ml-spectra-fitting - npm Package Compare versions

Comparing version 0.3.2 to 0.5.0

CHANGELOG.md

 # Changelog
 
+## [0.5.0](https://www.github.com/mljs/spectra-fitting/compare/v0.4.0...v0.5.0) (2020-11-06)
+
+
+### Features
+
+* optimize gaussian, lorentzian or pseudovoight ([a756ff7](https://www.github.com/mljs/spectra-fitting/commit/a756ff72a25661a6778ce4908b176c4bf8df5b63))
+* OptimizeLorentzianTrain and OptimizeGaussianTrain ([1650873](https://www.github.com/mljs/spectra-fitting/commit/165087356a10a1dce453a29b94700e07735b9f40))
+* update peak-shape-generator ([a76be80](https://www.github.com/mljs/spectra-fitting/commit/a76be80094b0599c78383b8469cb56b986b75bea))
+
+
+### Bug Fixes
+
+* add missing build script ([42e4ce3](https://www.github.com/mljs/spectra-fitting/commit/42e4ce3ced85258933164de586ceb238101a2353))
+* boundaries array bug ([#13](https://www.github.com/mljs/spectra-fitting/issues/13)) ([6c822e1](https://www.github.com/mljs/spectra-fitting/commit/6c822e14f25c5b091890cee750f34f7dd45bf136))
+* remove docs ([a625ee6](https://www.github.com/mljs/spectra-fitting/commit/a625ee645ca09bc923141238d24415650c844f09))
+* update dependencies to fix web compatibility ([2113eef](https://www.github.com/mljs/spectra-fitting/commit/2113eef2079032ea27fcd7ecf0388625d36687cb))
+
 ### [0.3.2](https://www.github.com/mljs/spectra-fitting/compare/v0.3.1...v0.3.2) (2020-11-04)
@@ -4,0 +21,0 @@

lib/index.js

@@ -27,9 +27,9 @@ 'use strict';
     for (let i = 0; i < nL; i++) {
-      let func = mlPeakShapeGenerator.pseudovoigtFct({
-        x: p[i],
-        y: p[i + nL],
-        width: p[i + nL * 2],
-        mu: p[i + nL * 3],
-      });
-      result += func(t);
+      result += mlPeakShapeGenerator.pseudovoigtFct(
+        p[i],
+        p[i + nL],
+        p[i + nL * 2],
+        p[i + nL * 3],
+        t,
+      );
     }
@@ -53,8 +53,3 @@ return result;
     for (let i = 0; i < nL; i++) {
-      let func = mlPeakShapeGenerator.gaussianFct({
-        x: p[i],
-        y: p[i + nL],
-        width: p[i + nL * 2],
-      });
-      result += func(t);
+      result += mlPeakShapeGenerator.gaussianFct(p[i], p[i + nL], p[i + nL * 2], t);
     }
@@ -78,8 +73,3 @@ return result;
     for (let i = 0; i < nL; i++) {
-      let func = mlPeakShapeGenerator.lorentzianFct({
-        x: p[i],
-        y: p[i + nL],
-        width: p[i + nL * 2],
-      });
-      result += func(t);
+      result += mlPeakShapeGenerator.lorentzianFct(p[i], p[i + nL], p[i + nL * 2], t);
     }
@@ -97,3 +87,3 @@ return result;
  * Fits a set of points to the sum of a set of bell functions.
- * @param {Object} input - An object containing the x and y data to be fitted.
+ * @param {Object} data - An object containing the x and y data to be fitted.
  * @param {Array} peakList - A list of initial parameters to be optimized. e.g. coming from a peak picking [{x, y, width}].
@@ -108,4 +98,9 @@ * @param {Object} [options = {}]
 
+  let x = data.x;
   let maxY = getMaxValue__default['default'](data.y);
-  data.y.forEach((_, i, arr) => (arr[i] /= maxY));
+  let y = data.y.map((e) => (e /= maxY));
+  let peaks = peakList.map((peak) => {
+    peak.y /= maxY;
+    return peak;
+  });
 
@@ -131,3 +126,3 @@ let nbParams;
 
-  let nL = peakList.length;
+  let nL = peaks.length;
   let pInit = new Float64Array(nL * nbParams);
@@ -139,3 +134,3 @@ let pMin = new Float64Array(nL * nbParams);
   for (let i = 0; i < nL; i++) {
-    let peak = peakList[i];
+    let peak = peaks[i];
     for (let s = 0; s < nbParams; s++) {
@@ -160,3 +155,3 @@ pInit[i + s * nL] = getValue(s, peak, STATE_INIT, dt);
   );
-  let pFit = LM__default['default'](data, paramsFunc, lmOptions);
+  let pFit = LM__default['default']({ x, y }, paramsFunc, lmOptions);
 
@@ -188,3 +183,3 @@ let { parameterError: error, iterations } = pFit;
     case 1:
-      value = key === STATE_INIT ? 1 : key === STATE_MIN ? 0 : 1.5;
+      value = key === STATE_INIT ? peak.y : key === STATE_MIN ? 0 : 1.5;
       break;
@@ -191,0 +186,0 @@ case 2:

package.json

 {
   "name": "ml-spectra-fitting",
-  "version": "0.3.2",
-  "description": "Fit spectra using guassian or lorentzian",
+  "version": "0.5.0",
+  "description": "Fit spectra using gaussian or lorentzian",
   "main": "lib/index.js",
@@ -29,3 +29,4 @@ "module": "src/index.js",
     "Lorentzian",
-    "Guassian"
+    "Gaussian",
+    "pseudovoigt"
   ],
@@ -62,7 +63,8 @@ "author": "Andres Castillo",
   "dependencies": {
+    "esm": "^3.2.25",
     "ml-array-max": "^1.2.0",
     "ml-levenberg-marquardt": "^2.1.1",
-    "ml-peak-shape-generator": "^0.6.1",
+    "ml-peak-shape-generator": "^0.7.0",
     "spectrum-generator": "^4.4.0"
   }
 }

README.md

@@ -1,2 +0,2 @@
-[![NPM version][npm-image]][npm-url] [![build status][travis-image]][travis-url] [![npm download][download-image]][download-url]
+[![NPM version][npm-image]][npm-url] [![npm download][download-image]][download-url]
 
@@ -7,3 +7,3 @@ # ml-spectra-fitting
 
-This is spectra fitting package optimize the position (x), max intensity (y), full width at half maximum (width) and the percent of gaussian (mu). It supports three kind of shapes:
+This is a spectra fitting package to optimize the position (x), max intensity (y), full width at half maximum (FWHM = width) and the ratio of gaussian contribution (mu) if it's required. It supports three kind of shapes:
 
@@ -18,3 +18,3 @@ | Name         |                                                                                                                            Equation                                                                                                                             |
 
-| <img src="https://tex.cheminfo.org/?tex=%5Cdelta%20%3D%20%5Cleft(t%20-%20x%5Cright)%5E2%0A"/> | <img src="https://tex.cheminfo.org/?tex=%5Csigma%20%3D%20%5Cfrac%7Bwidth%7D%7B2%5Csqrt%7B2%20%5Ccdot%20Log(2)%7D%7D"/> | <img src="https://tex.cheminfo.org/?tex=%5Cgamma%3D%5Cleft(width%5Cright)%5E2"/> |
+| <img src="https://tex.cheminfo.org/?tex=%5Cdelta%20%3D%20%5Cleft(t%20-%20x%5Cright)%5E2%0A"/> | <img src="https://tex.cheminfo.org/?tex=%5Csigma%20%3D%20%5Cfrac%7Bwidth%7D%7B2%5Csqrt%7B2%20%5Ccdot%20Ln(2)%7D%7D"/> | <img src="https://tex.cheminfo.org/?tex=%5Cgamma%3D%5Cleft(width%5Cright)%5E2"/> |
 | --------------------------------------------------------------------------------------------- | :--------------------------------------------------------------------------------------------------------------------: | :--------------------------------------------------------------------------------------------------- |
@@ -59,7 +59,7 @@
 
-// the function recive a peaklist with {x, y, width} as a guess
-// and return a list of objects
+// the function receive an array of peaks {x, y, width} as a guess
+// and returns an array of peaks
 
-let fittedParams = optimize(data, peakList);
-console.log(fittedParams);
+let fittedPeaks = optimize(data, peakList);
+console.log(fittedPeaks);
 /**
@@ -164,5 +164,3 @@ {
 [npm-url]: https://npmjs.org/package/ml-spectra-fitting
-[travis-image]: https://img.shields.io/travis/mljs/spectra-fitting/master.svg?style=flat-square
-[travis-url]: https://travis-ci.org/mljs/spectra-fitting
 [download-image]: https://img.shields.io/npm/dm/ml-spectra-fitting.svg?style=flat-square
 [download-url]: https://npmjs.org/package/ml-spectra-fitting

src/index.js

@@ -15,3 +15,3 @@ import getMaxValue from 'ml-array-max';
  * Fits a set of points to the sum of a set of bell functions.
- * @param {Object} input - An object containing the x and y data to be fitted.
+ * @param {Object} data - An object containing the x and y data to be fitted.
  * @param {Array} peakList - A list of initial parameters to be optimized. e.g. coming from a peak picking [{x, y, width}].
@@ -26,4 +26,9 @@ * @param {Object} [options = {}]
 
+  let x = data.x;
   let maxY = getMaxValue(data.y);
-  data.y.forEach((_, i, arr) => (arr[i] /= maxY));
+  let y = data.y.map((e) => (e /= maxY));
+  let peaks = peakList.map((peak) => {
+    peak.y /= maxY;
+    return peak;
+  });
 
@@ -49,3 +54,3 @@ let nbParams;
 
-  let nL = peakList.length;
+  let nL = peaks.length;
   let pInit = new Float64Array(nL * nbParams);
@@ -57,3 +62,3 @@ let pMin = new Float64Array(nL * nbParams);
   for (let i = 0; i < nL; i++) {
-    let peak = peakList[i];
+    let peak = peaks[i];
     for (let s = 0; s < nbParams; s++) {
@@ -78,3 +83,3 @@ pInit[i + s * nL] = getValue(s, peak, STATE_INIT, dt);
   );
-  let pFit = LM(data, paramsFunc, lmOptions);
+  let pFit = LM({ x, y }, paramsFunc, lmOptions);
 
@@ -106,3 +111,3 @@ let { parameterError: error, iterations } = pFit;
     case 1:
-      value = key === STATE_INIT ? 1 : key === STATE_MIN ? 0 : 1.5;
+      value = key === STATE_INIT ? peak.y : key === STATE_MIN ? 0 : 1.5;
       break;
@@ -109,0 +114,0 @@ case 2:

src/shapes/sumOfGaussianLorentzians.js

@@ -16,9 +16,9 @@ import { pseudovoigtFct } from 'ml-peak-shape-generator';
     for (let i = 0; i < nL; i++) {
-      let func = pseudovoigtFct({
-        x: p[i],
-        y: p[i + nL],
-        width: p[i + nL * 2],
-        mu: p[i + nL * 3],
-      });
-      result += func(t);
+      result += pseudovoigtFct(
+        p[i],
+        p[i + nL],
+        p[i + nL * 2],
+        p[i + nL * 3],
+        t,
+      );
     }
@@ -25,0 +25,0 @@ return result;

src/shapes/sumOfGaussians.js

@@ -15,8 +15,3 @@ import { gaussianFct } from 'ml-peak-shape-generator';
     for (let i = 0; i < nL; i++) {
-      let func = gaussianFct({
-        x: p[i],
-        y: p[i + nL],
-        width: p[i + nL * 2],
-      });
-      result += func(t);
+      result += gaussianFct(p[i], p[i + nL], p[i + nL * 2], t);
     }
@@ -23,0 +18,0 @@ return result;

src/shapes/sumOfLorentzians.js

@@ -16,8 +16,3 @@ import { lorentzianFct } from 'ml-peak-shape-generator';
     for (let i = 0; i < nL; i++) {
-      let func = lorentzianFct({
-        x: p[i],
-        y: p[i + nL],
-        width: p[i + nL * 2],
-      });
-      result += func(t);
+      result += lorentzianFct(p[i], p[i + nL], p[i + nL * 2], t);
     }
@@ -24,0 +19,0 @@ return result;

New alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Fixed alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Improved metrics

Total package byte prevSize

24615

increased by3.73%

Worsened metrics

Dependency count

5

increased by25%

Lines of code

424

decreased by-2.3%

Number of lines in readme file

163

decreased by-1.21%

Dependency changes

• + Addedesm@^3.2.25

• + Addedesm@3.2.25(transitive)

• + Addedml-peak-shape-generator@0.7.0(transitive)

• - Removedml-peak-shape-generator@0.6.1(transitive)

• Updatedml-peak-shape-generator@^0.7.0