Detect the broadPeaks

GSD fails to detect very broad peaks. It returns instead, a lot of
sharp peaks. The optimisation procedure aims to convert all those sharp
little signals in a single broad peak. A test case is included where
the broad peak overlaps with some normal peaks.

Author: andcastillo

src/gsd.js

@@ -5,7 +5,7 @@ var SG = require('ml-savitzky-golay-generalized');
 
 var sgDefOptions = {
     windowSize: 5,
-    polynomial: 3,
+    polynomial: 3
 };
 
 

src/index.js

@@ -1,3 +1,3 @@
 
-module.exports.optimize = require("../src/optimize");
+module.exports.post = require("../src/optimize");
 module.exports.gsd = require("../src/gsd");

src/optimize.js

@@ -159,6 +159,67 @@ function groupPeaks(peakList,nL){
     }
     return groups;
 }
+/**
+ * This function try to join the peaks that seems to belong to a broad signal in a single broad peak.
+ * @param peakList
+ * @param options
+ */
+function joinBroadPeaks(peakList, options){
+    var width = options.width;
+    var broadLines=[];
+    //Optimize the possible broad lines
+    var max=0, maxI=0,count=1;
+    var isPartOf = false;
+    for(var i=peakList.length-1;i>=0;i--){
+        if(peakList[i].soft){
+            broadLines.push(peakList.splice(i,1)[0]);
+        }
+    }
+    //Push a feak peak
+    broadLines.push({x:Number.MAX_VALUE});
+
+    var candidates = [[broadLines[0].x,
+                        broadLines[0].y]];
+    var indexes = [0];
+
+    for(var i=1;i<broadLines.length;i++){
+        //console.log(broadLines[i-1].x+" "+broadLines[i].x);
+        if(Math.abs(broadLines[i-1].x-broadLines[i].x)<width){
+            candidates.push([broadLines[i].x,broadLines[i].y]);
+            if(broadLines[i].y>max){
+                max = broadLines[i].y;
+                maxI = i;
+            }
+            indexes.push(i);
+            count++;
+        }
+        else{
+            if(count>2){
+                var fitted =  Opt.optimizeSingleLorentzian(candidates,
+                    {x: broadLines[maxI].x, y:max, width: Math.abs(candidates[0][0]-candidates[candidates.length-1][0])});
+                //console.log(fitted)
+                peakList.push({x:fitted[0][0],y:fitted[1][0],width:fitted[2][0],soft:false});
+
+            }
+            else{
+                //Put back the candidates to the signals list
+                indexes.map(function(index){peakList.push(broadLines[index])});
+            }
+            candidates = [[broadLines[i].x,broadLines[i].y]];
+            indexes = [i];
+            max = broadLines[i].y;
+            maxI = i;
+            count = 1;
+        }
+    }
+
+    peakList.sort(function (a, b) {
+        return a.x - b.x;
+    });
+
+    return peakList;
+
+}
 
 /*if(options.broadRatio>0){
  var broadLines=[[Number.MAX_VALUE,0,0]];
@@ -208,5 +269,5 @@ function groupPeaks(peakList,nL){
  }
  }*/
 
-module.exports=optimizePeaks;
+module.exports={optimizePeaks:optimizePeaks,joinBroadPeaks:joinBroadPeaks};
 

test/broadNMR.js

@@ -0,0 +1,27 @@
+'use strict';
+
+var fs = require('fs');
+var peakPicking = require("../src/index");
+
+describe('Global spectra deconvolution NMR spectra', function () {
+
+    // Test case obtained from Pag 443, Chap 8.
+    it('Should give 1 broad peak and around 14 other peaks', function () {
+        var spectrum=JSON.parse(fs.readFileSync('./test/broadNMR.json', 'utf-8'));
+        var result = peakPicking.gsd(spectrum[0],spectrum[1], {noiseLevel: 1049200.537996172/2,
+                                                                minMaxRatio:0.01,
+                                                                broadRatio:0.0025,
+                                                                sgOptions:{windowSize: 9,
+                                                                    polynomial: 3}
+        }
+        );
+        var last = peakPicking.post.joinBroadPeaks(result,{width:0.25});
+
+        result.length.should.approximately(15,1);
+        result.map(function(peak){
+            if(Math.abs(peak.x-4.31)<0.01){
+                peak.width.should.approximately(0.4,0.02);
+            }
+        });
+    });
+});