344,3 @@ * @param {number} [options.sd] - Standard deviation, if it's defined options.fwhm will be ignored and the value will be computed sd * Math.sqrt(8 * Math.LN2);
    * @param {object} [options={}]
-   * @param {number} [options.height=x] Define the height of the peak, by default area=1 (normalized)
+   * @param {number} [options.height=1/(mu*FWHM/sqrt(4*LN2/PI)+(1-mu)*fwhm*PI*0.5)] Define the height of the peak, by default area=1 (normalized)
    * @param {number} [options.fwhm=500] - Full Width at Half Maximum in the number of points in FWHM.
@@ -512,2 +512,216 @@ * @param {number} [options.mu=0.5] - ratio of gaussian contribution.
 
+let axis = ['x', 'y'];
+
+class Gaussian2D {
+  /**
+   * @param {object} [options = {}]
+   * @param {number} [options.height=4*LN2/(PI*xFWHM*yFWHM)] Define the height of the peak, by default area=1 (normalized).
+   * @param {number} [options.fwhm = 500] - Full Width at Half Maximum in the number of points in FWHM used if x or y has not the fwhm property.
+   * @param {object} [options.x] - Options for x axis.
+   * @param {number} [options.x.fwhm = fwhm] - Full Width at Half Maximum in the number of points in FWHM for x axis.
+   * @param {number} [options.x.sd] - Standard deviation for x axis, if it's defined options.x.fwhm will be ignored and the value will be computed sd * Math.sqrt(8 * Math.LN2);
+   * @param {object} [options.y] - Options for y axis.
+   * @param {number} [options.y.fwhm = fwhm] - Full Width at Half Maximum in the number of points in FWHM for y axis.
+   * @param {number} [options.y.sd] - Standard deviation for y axis, if it's defined options.y.fwhm will be ignored and the value will be computed sd * Math.sqrt(8 * Math.LN2);
+   */
+  constructor(options = {}) {
+    let { fwhm: globalFWHM = 500 } = options;
+
+    for (let i of axis) {
+      let fwhm;
+      if (!options[i]) {
+        fwhm = globalFWHM;
+      } else {
+        fwhm = options[i].sd
+          ? Gaussian2D.widthToFWHM(2 * options[i].sd)
+          : options[i].fwhm || globalFWHM;
+      }
+      this[i] = { fwhm };
+    }
+
+    this.height =
+      options.height === undefined
+        ? -GAUSSIAN_EXP_FACTOR / Math.PI / this.x.fwhm / this.y.fwhm
+        : options.height;
+  }
+  /**
+   * Calculate a Gaussian2D shape
+   * @param {object} [options = {}]
+   * @param {number} [options.factor] - Number of time to take fwhm to calculate length. Default covers 99.99 % of area.
+   * @param {object} [options.x] - parameter for x axis.
+   * @param {number} [options.x.length=fwhm*factor+1] - length on x axis.
+   * @param {number} [options.x.factor=factor] - Number of time to take fwhm to calculate length. Default covers 99.99 % of area.
+   * @param {object} [options.y] - parameter for y axis.
+   * @param {number} [options.y.length=fwhm*factor+1] - length on y axis.
+   * @param {number} [options.y.factor=factor] - Number of time to take fwhm to calculate length. Default covers 99.99 % of area.
+   * @return {Array<Float64Array>} - z values.
+   */
+
+  getData(options = {}) {
+    let { x = {}, y = {}, factor = this.getFactor(), length } = options;
+
+    let xLength = x.length || length;
+    if (!xLength) {
+      let { factor: xFactor = factor } = x;
+      xLength = Math.min(Math.ceil(this.x.fwhm * xFactor), Math.pow(2, 25) - 1);
+      if (xLength % 2 === 0) xLength++;
+    }
+
+    let yLength = y.length || length;
+    if (!yLength) {
+      let { factor: yFactor = factor } = y;
+      yLength = Math.min(Math.ceil(this.y.fwhm * yFactor), Math.pow(2, 25) - 1);
+      if (yLength % 2 === 0) yLength++;
+    }
+
+    const xCenter = (xLength - 1) / 2;
+    const yCenter = (yLength - 1) / 2;
+    const data = new Array(xLength);
+    for (let i = 0; i < xLength; i++) {
+      data[i] = new Array(yLength);
+    }
+
+    for (let i = 0; i < xLength; i++) {
+      for (let j = 0; j < yLength; j++) {
+        data[i][j] = this.fct(i - xCenter, j - yCenter) * this.height;
+      }
+    }
+
+    return data;
+  }
+
+  /**
+   * Return the intensity value of a 2D gaussian shape (see README for equation).
+   * @param {number} x - x value to calculate.
+   * @param {number} y - y value to calculate.
+   * @returns {number} - the z value of bi-dimensional gaussian with the current parameters.
+   */
+  fct(x, y) {
+    return Gaussian2D.fct(x, y, this.x.fwhm, this.y.fwhm);
+  }
+
+  /**
+   * Calculate the number of times FWHM allows to reach a specific volume coverage.
+   * @param {number} [volume=0.9999]
+   * @returns {number}
+   */
+  getFactor(volume = 0.9999) {
+    return Gaussian2D.getFactor(volume);
+  }
+
+  /**
+   * Calculate the volume of the shape.
+   * @returns {number} - returns the volume.
+   */
+
+  getVolume() {
+    return Gaussian2D.getVolume(this.x.fwhm, this.y.fwhm, {
+      height: this.height,
+    });
+  }
+
+  /**
+   * Compute the value of Full Width at Half Maximum (FWHM) from the width between the inflection points.
+   * //https://mathworld.wolfram.com/Gaussian2DFunction.html
+   * @param {number} width - Width between the inflection points
+   * @returns {number} fwhm
+   */
+  widthToFWHM(width) {
+    //https://mathworld.wolfram.com/Gaussian2DFunction.html
+    return Gaussian2D.widthToFWHM(width);
+  }
+
+  /**
+   * Compute the value of width between the inflection points from Full Width at Half Maximum (FWHM).
+   * //https://mathworld.wolfram.com/Gaussian2DFunction.html
+   * @param {number} fwhm - Full Width at Half Maximum.
+   * @returns {number} width
+   */
+  fwhmToWidth(fwhm = this.x.fwhm) {
+    return Gaussian2D.fwhmToWidth(fwhm);
+  }
+
+  /**
+   * set a new full width at half maximum
+   * @param {number} fwhm - full width at half maximum
+   * @param {string|Array<string>} axisLabel - label of axis, if it is undefined fwhm is set to both axis.
+   */
+  setFWHM(fwhm, axisLabel) {
+    if (!axisLabel) axisLabel = axis;
+    if (!Array.isArray(axisLabel)) axisLabel = [axisLabel];
+    for (let i of axisLabel) {
+      let axisName = i.toLowerCase();
+      if (axisName !== 'y' && axisName !== 'x') {
+        throw new Error('axis label should be x or y');
+      }
+      this[axisName].fwhm = fwhm;
+    }
+  }
+
+  /**
+   * set a new height
+   * @param {number} height - The maximal intensity of the shape.
+   */
+  setHeight(height) {
+    this.height = height;
+  }
+}
+
+/**
+ * Return a parameterized function of a Gaussian2D shape (see README for equation).
+ * @param {number} x - x value to calculate.
+ * @param {number} y - y value to calculate.
+ * @param {number} fwhmX - full width half maximum in the x axis.
+ * @param {number} fwhmY - full width half maximum in the y axis.
+ * @returns {number} - the z value of bi-dimensional gaussian with the current parameters.
+ */
+Gaussian2D.fct = function fct(x, y, xFWHM = 500, yFWHM = 500) {
+  return Math.exp(
+    GAUSSIAN_EXP_FACTOR * (Math.pow(x / xFWHM, 2) + Math.pow(y / yFWHM, 2)),
+  );
+};
+
+/**
+ * Compute the value of Full Width at Half Maximum (FWHM) from the width between the inflection points.
+ * //https://mathworld.wolfram.com/Gaussian2DFunction.html
+ * @param {number} width - Width between the inflection points
+ * @returns {number} fwhm
+ */
+Gaussian2D.widthToFWHM = function widthToFWHM(width) {
+  return width * ROOT_2LN2;
+};
+
+/**
+ * Compute the value of width between the inflection points from Full Width at Half Maximum (FWHM).
+ * //https://mathworld.wolfram.com/Gaussian2DFunction.html
+ * @param {number} fwhm - Full Width at Half Maximum.
+ * @returns {number} width
+ */
+Gaussian2D.fwhmToWidth = function fwhmToWidth(fwhm) {
+  return fwhm / ROOT_2LN2;
+};
+
+/**
+ * Calculate the volume of a specific shape.
+ * @param {number} xFWHM - Full width at half maximum for x axis.
+ * @param {number} yFWHM - Full width at half maximum for y axis.
+ * @param {object} [options = {}] - options.
+ * @param {number} [options.height = 1] - Maximum z value of the shape.
+ * @returns {number} - returns the area of the specific shape and parameters.
+ */
+
+Gaussian2D.getVolume = function getVolume(xFWHM, yFWHM, options = {}) {
+  let { height = 1 } = options;
+  return (height * Math.PI * xFWHM * yFWHM) / Math.LN2 / 4;
+};
+
+/**@TODO look for a better factor
+ * Calculate the number of times FWHM allows to reach a specific volume coverage.
+ * @param {number} [volume=0.9999]
+ * @returns {number}
+ */
+Gaussian2D.getFactor = function getFactor(volume = 0.9999) {
+  return Math.sqrt(2) * erfinv(volume);
+};
+
 function getShapeGenerator(options) {
@@ -522,2 +736,4 @@ let { kind = 'Gaussian', options: shapeOptions } = options;
       return new PseudoVoigt(shapeOptions);
+    case 'gaussian2d':
+      return new Gaussian2D(shapeOptions);
     default:
@@ -529,4 +745,5 @@ throw new Error(`Unknown kind: ${kind}`);
 exports.Gaussian = Gaussian;
+exports.Gaussian2D = Gaussian2D;
 exports.Lorentzian = Lorentzian;
 exports.PseudoVoigt = PseudoVoigt;
 exports.getShapeGenerator = getShapeGenerator;

package.json

 {
   "name": "ml-peak-shape-generator",
-  "version": "0.12.0",
+  "version": "0.13.0",
   "description": "",
@@ -5,0 +5,0 @@ "main": "lib/index.js",

src/classes/Gaussian.js

@@ -11,3 +11,3 @@ import {
    * @param {object} [options = {}]
-   * @param {number} [options.height=x] Define the height of the peak, by default area=1 (normalized)
+   * @param {number} [options.height=4*LN2/(PI*FWHM)] Define the height of the peak, by default area=1 (normalized)
    * @param {number} [options.fwhm = 500] - Full Width at Half Maximum in the number of points in FWHM.
@@ -14,0 +14,0 @@ * @param {number} [options.sd] - Standard deviation, if it's defined options.fwhm will be ignored and the value will be computed sd * Math.sqrt(8 * Math.LN2);

src/classes/Lorentzian.js

@@ -6,3 +6,3 @@ import { ROOT_THREE } from '../util/constants';
    * @param {object} [options = {}]
-   * @param {number} [options.height=x] Define the height of the peak, by default area=1 (normalized)
+   * @param {number} [options.height=2/(PI*FWHM)] Define the height of the peak, by default area=1 (normalized)
    * @param {number} [options.fwhm = 500] - Full Width at Half Maximum in the number of points in FWHM.
@@ -9,0 +9,0 @@ * @param {number} [options.sd] - Standard deviation, if it's defined options.fwhm will be ignored and the value will be computed sd * Math.sqrt(8 * Math.LN2);

src/classes/PseudoVoigt.js

@@ -13,3 +13,3 @@ import {
    * @param {object} [options={}]
-   * @param {number} [options.height=x] Define the height of the peak, by default area=1 (normalized)
+   * @param {number} [options.height=1/(mu*FWHM/sqrt(4*LN2/PI)+(1-mu)*fwhm*PI*0.5)] Define the height of the peak, by default area=1 (normalized)
    * @param {number} [options.fwhm=500] - Full Width at Half Maximum in the number of points in FWHM.
@@ -16,0 +16,0 @@ * @param {number} [options.mu=0.5] - ratio of gaussian contribution.

src/index.js

 export * from './classes/Gaussian';
 export * from './classes/Lorentzian';
 export * from './classes/PseudoVoigt';
+export * from './classes/Gaussian2D';
 export * from './util/getShapeGenerator';

src/util/getShapeGenerator.js

 import { Gaussian } from '../classes/Gaussian';
+import { Gaussian2D } from '../classes/Gaussian2D';
 import { Lorentzian } from '../classes/Lorentzian';
@@ -14,2 +15,4 @@ import { PseudoVoigt } from '../classes/PseudoVoigt';
       return new PseudoVoigt(shapeOptions);
+    case 'gaussian2d':
+      return new Gaussian2D(shapeOptions);
     default:
@@ -16,0 +19,0 @@ throw new Error(`Unknown kind: ${kind}`);

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increased by32.89%

Number of package files

13

increased by8.33%

Lines of code

1334

increased by41.16%

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