spectrum-generator - npm Package Compare versions

Comparing version 4.6.0 to 4.7.0

CHANGELOG.md

 # Changelog
 
+## [4.7.0](https://www.github.com/cheminfo/spectrum-generator/compare/v4.6.0...v4.7.0) (2021-01-06)
+
+
+### Features
+
+* Use gaussian ration directly from peaks ([#28](https://www.github.com/cheminfo/spectrum-generator/issues/28)) ([36e1051](https://www.github.com/cheminfo/spectrum-generator/commit/36e1051171aa1bd59821f8d116dec81137231fc4))
+
 ## [4.6.0](https://www.github.com/cheminfo/spectrum-generator/compare/v4.5.0...v4.6.0) (2020-12-11)
@@ -4,0 +11,0 @@

lib/index.js

@@ -64,2 +64,13 @@ 'use strict';
 class SpectrumGenerator {
+  /**
+   *
+   * @param {object} [options={}]
+   * @param {number} [options.from=0]
+   * @param {number} [options.to=0]
+   * @param {function} [options.nbPoints=10001]
+   * @param {number} [options.factor] default value depends of the shape in order to cover 99.99% of the surface
+   * @param {object} [options.shape={kind:'gaussian'}]
+   * @param {string} [options.shape.kind] kind of shape, gaussian, lorentzian or pseudovoigt
+   * @param {object} [options.shape.options] options for the shape (like `mu` for pseudovoigt)
+   */
   constructor(options = {}) {
@@ -132,2 +143,7 @@ options = Object.assign(
 
+  /**
+   *
+   * @param {[x,y]|[x,y,w]|{x,y,width}} [peak]
+   * @param {*} options
+   */
   addPeak(peak, options = {}) {
@@ -148,4 +164,5 @@ if (
     let peakWidth;
+    let peakOptions;
     if (Array.isArray(peak)) {
-      [xPosition, intensity, peakWidth] = peak;
+      [xPosition, intensity, peakWidth, peakOptions] = peak;
     } else {
@@ -155,2 +172,3 @@ xPosition = peak.x;
       peakWidth = peak.width;
+      peakOptions = peak.options;
     }
@@ -169,2 +187,6 @@
 
+    if (peakOptions) {
+      Object.assign(shapeOptions || {}, peakOptions || {});
+    }
+
     let shapeGenerator = shapeOptions
@@ -171,0 +193,0 @@ ? mlPeakShapeGenerator.getShapeGenerator(shapeOptions)

package.json

 {
   "name": "spectrum-generator",
-  "version": "4.6.0",
+  "version": "4.7.0",
   "description": "generate a spectrum from discrete peaks",
@@ -53,2 +53,3 @@ "main": "lib/index.js",
     "jest": "^26.6.3",
+    "ml-savitzky-golay-generalized": "^2.0.3",
     "ml-spectra-processing": "^4.10.0",
@@ -55,0 +56,0 @@ "pnpm": "^5.13.5",

README.md

@@ -7,8 +7,4 @@ # spectrum-generator
 
-Generates a spectrum from discrete peaks. The shape of the peaks can be customised.
+Generates a spectrum from discrete peaks. The shape of the peaks can be customized.
 
-In order to increase the speed a `shape` is first generated and then the peaks in the final
-spectrum are resulting from sampling the `shape`. A `shape` will therefore be generated with
-much more points (typically fwhm:1000).
-
 The shape is generated using [ml-peak-shape-generator](https://github.com/mljs/peak-shape-generator) and you may use all the corresponding [options](https://mljs.github.io/peak-shape-generator/#getshape) of getShape.
@@ -22,5 +18,2 @@
 
-The spectrum generator takes an array of discrete peaks (value and intensity)
-and generates peaks with a gaussian distribution (by default).
-
 ### generateSpectrum
@@ -41,2 +34,6 @@
   nbPoints: 10001, // default value: 10001
+  factor: 3, // default value would covers 99.99% of the surface and depends on the shape
+  shape: {
+    kind: 'gaussian', // default value is gaussian
+  },
 });
@@ -61,2 +58,3 @@ ```
 - const peaks = {x:[1,2,3,4], y:[10,30,1,76]}
+- const peaks = [ [1,10,5], [2,30,10] ] // third argument is the peak width
 */
@@ -70,6 +68,2 @@
     kind: 'lorentzian',
-    options: {
-      fwhm: 1000,
-      length: 10001,
-    },
   },
@@ -98,7 +92,5 @@ });
   width: 0.1, // width of peak is FWHM
+  factor: 10, // 10 times fwhm. Lorentzian are rather flat
   shape: {
     kind: 'lorentzian',
-    options: {
-      factor: 10, // 10 times fwhm. Lorentzian are rather flat
-    },
   }
@@ -113,6 +105,2 @@ });
     kind: 'gaussian',
-    options: {
-      fwhm: 1000,
-      length: 10001,
-    },
   }
@@ -119,0 +107,0 @@ });

src/__tests__/generateSpectrum.test.js

@@ -64,3 +64,2 @@ import { xyMaxYPoint } from 'ml-spectra-processing';
         options: {
-          length: 17,
           fwhm: 4,
@@ -87,3 +86,2 @@ },
         options: {
-          length: 10,
           fwhm: 3,
@@ -107,6 +105,2 @@ },
         kind: 'gaussian',
-        options: {
-          fwhm: 4,
-          length: 13,
-        },
       },
@@ -128,6 +122,2 @@ });
         kind: 'gaussian',
-        options: {
-          fwhm: 500,
-          length: 1501,
-        },
       },
@@ -134,0 +124,0 @@ });

src/__tests__/SpectrumGenerator.shapes.test.js

@@ -15,6 +15,2 @@ import { Lorentzian } from 'ml-peak-shape-generator';
         kind: 'gaussian',
-        options: {
-          fwhm: 1000,
-          length: 5001,
-        },
       },
@@ -30,6 +26,2 @@ });
           kind: 'lorentzian',
-          options: {
-            fwhm: 1000,
-            length: 5001,
-          },
         },
@@ -48,2 +40,46 @@ },
 
+  it('full generation with {x,y}', () => {
+    const generator = new SpectrumGenerator({
+      from: 0,
+      to: 10,
+      nbPoints: 101,
+      peakWidthFct: () => 1,
+      shape: {
+        kind: 'gaussian',
+      },
+    });
+
+    generator.addPeak({
+      x: 3,
+      y: 10,
+      options: { kind: 'pseudovoigt', options: { mu: 1 } },
+    });
+
+    generator.addPeak(
+      { x: 7, y: 5 },
+      {
+        shape: {
+          kind: 'lorentzian',
+        },
+      },
+    );
+
+    generator.addPeak(
+      { x: 7, y: 5, options: { options: { mu: 0 } } },
+      {
+        shape: {
+          kind: 'pseudovoigt',
+        },
+      },
+    );
+
+    const spectrum = generator.getSpectrum();
+
+    const ys = spectrum.y;
+    expect(ys[30]).toBeCloseTo(10 + 10 * Lorentzian.fct(3 - 7, 1), 7);
+    expect(ys[70]).toBeCloseTo(10, 7);
+
+    expect(ys[31] !== ys[71]).toBe(true);
+  });
+
   it('second test', () => {
@@ -57,6 +93,2 @@ let spectrumGenerator = new SpectrumGenerator({
         kind: 'lorentzian',
-        options: {
-          length: 13,
-          fwhm: 4,
-        },
       },
@@ -83,6 +115,2 @@ });
           kind: 'gaussian',
-          options: {
-            length: 13,
-            fwhm: 4,
-          },
         },
@@ -132,6 +160,2 @@ },
         kind: 'lorentzian',
-        options: {
-          length: 13,
-          fwhm: 4,
-        },
       },
@@ -138,0 +162,0 @@ });

src/index.js

@@ -7,2 +7,13 @@ import { getShapeGenerator } from 'ml-peak-shape-generator';
 export class SpectrumGenerator {
+  /**
+   *
+   * @param {object} [options={}]
+   * @param {number} [options.from=0]
+   * @param {number} [options.to=0]
+   * @param {function} [options.nbPoints=10001]
+   * @param {number} [options.factor] default value depends of the shape in order to cover 99.99% of the surface
+   * @param {object} [options.shape={kind:'gaussian'}]
+   * @param {string} [options.shape.kind] kind of shape, gaussian, lorentzian or pseudovoigt
+   * @param {object} [options.shape.options] options for the shape (like `mu` for pseudovoigt)
+   */
   constructor(options = {}) {
@@ -75,2 +86,7 @@ options = Object.assign(
 
+  /**
+   *
+   * @param {[x,y]|[x,y,w]|{x,y,width}} [peak]
+   * @param {*} options
+   */
   addPeak(peak, options = {}) {
@@ -91,4 +107,5 @@ if (
     let peakWidth;
+    let peakOptions;
     if (Array.isArray(peak)) {
-      [xPosition, intensity, peakWidth] = peak;
+      [xPosition, intensity, peakWidth, peakOptions] = peak;
     } else {
@@ -98,2 +115,3 @@ xPosition = peak.x;
       peakWidth = peak.width;
+      peakOptions = peak.options;
     }
@@ -112,2 +130,6 @@
 
+    if (peakOptions) {
+      Object.assign(shapeOptions || {}, peakOptions || {});
+    }
+
     let shapeGenerator = shapeOptions
@@ -114,0 +136,0 @@ ? getShapeGenerator(shapeOptions)

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Improved metrics

Total package byte prevSize

50353

increased by4.04%

Lines of code

1280

increased by3.98%

Worsened metrics

Dev dependency count

16

increased by6.67%

Number of lines in readme file

116

decreased by-9.37%

No dependency changes