Optimize: Tested for NMR spectra

Author: andcastillo

README.md

@@ -1 +1,21 @@
 # global-spectral-deconvolution
+
+Global Spectra Deconvolution + Peak optimizer
+
+## Example
+``
+var CC = require('chemcalc');
+var Stat = require('ml-stat');
+var peakPicking = require("../src/index");
+
+
+var spectrum=CC.analyseMF("Cl2.Br2", {isotopomers:'arrayXXYY', fwhm:0.01, gaussianWidth: 11});
+var xy=spectrum.arrayXXYY;
+var x=xy[0];
+var y=xy[1];
+//Just a fake noiseLevel
+var noiseLevel=Stat.array.median(y.filter(function(a) {return (a>0)}))*3;
+
+var result=peakPicking.gsd(x, y,  {noiseLevel: noiseLevel, minMaxRatio:0, broadRatio:0,smoothY:false});
+result = peakPicking.optimize(result,x,y,1,"gaussian");`
+```

bower.json

@@ -1,6 +1,6 @@
 {
   "name": "ml-gsd",
-  "version": "0.0.1",
+  "version": "0.1.0",
   "description": "Global Spectra Deconvolution",
   "keywords": [
     "optimization",

dist/ml-gsd.js

@@ -1,22 +1,26 @@
 {
   "name": "ml-gsd",
-  "version": "0.0.1",
+  "version": "0.1.0",
   "description": "Global Spectra Deconvolution",
   "main": "src/index.js",
   "directories": {
     "lib": "src",
     "test": "test"
   },
   "scripts": {
-    "build": "gulp build",
+    "build": "cheminfo build",
     "test": "mocha --require should --reporter mocha-better-spec-reporter --recursive"
   },
   "repository": {
     "type": "git",
     "url": "https://github.com/mljs/global-spectra-deconvolution.git"
   },
   "keywords": [
-    "Global Spectra Deconvolution"
+    "Global Spectra Deconvolution",
+    "peak",
+    "picking",
+    "optimization",
+    "gsd"
   ],
   "author": "Andres Castillo",
   "license": "MIT",
@@ -39,10 +43,11 @@
     "should": "^7.0.2",
     "xy-parser": "^1.0.0",
     "chemcalc": "^3.0.1",
-    "ml-stat": "^1.0.1"
+    "ml-stat": "^1.0.1",
+    "cheminfo-tools": "^1.0.2"
   },
   "dependencies": {
-    "ml-optimize-lorentzian": "../optimize-lorentzian",
+    "ml-optimize-lorentzian": "0.0.2",
     "ml-stat": "^1.0.1",
     "xy-parser": "^1.1.0"
   }

dist/ml-gsd.min.js

@@ -1,5 +1,4 @@
-
-var optimizePeaks = require("../src/optimize");
+var Opt = require("ml-optimize-lorentzian");
 
 function gsd(x, y, options){
     var options=Object.create(options || {});
@@ -174,9 +173,11 @@ function gsd(x, y, options){
                     }
                 }
                 else{
-                    var fitted =  optimizePeaks.optimizeSingleLorentzian(candidates);
+                    var fitted =  Opt.optimizeSingleLorentzian(candidates,{x:candidates[maxI][0],
+                        width:Math.abs(candidates[0][0]-candidates[candidates.length-1][0])},
+                        []);
                     //console.log(fitted);
-                    signals.push(fitted);
+                    signals.push([fitted[0][0],fitted[0][1],fitted[0][2]]);
                 }
                 candidates = [];
                 max = 0;

dist/ml-gsd.min.js.map

@@ -4,29 +4,30 @@
 var Opt = require("ml-optimize-lorentzian");
 
 function sampleFunction(from, to, x, y, lastIndex){
-    //console.log(from+" "+to);
-    //console.log(lastIndex+" "+x[lastIndex[0]]);
     var nbPoints = x.length;
     var sampleX = [];
     var sampleY = [];
     var direction = Math.sign(x[1]-x[0]);//Direction of the derivative
-    var delta = (to-from)/2;
+    if(direction==-1){
+        lastIndex[0]= x.length-1;
+    }
+
+    var delta = Math.abs(to-from)/2;
     var mid = (from+to)/2;
     var stop = false;
     var index = lastIndex[0];
-    while(!stop&&index<nbPoints){
+    while(!stop&&index<nbPoints&&index>=0){
         if(Math.abs(x[index]-mid)<=delta){
             sampleX.push(x[index]);
             sampleY.push(y[index]);
-            index++;
-
+            index+=direction;
         }
         //It is outside the range.
         else{
 
-            if(Math.sign(mid-x[index])==direction){
+            if(Math.sign(mid-x[index])==1){
                 //We'll reach the mid going in the current direction
-                index++;
+                index+=direction;
             }
             else{
                 //There is not more peaks in the current range
@@ -46,13 +47,12 @@ function optimizePeaks(peakList,x,y,n, fnType){
     var factor = 1;
     if(fnType=="gaussian")
         factor = 1.17741;//From https://en.wikipedia.org/wiki/Gaussian_function#Properties
-    //console.log(x[0]+" "+x[1]);
     for(i=0;i<groups.length;i++){
-        //console.log(peakList[i]);
         var peaks = groups[i].group;
         if(peaks.length>1){
             //Multiple peaks
             //console.log("Pending group of overlaped peaks "+peaks.length);
+            //console.log("here1");
             //console.log(groups[i].limits);
             var sampling = sampleFunction(groups[i].limits[0]-groups[i].limits[1],groups[i].limits[0]+groups[i].limits[1],x,y,lastIndex);
             //console.log(sampling);
@@ -68,8 +68,9 @@ function optimizePeaks(peakList,x,y,n, fnType){
                         optPeaks = Opt.optimizeLorentzianSum(sampling, peaks, opts);
                     }
                 }
+                //console.log(optPeak);
                 for(j=0;j<optPeaks.length;j++){
-                    result.push({x:optPeaks[j][0],y:optPeaks[j][1],width:optPeaks[j][2]*factor});
+                    result.push({x:optPeaks[j][0][0],y:optPeaks[j][1][0],width:optPeaks[j][2][0]*factor});
                 }
             }
         }
@@ -78,7 +79,8 @@ function optimizePeaks(peakList,x,y,n, fnType){
             peaks = peaks[0];
             var sampling = sampleFunction(peaks.x-n*peaks.width,
                 peaks.x+n*peaks.width,x,y,lastIndex);
-            //console.log(sampling);
+            //console.log("here2");
+            //console.log(groups[i].limits);
             if(sampling[0].length>5){
                 var error = peaks.width/1000;
                 var opts = [  3,    100, error, error, error, error*10, error*10,    11,    9,        1 ];
@@ -92,7 +94,8 @@ function optimizePeaks(peakList,x,y,n, fnType){
                         var optPeak = Opt.optimizeSingleLorentzian([sampling[0],sampling[1]], peaks,  opts);
                     }
                 }
-                result.push({x:optPeak[0],y:optPeak[1],width:optPeak[2]*factor}); // From https://en.wikipedia.org/wiki/Gaussian_function#Properties}
+                //console.log(optPeak);
+                result.push({x:optPeak[0][0],y:optPeak[1][0],width:optPeak[2][0]*factor}); // From https://en.wikipedia.org/wiki/Gaussian_function#Properties}
             }
         }
 

package.json

@@ -22,7 +22,7 @@ console.log(result);
 describe.only('Check the peak picking of a simulated mass spectrum', function () {
 
     it('Check result', function () {
-        
+
     });
 });
 

src/gsd.js

@@ -32,11 +32,11 @@ describe('Global spectra deconvolution2', function () {
     console.log("Parsing + gsd + optimization time: "+(d.getTime()-n));
 
 
-    for(var i=0;i<result.length;i++){
+   /* for(var i=0;i<result.length;i++){
         //if(result[i].width<0.05)
         console.log(result[i].x+" "+result[i].y+" "+result[i].width);
     }
-    console.log(result.length);
+    console.log(result.length);*/
 
     // Test case obtained from Pag 443, Chap 8.
     it('Should provide the right result ...', function () {