ml-spectra-fitting - npm Package Compare versions

Comparing version 0.11.0 to 0.12.0

CHANGELOG.md

 # Changelog
 
+## [0.12.0](https://www.github.com/mljs/spectra-fitting/compare/v0.11.0...v0.12.0) (2021-01-13)
+
+
+### Features
+
+* remove  twice declaration ([bb8d013](https://www.github.com/mljs/spectra-fitting/commit/bb8d013e22c89b79fafaa0fefa2fe341b5d2fdc4))
+* use gradientDifference from peak too ([#48](https://www.github.com/mljs/spectra-fitting/issues/48)) ([fb81ac2](https://www.github.com/mljs/spectra-fitting/commit/fb81ac235fa73ee8814ecd65bf40353e8a54f53b))
+* x search space depending on peak width ([#45](https://www.github.com/mljs/spectra-fitting/issues/45)) ([63375d3](https://www.github.com/mljs/spectra-fitting/commit/63375d33805983e2288718d5763364111a08bb0e))
+
 ## [0.11.0](https://www.github.com/mljs/spectra-fitting/compare/v0.10.0...v0.11.0) (2020-12-20)
@@ -4,0 +13,0 @@

lib/index.js

@@ -116,4 +116,9 @@ 'use strict';
 const STATE_MAX = 2;
-const STATE_GS = 3;
+const STATE_GRADIENT_DIFFERENCE = 3;
 
+const X = 0;
+const Y = 1;
+const WIDTH = 2;
+const MU = 3;
+
 const keys = ['x', 'y', 'width', 'mu'];
@@ -129,4 +134,7 @@ /**
  * @param {object} [options.optimization.kind = 'lm'] - kind of algorithm. By default it's levenberg-marquardt.
+ * @param {object} [options.optimization.options = {}] - options for the specific kind of algorithm.
  * @param {number} [options.optimization.options.timeout] - maximum time running before break in seconds.
- * @param {object} [options.optimization.options = {}] - options for the specific kind of algorithm.
+ * @param {number} [options.optimization.options.damping=1.5]
+ * @param {number} [options.optimization.options.maxIterations=100]
+ * @param {number} [options.optimization.options.errorTolerance=1e-8]
  * @returns {object} - A object with fitting error and the list of optimized parameters { parameters: [ {x, y, width} ], error } if the kind of shape is pseudoVoigt mu parameter is optimized.
@@ -142,2 +150,17 @@ */
 
+  let {
+    minFactorWidth = 0.25,
+    maxFactorWidth = 4,
+    minFactorX = 2,
+    maxFactorX = 2,
+    minFactorY = 0,
+    maxFactorY = 1.5,
+    minMuValue = 0,
+    maxMuValue = 1,
+    xGradientDifference,
+    yGradientDifference = 1e-3,
+    widthGradientDifference,
+    muGradientDifference = 0.01,
+  } = optimization;
+
   peaks = JSON.parse(JSON.stringify(peaks));
@@ -177,21 +200,33 @@
 
+  const getValueOptions = {
+    maxY,
+    minFactorX,
+    maxFactorX,
+    minFactorY,
+    maxFactorY,
+    minMuValue,
+    maxMuValue,
+    minFactorWidth,
+    maxFactorWidth,
+    xGradientDifference,
+    yGradientDifference,
+    widthGradientDifference,
+    muGradientDifference,
+  };
   let nbShapes = peaks.length;
-  let pInit = new Float64Array(nbShapes * nbParams);
   let pMin = new Float64Array(nbShapes * nbParams);
   let pMax = new Float64Array(nbShapes * nbParams);
+  let pInit = new Float64Array(nbShapes * nbParams);
   let gradientDifference = new Float64Array(nbShapes * nbParams);
-  let deltaX = Math.abs(data.x[0] - data.x[1]);
-
   for (let i = 0; i < nbShapes; i++) {
     let peak = peaks[i];
     for (let s = 0; s < nbParams; s++) {
-      pInit[i + s * nbShapes] = getValue(s, peak, STATE_INIT, deltaX, maxY);
-      pMin[i + s * nbShapes] = getValue(s, peak, STATE_MIN, deltaX, maxY);
-      pMax[i + s * nbShapes] = getValue(s, peak, STATE_MAX, deltaX, maxY);
+      pInit[i + s * nbShapes] = getValue(s, peak, STATE_INIT, getValueOptions);
+      pMin[i + s * nbShapes] = getValue(s, peak, STATE_MIN, getValueOptions);
+      pMax[i + s * nbShapes] = getValue(s, peak, STATE_MAX, getValueOptions);
       gradientDifference[i + s * nbShapes] = getValue(
         s,
         peak,
-        STATE_GS,
-        deltaX,
-        maxY,
+        STATE_GRADIENT_DIFFERENCE,
+        getValueOptions,
       );
@@ -219,51 +254,78 @@ }
   }
+
   return result;
 }
 
-function getValue(parameterIndex, peak, key, dt, maxY) {
-  let value;
-  switch (parameterIndex) {
-    case 0:
-      value =
-        key === STATE_INIT
-          ? peak.x
-          : key === STATE_GS
-          ? dt / 1000
-          : key === STATE_MIN
-          ? peak.x - dt
-          : peak.x + dt;
-      break;
-    case 1:
-      value =
-        key === STATE_INIT
-          ? peak.y / maxY
-          : key === STATE_GS
-          ? 1e-3
-          : key === STATE_MIN
-          ? 0
-          : 1.5;
-      break;
-    case 2:
-      value =
-        key === STATE_INIT
-          ? peak.width
-          : key === STATE_GS
-          ? dt / 1000
-          : key === STATE_MIN
-          ? peak.width / 4
-          : peak.width * 4;
-      break;
+function getValue(parameterIndex, peak, state, options) {
+  let maxY = options.maxY;
+  switch (state) {
+    case STATE_INIT:
+      switch (parameterIndex) {
+        case X:
+          return peak.x;
+        case Y:
+          return peak.y / maxY;
+        case WIDTH:
+          return peak.width;
+        case MU:
+          return peak.mu || 0.5;
+        default:
+          throw new Error('The parameter is not supported');
+      }
+    case STATE_GRADIENT_DIFFERENCE:
+      switch (parameterIndex) {
+        case X:
+          return peak.xGradientDifference !== undefined
+            ? peak.xGradientDifference
+            : options.xGradientDifference !== undefined
+            ? options.xGradientDifference
+            : peak.width / 2e3;
+        case Y:
+          return peak.yGradientDifference !== undefined
+            ? peak.yGradientDifference
+            : options.yGradientDifference;
+        case WIDTH:
+          return peak.widthGradientDifference !== undefined
+            ? peak.widthGradientDifference
+            : options.widthGradientDifference !== undefined
+            ? options.widthGradientDifference
+            : peak.width / 2e3;
+        case MU:
+          return peak.muGradientDifference !== undefined
+            ? peak.muGradientDifference
+            : options.muGradientDifference;
+        default:
+          throw new Error('The parameter is not supported');
+      }
+    case STATE_MIN:
+      switch (parameterIndex) {
+        case X:
+          return peak.x - peak.width * options.minFactorX;
+        case Y:
+          return (peak.y / maxY) * options.minFactorY;
+        case WIDTH:
+          return peak.width * options.minFactorWidth;
+        case MU:
+          return options.minMuValue;
+        default:
+          throw new Error('The parameter is not supported');
+      }
+    case STATE_MAX:
+      switch (parameterIndex) {
+        case X:
+          return peak.x + peak.width * options.maxFactorX;
+        case Y:
+          return (peak.y / maxY) * options.maxFactorY;
+        case WIDTH:
+          return peak.width * options.maxFactorWidth;
+        case MU:
+          return options.maxMuValue;
+        default:
+          throw new Error('The parameter is not supported');
+      }
     default:
-      value =
-        key === STATE_INIT
-          ? 0.5
-          : key === STATE_GS
-          ? 0.01
-          : key === STATE_MIN
-          ? 0
-          : 1;
+      throw Error('the state is not supported');
   }
-  return value;
 }
 
 exports.optimize = optimize;

package.json

 {
   "name": "ml-spectra-fitting",
-  "version": "0.11.0",
+  "version": "0.12.0",
   "description": "Fit spectra using gaussian or lorentzian",
@@ -5,0 +5,0 @@ "main": "lib/index.js",

src/__tests__/optimize.test.js

@@ -39,3 +39,2 @@ import { optimize } from '../index';
     let yData = sumOfGaussians(pTrue);
-
     let result = optimize(
@@ -71,5 +70,5 @@ { x, y: x.map((i) => yData(i)) },
     ];
-    let yData = sumOfGaussianLorentzians(pTrue);
+    let func = sumOfGaussianLorentzians(pTrue);
     let result = optimize(
-      { x, y: x.map(yData) },
+      { x, y: x.map(func) },
       [
@@ -76,0 +75,0 @@ { x: 0.1, y: 0.0009, width: (xFactor * nbPoints) / 6 },

src/index.js

@@ -11,4 +11,9 @@ import getMaxValue from 'ml-array-max';
 const STATE_MAX = 2;
-const STATE_GS = 3;
+const STATE_GRADIENT_DIFFERENCE = 3;
 
+const X = 0;
+const Y = 1;
+const WIDTH = 2;
+const MU = 3;
+
 const keys = ['x', 'y', 'width', 'mu'];
@@ -24,4 +29,7 @@ /**
  * @param {object} [options.optimization.kind = 'lm'] - kind of algorithm. By default it's levenberg-marquardt.
+ * @param {object} [options.optimization.options = {}] - options for the specific kind of algorithm.
  * @param {number} [options.optimization.options.timeout] - maximum time running before break in seconds.
- * @param {object} [options.optimization.options = {}] - options for the specific kind of algorithm.
+ * @param {number} [options.optimization.options.damping=1.5]
+ * @param {number} [options.optimization.options.maxIterations=100]
+ * @param {number} [options.optimization.options.errorTolerance=1e-8]
  * @returns {object} - A object with fitting error and the list of optimized parameters { parameters: [ {x, y, width} ], error } if the kind of shape is pseudoVoigt mu parameter is optimized.
@@ -37,2 +45,17 @@ */
 
+  let {
+    minFactorWidth = 0.25,
+    maxFactorWidth = 4,
+    minFactorX = 2,
+    maxFactorX = 2,
+    minFactorY = 0,
+    maxFactorY = 1.5,
+    minMuValue = 0,
+    maxMuValue = 1,
+    xGradientDifference,
+    yGradientDifference = 1e-3,
+    widthGradientDifference,
+    muGradientDifference = 0.01,
+  } = optimization;
+
   peaks = JSON.parse(JSON.stringify(peaks));
@@ -72,21 +95,33 @@
 
+  const getValueOptions = {
+    maxY,
+    minFactorX,
+    maxFactorX,
+    minFactorY,
+    maxFactorY,
+    minMuValue,
+    maxMuValue,
+    minFactorWidth,
+    maxFactorWidth,
+    xGradientDifference,
+    yGradientDifference,
+    widthGradientDifference,
+    muGradientDifference,
+  };
   let nbShapes = peaks.length;
-  let pInit = new Float64Array(nbShapes * nbParams);
   let pMin = new Float64Array(nbShapes * nbParams);
   let pMax = new Float64Array(nbShapes * nbParams);
+  let pInit = new Float64Array(nbShapes * nbParams);
   let gradientDifference = new Float64Array(nbShapes * nbParams);
-  let deltaX = Math.abs(data.x[0] - data.x[1]);
-
   for (let i = 0; i < nbShapes; i++) {
     let peak = peaks[i];
     for (let s = 0; s < nbParams; s++) {
-      pInit[i + s * nbShapes] = getValue(s, peak, STATE_INIT, deltaX, maxY);
-      pMin[i + s * nbShapes] = getValue(s, peak, STATE_MIN, deltaX, maxY);
-      pMax[i + s * nbShapes] = getValue(s, peak, STATE_MAX, deltaX, maxY);
+      pInit[i + s * nbShapes] = getValue(s, peak, STATE_INIT, getValueOptions);
+      pMin[i + s * nbShapes] = getValue(s, peak, STATE_MIN, getValueOptions);
+      pMax[i + s * nbShapes] = getValue(s, peak, STATE_MAX, getValueOptions);
       gradientDifference[i + s * nbShapes] = getValue(
         s,
         peak,
-        STATE_GS,
-        deltaX,
-        maxY,
+        STATE_GRADIENT_DIFFERENCE,
+        getValueOptions,
       );
@@ -114,49 +149,76 @@ }
   }
+
   return result;
 }
 
-function getValue(parameterIndex, peak, key, dt, maxY) {
-  let value;
-  switch (parameterIndex) {
-    case 0:
-      value =
-        key === STATE_INIT
-          ? peak.x
-          : key === STATE_GS
-          ? dt / 1000
-          : key === STATE_MIN
-          ? peak.x - dt
-          : peak.x + dt;
-      break;
-    case 1:
-      value =
-        key === STATE_INIT
-          ? peak.y / maxY
-          : key === STATE_GS
-          ? 1e-3
-          : key === STATE_MIN
-          ? 0
-          : 1.5;
-      break;
-    case 2:
-      value =
-        key === STATE_INIT
-          ? peak.width
-          : key === STATE_GS
-          ? dt / 1000
-          : key === STATE_MIN
-          ? peak.width / 4
-          : peak.width * 4;
-      break;
+function getValue(parameterIndex, peak, state, options) {
+  let maxY = options.maxY;
+  switch (state) {
+    case STATE_INIT:
+      switch (parameterIndex) {
+        case X:
+          return peak.x;
+        case Y:
+          return peak.y / maxY;
+        case WIDTH:
+          return peak.width;
+        case MU:
+          return peak.mu || 0.5;
+        default:
+          throw new Error('The parameter is not supported');
+      }
+    case STATE_GRADIENT_DIFFERENCE:
+      switch (parameterIndex) {
+        case X:
+          return peak.xGradientDifference !== undefined
+            ? peak.xGradientDifference
+            : options.xGradientDifference !== undefined
+            ? options.xGradientDifference
+            : peak.width / 2e3;
+        case Y:
+          return peak.yGradientDifference !== undefined
+            ? peak.yGradientDifference
+            : options.yGradientDifference;
+        case WIDTH:
+          return peak.widthGradientDifference !== undefined
+            ? peak.widthGradientDifference
+            : options.widthGradientDifference !== undefined
+            ? options.widthGradientDifference
+            : peak.width / 2e3;
+        case MU:
+          return peak.muGradientDifference !== undefined
+            ? peak.muGradientDifference
+            : options.muGradientDifference;
+        default:
+          throw new Error('The parameter is not supported');
+      }
+    case STATE_MIN:
+      switch (parameterIndex) {
+        case X:
+          return peak.x - peak.width * options.minFactorX;
+        case Y:
+          return (peak.y / maxY) * options.minFactorY;
+        case WIDTH:
+          return peak.width * options.minFactorWidth;
+        case MU:
+          return options.minMuValue;
+        default:
+          throw new Error('The parameter is not supported');
+      }
+    case STATE_MAX:
+      switch (parameterIndex) {
+        case X:
+          return peak.x + peak.width * options.maxFactorX;
+        case Y:
+          return (peak.y / maxY) * options.maxFactorY;
+        case WIDTH:
+          return peak.width * options.maxFactorWidth;
+        case MU:
+          return options.maxMuValue;
+        default:
+          throw new Error('The parameter is not supported');
+      }
     default:
-      value =
-        key === STATE_INIT
-          ? 0.5
-          : key === STATE_GS
-          ? 0.01
-          : key === STATE_MIN
-          ? 0
-          : 1;
+      throw Error('the state is not supported');
   }
-  return value;
 }

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Found 1 instance in 1 package

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Total package byte prevSize

36768

16.03%

Lines of code

695

20.87%

Worsened metrics

Number of low supply chain risk alerts

2

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