ml-gsd - npm Package Compare versions

Comparing version 5.0.1 to 5.0.2

lib/index.js

@@ -5,7 +5,9 @@ 'use strict';
 
-function _interopDefault (ex) { return (ex && (typeof ex === 'object') && 'default' in ex) ? ex['default'] : ex; }
-
-var SG = _interopDefault(require('ml-savitzky-golay-generalized'));
+var SG = require('ml-savitzky-golay-generalized');
 var mlOptimizeLorentzian = require('ml-optimize-lorentzian');
 
+function _interopDefaultLegacy (e) { return e && typeof e === 'object' && 'default' in e ? e : { 'default': e }; }
+
+var SG__default = /*#__PURE__*/_interopDefaultLegacy(SG);
+
 /**
@@ -28,3 +30,2 @@ * Global spectra deconvolution
  * @param {number} [options.heightFactor = 0] - Factor to multiply the calculated height (usually 2)
- * @param {boolean} [options.boundaries = false] - Return also the inflection points of the peaks
  * @param {number} [options.derivativeThreshold = -1] - Filters based on the amplitude of the first derivative
@@ -74,3 +75,3 @@ * @return {Array<object>}
   // we can assume it to be equally spaced variable
-  let Y = y;
+  let yData = y;
   let dY, ddY;
@@ -81,3 +82,3 @@ const { windowSize, polynomial } = sgOptions;
     if (smoothY) {
-      Y = SG(y, x[1] - x[0], {
+      yData = SG__default['default'](y, x[1] - x[0], {
         windowSize,
@@ -88,3 +89,3 @@ polynomial,
     }
-    dY = SG(y, x[1] - x[0], {
+    dY = SG__default['default'](y, x[1] - x[0], {
       windowSize,
@@ -94,3 +95,3 @@ polynomial,
     });
-    ddY = SG(y, x[1] - x[0], {
+    ddY = SG__default['default'](y, x[1] - x[0], {
       windowSize,
@@ -102,3 +103,3 @@ polynomial,
     if (smoothY) {
-      Y = SG(y, x, {
+      yData = SG__default['default'](y, x, {
         windowSize,
@@ -109,3 +110,3 @@ polynomial,
     }
-    dY = SG(y, x, {
+    dY = SG__default['default'](y, x, {
       windowSize,
@@ -115,3 +116,3 @@ polynomial,
     });
-    ddY = SG(y, x, {
+    ddY = SG__default['default'](y, x, {
       windowSize,
@@ -122,13 +123,13 @@ polynomial,
   }
-  // console.log('this is 2', y)
-  const X = x;
-  const dx = x[1] - x[0];
+
+  const xData = x;
+  const dX = x[1] - x[0];
   let maxDdy = 0;
   let maxY = 0;
-  for (let i = 0; i < Y.length; i++) {
+  for (let i = 0; i < yData.length; i++) {
     if (Math.abs(ddY[i]) > maxDdy) {
       maxDdy = Math.abs(ddY[i]);
     }
-    if (Math.abs(Y[i]) > maxY) {
-      maxY = Math.abs(Y[i]);
+    if (Math.abs(yData[i]) > maxY) {
+      maxY = Math.abs(yData[i]);
     }
@@ -139,6 +140,6 @@ }
   let lastMin = null;
-  let minddY = new Array(Y.length - 2);
-  let intervalL = new Array(Y.length);
-  let intervalR = new Array(Y.length);
-  let broadMask = new Array(Y.length - 2);
+  let minddY = new Array(yData.length - 2);
+  let intervalL = new Array(yData.length);
+  let intervalR = new Array(yData.length);
+  let broadMask = new Array(yData.length - 2);
   let minddYLen = 0;
@@ -149,3 +150,3 @@ let intervalLLen = 0;
   // By the intermediate value theorem We cannot find 2 consecutive maximum or minimum
-  for (let i = 1; i < Y.length - 1; ++i) {
+  for (let i = 1; i < yData.length - 1; ++i) {
     // filter based on derivativeThreshold
@@ -160,6 +161,6 @@ // console.log('pasa', y[i], dY[i], ddY[i]);
         lastMin = {
-          x: X[i],
+          x: xData[i],
           index: i,
         };
-        if (dx > 0 && lastMax !== null) {
+        if (dX > 0 && lastMax !== null) {
           intervalL[intervalLLen++] = lastMax;
@@ -176,6 +177,6 @@ intervalR[intervalRLen++] = lastMin;
         lastMax = {
-          x: X[i],
+          x: xData[i],
           index: i,
         };
-        if (dx < 0 && lastMin !== null) {
+        if (dX < 0 && lastMin !== null) {
           intervalL[intervalLLen++] = lastMax;
@@ -190,3 +191,3 @@ intervalR[intervalRLen++] = lastMin;
       // TODO should we change this to have 3 arrays ? Huge overhead creating arrays
-      minddY[minddYLen++] = i; // ( [X[i], Y[i], i] );
+      minddY[minddYLen++] = i; // ( [xData[i], yData[i], i] );
       broadMask[broadMaskLen++] = Math.abs(ddY[i]) <= broadRatio * maxDdy;
@@ -205,3 +206,3 @@ }
   for (let j = 0; j < minddY.length; ++j) {
-    frequency = X[minddY[j]];
+    frequency = xData[minddY[j]];
     possible = -1;
@@ -229,7 +230,7 @@ let k = lastK + 1;
     if (possible !== -1) {
-      if (Math.abs(Y[minddY[j]]) > minMaxRatio * maxY) {
+      if (Math.abs(yData[minddY[j]]) > minMaxRatio * maxY) {
         signals[signalsLen++] = {
           index: minddY[j],
           x: frequency,
-          y: (Y[minddY[j]] + yCorrection.b) / yCorrection.m,
+          y: (yData[minddY[j]] + yCorrection.b) / yCorrection.m,
           width: Math.abs(intervalR[possible].x - intervalL[possible].x), // widthCorrection
@@ -243,4 +244,4 @@ soft: broadMask[j],
         if (heightFactor) {
-          let yLeft = Y[intervalL[possible].index];
-          let yRight = Y[intervalR[possible].index];
+          let yLeft = yData[intervalL[possible].index];
+          let yRight = yData[intervalR[possible].index];
           signals[signalsLen - 1].height =
@@ -255,3 +256,3 @@ heightFactor * (signals[signalsLen - 1].y - (yLeft + yRight) / 2);
   if (realTopDetection) {
-    determineRealTop(signals, X, Y);
+    determineRealTop(signals, xData, yData);
   }
@@ -258,0 +259,0 @@

package.json

 {
   "name": "ml-gsd",
-  "version": "5.0.1",
+  "version": "5.0.2",
   "description": "Global Spectra Deconvolution",
@@ -44,14 +44,14 @@ "main": "lib/index.js",
   "devDependencies": {
-    "@babel/plugin-transform-modules-commonjs": "^7.9.6",
+    "@babel/plugin-transform-modules-commonjs": "^7.10.4",
     "chemcalc": "^3.4.1",
     "cheminfo-tools": "^1.23.3",
-    "eslint": "^7.0.0",
+    "eslint": "^7.9.0",
     "eslint-config-cheminfo": "^3.0.0",
-    "eslint-plugin-import": "^2.20.2",
-    "eslint-plugin-jest": "^23.13.1",
-    "eslint-plugin-prettier": "^3.1.3",
-    "jest": "^26.0.1",
+    "eslint-plugin-import": "^2.22.0",
+    "eslint-plugin-jest": "^23.20.0",
+    "eslint-plugin-prettier": "^3.1.4",
+    "jest": "^26.4.2",
     "ml-stat": "^1.3.3",
-    "prettier": "^2.0.5",
-    "rollup": "^2.10.4",
+    "prettier": "^2.1.2",
+    "rollup": "^2.28.2",
     "spectrum-generator": "^4.0.2",
@@ -58,0 +58,0 @@ "xy-parser": "^3.0.0"

README.md

@@ -46,6 +46,2 @@ # global-spectral-deconvolution
 
-#### boundaries=false
-
-Return also the inflection points of the peaks
-
 #### derivativeThreshold=0
@@ -52,0 +48,0 @@

src/gsd.js

@@ -20,3 +20,2 @@ import SG from 'ml-savitzky-golay-generalized';
  * @param {number} [options.heightFactor = 0] - Factor to multiply the calculated height (usually 2)
- * @param {boolean} [options.boundaries = false] - Return also the inflection points of the peaks
  * @param {number} [options.derivativeThreshold = -1] - Filters based on the amplitude of the first derivative
@@ -66,3 +65,3 @@ * @return {Array<object>}
   // we can assume it to be equally spaced variable
-  let Y = y;
+  let yData = y;
   let dY, ddY;
@@ -73,3 +72,3 @@ const { windowSize, polynomial } = sgOptions;
     if (smoothY) {
-      Y = SG(y, x[1] - x[0], {
+      yData = SG(y, x[1] - x[0], {
         windowSize,
@@ -92,3 +91,3 @@ polynomial,
     if (smoothY) {
-      Y = SG(y, x, {
+      yData = SG(y, x, {
         windowSize,
@@ -110,13 +109,13 @@ polynomial,
   }
-  // console.log('this is 2', y)
-  const X = x;
-  const dx = x[1] - x[0];
+
+  const xData = x;
+  const dX = x[1] - x[0];
   let maxDdy = 0;
   let maxY = 0;
-  for (let i = 0; i < Y.length; i++) {
+  for (let i = 0; i < yData.length; i++) {
     if (Math.abs(ddY[i]) > maxDdy) {
       maxDdy = Math.abs(ddY[i]);
     }
-    if (Math.abs(Y[i]) > maxY) {
-      maxY = Math.abs(Y[i]);
+    if (Math.abs(yData[i]) > maxY) {
+      maxY = Math.abs(yData[i]);
     }
@@ -127,6 +126,6 @@ }
   let lastMin = null;
-  let minddY = new Array(Y.length - 2);
-  let intervalL = new Array(Y.length);
-  let intervalR = new Array(Y.length);
-  let broadMask = new Array(Y.length - 2);
+  let minddY = new Array(yData.length - 2);
+  let intervalL = new Array(yData.length);
+  let intervalR = new Array(yData.length);
+  let broadMask = new Array(yData.length - 2);
   let minddYLen = 0;
@@ -137,3 +136,3 @@ let intervalLLen = 0;
   // By the intermediate value theorem We cannot find 2 consecutive maximum or minimum
-  for (let i = 1; i < Y.length - 1; ++i) {
+  for (let i = 1; i < yData.length - 1; ++i) {
     // filter based on derivativeThreshold
@@ -148,6 +147,6 @@ // console.log('pasa', y[i], dY[i], ddY[i]);
         lastMin = {
-          x: X[i],
+          x: xData[i],
           index: i,
         };
-        if (dx > 0 && lastMax !== null) {
+        if (dX > 0 && lastMax !== null) {
           intervalL[intervalLLen++] = lastMax;
@@ -164,6 +163,6 @@ intervalR[intervalRLen++] = lastMin;
         lastMax = {
-          x: X[i],
+          x: xData[i],
           index: i,
         };
-        if (dx < 0 && lastMin !== null) {
+        if (dX < 0 && lastMin !== null) {
           intervalL[intervalLLen++] = lastMax;
@@ -178,3 +177,3 @@ intervalR[intervalRLen++] = lastMin;
       // TODO should we change this to have 3 arrays ? Huge overhead creating arrays
-      minddY[minddYLen++] = i; // ( [X[i], Y[i], i] );
+      minddY[minddYLen++] = i; // ( [xData[i], yData[i], i] );
       broadMask[broadMaskLen++] = Math.abs(ddY[i]) <= broadRatio * maxDdy;
@@ -193,3 +192,3 @@ }
   for (let j = 0; j < minddY.length; ++j) {
-    frequency = X[minddY[j]];
+    frequency = xData[minddY[j]];
     possible = -1;
@@ -217,7 +216,7 @@ let k = lastK + 1;
     if (possible !== -1) {
-      if (Math.abs(Y[minddY[j]]) > minMaxRatio * maxY) {
+      if (Math.abs(yData[minddY[j]]) > minMaxRatio * maxY) {
         signals[signalsLen++] = {
           index: minddY[j],
           x: frequency,
-          y: (Y[minddY[j]] + yCorrection.b) / yCorrection.m,
+          y: (yData[minddY[j]] + yCorrection.b) / yCorrection.m,
           width: Math.abs(intervalR[possible].x - intervalL[possible].x), // widthCorrection
@@ -231,4 +230,4 @@ soft: broadMask[j],
         if (heightFactor) {
-          let yLeft = Y[intervalL[possible].index];
-          let yRight = Y[intervalR[possible].index];
+          let yLeft = yData[intervalL[possible].index];
+          let yRight = yData[intervalR[possible].index];
           signals[signalsLen - 1].height =
@@ -243,3 +242,3 @@ heightFactor * (signals[signalsLen - 1].y - (yLeft + yRight) / 2);
   if (realTopDetection) {
-    determineRealTop(signals, X, Y);
+    determineRealTop(signals, xData, yData);
   }
@@ -246,0 +245,0 @@

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Improved metrics

Total package byte prevSize

5856330

Worsened metrics

Lines of code

1729

decreased by-0.17%

Number of lines in readme file

107

decreased by-3.6%

No dependency changes