Feat(GSD): Option smoothY

Author: andcastillo

package.json

@@ -1,6 +1,6 @@
 {
   "name": "ml-gsd",
-  "version": "1.1.0",
+  "version": "1.1.1",
   "description": "Global Spectra Deconvolution",
   "main": "src/index.js",
   "directories": {
@@ -13,7 +13,7 @@
   },
   "repository": {
     "type": "git",
-    "url": "https://github.com/mljs/global-spectra-deconvolution.git"
+    "url": "https://github.com/mljs/global-spectral-deconvolution.git"
   },
   "keywords": [
     "Global Spectra Deconvolution",
@@ -25,23 +25,21 @@
   "author": "Andres Castillo",
   "license": "MIT",
   "bugs": {
-    "url": "https://github.com/mljs/global-spectra-deconvolution/issues"
+    "url": "https://github.com/mljs/global-spectral-deconvolution/issues"
   },
-  "homepage": "https://github.com/mljs/global-spectra-deconvolution",
+  "homepage": "https://github.com/mljs/global-spectral-deconvolution",
   "devDependencies": {
     "cheminfo-tools": "^1.0.2",
     "mocha": "^2.2.5",
     "mocha-better-spec-reporter": "^2.1.1",
     "should": "^7.0.2",
-    "xy-parser": "^1.0.0",
-    "chemcalc": "^3.0.1",
-    "ml-stat": "^1.0.1"
+    "chemcalc": "^3.0.1"
   },
   "dependencies": {
     "ml-optimize-lorentzian": "0.0.2",
     "ml-stat": "^1.0.1",
     "xy-parser": "^1.1.0",
-    "ml-savitzky-golay-generalized": "1.0.0",
+    "ml-savitzky-golay-generalized": "1.0.3",
     "extend": "3.0.0"
   }
 }

src/gsd.js

@@ -4,7 +4,7 @@ var extend = require('extend');
 var SG = require('ml-savitzky-golay-generalized');
 
 var sgDefOptions = {
-    windowSize: 5,
+    windowSize: 9,
     polynomial: 3
 };
 
@@ -53,13 +53,16 @@ function gsd(x, y, options){
         }
     }
     //If the max difference between delta x is less than 5%, then, we can assume it to be equally spaced variable
+    var Y = y;
     if((maxDx-minDx)/maxDx<0.05){
-        var Y = SG(y, x[1]-x[0], {windowSize:sgOptions.windowSize, polynomial:sgOptions.polynomial,derivative:0});
+        if(options.smoothY)
+            Y = SG(y, x[1]-x[0], {windowSize:sgOptions.windowSize, polynomial:sgOptions.polynomial,derivative:0});
         var dY = SG(y, x[1]-x[0], {windowSize:sgOptions.windowSize, polynomial:sgOptions.polynomial,derivative:1});
         var ddY = SG(y, x[1]-x[0], {windowSize:sgOptions.windowSize, polynomial:sgOptions.polynomial,derivative:2});
     }
     else{
-        var Y = SG(y, x, {windowSize:sgOptions.windowSize, polynomial:sgOptions.polynomial,derivative:0});
+        if(options.smoothY)
+            Y = SG(y, x, {windowSize:sgOptions.windowSize, polynomial:sgOptions.polynomial,derivative:0});
         var dY = SG(y, x, {windowSize:sgOptions.windowSize, polynomial:sgOptions.polynomial,derivative:1});
         var ddY = SG(y, x, {windowSize:sgOptions.windowSize, polynomial:sgOptions.polynomial,derivative:2});
     }
@@ -171,6 +174,9 @@ function gsd(x, y, options){
 }
 
 function realTopDetection(peakList, x, y){
+    //console.log(peakList);
+    //console.log(x);
+    //console.log(y);
     var listP = [];
     var alpha, beta, gamma, p,currentPoint;
     for(var j=0;j<peakList.length;j++){

test/ethylvinylether.js

@@ -8,8 +8,12 @@ describe('Global spectra deconvolution NMR spectra', function () {
     // Test case obtained from Pag 443, Chap 8.
     it('Ethylvinylether should have 21 peaks', function () {
         var spectrum=JSON.parse(fs.readFileSync('./test//ethylvinylether.json', 'utf-8'));
-        var result = peakPicking.gsd(spectrum[0],spectrum[1], {noiseLevel: 1049200.537996172, minMaxRatio:0.03});
-        //console.log(result)
+        var result = peakPicking.gsd(spectrum[0],spectrum[1],
+            {noiseLevel: 1049200.537996172,
+            minMaxRatio: 0.03,
+            smoothY:false,
+            sgOptions:{windowSize:5, polynomial:3}
+            });
         result.length.should.equal(21);
     });
 });

test/test.js

@@ -8,14 +8,18 @@ describe('Global spectra deconvolution simple simulated spectrum', function () {
     // Test case obtained from Pag 443, Chap 8.
     it('Should provide the right result ...', function () {
         var spectrum=JSON.parse(fs.readFileSync('./test//C2.json', 'utf-8'));
-        var result = peakPicking.gsd(spectrum[0],spectrum[1], {noiseLevel: 0.001, minMaxRatio:0,realTopDetection:true});
+        var result = peakPicking.gsd(spectrum[0],spectrum[1], {noiseLevel: 0.001,
+            minMaxRatio:0,
+            realTopDetection:true,
+            smoothY:false
+        });
 
         result[0].x.should.approximately(24,0.02);
-        result[0].y.should.approximately(0.09394372786996513,0.0005);
+        result[0].y.should.approximately(0.09394372786996513,0.00005);
         //result[0].width.should.approximately(0.008,5e-4);
 
         result[1].x.should.approximately(25,0.02);
-        result[1].y.should.approximately(0.0020321396708958394,0.0005);
+        result[1].y.should.approximately(0.0020321396708958394,0.00005);
         //result[1].width.should.approximately(0.006,5e-4);
 
     });