fix: Do not modify y within the function. style.

Solve #3

Author: andcastillo

src/gsd.js

@@ -9,7 +9,7 @@ var sgDefOptions = {
 };
 
 
-function gsd(xIn, yIn, options){
+function gsd(x, yIn, options){
     //options = extend({}, defaultOptions, options);
     var options=Object.create(options || {});
     if (options.minMaxRatio===undefined) options.minMaxRatio=0.00025;
@@ -21,147 +21,138 @@ function gsd(xIn, yIn, options){
     if (options.realTopDetection===undefined) options.realTopDetection=false;
 
     var sgOptions = extend({}, sgDefOptions, options.sgOptions);
+    const y = [].concat(yIn);
 
-    //console.log(JSON.stringify(stats.array.minMax(y)));
-    if(options.noiseLevel===undefined){
+    var i, j, k;
+
+    if(options.noiseLevel === undefined){
         //We have to know if x is equally spaced
-        var maxDx=0, minDx=Number.MAX_VALUE,tmp;
-        for(var i=0;i< x.length-1;i++){
-            var tmp = Math.abs(x[i+1]-x[i]);
-            if(tmp<minDx){
+        var maxDx = 0, minDx = Number.MAX_VALUE, tmp;
+        for(i = 0;i < x.length - 1; i++) {
+            tmp = Math.abs(x[i+1] - x[i]);
+            if(tmp < minDx) {
                 minDx = tmp;
             }
-            if(tmp>maxDx){
+            if(tmp > maxDx) {
                 maxDx = tmp;
             }
         }
 
-        if((maxDx-minDx)/maxDx<0.05){
-
+        if((maxDx-minDx)/maxDx < 0.05) {
             options.noiseLevel = getNoiseLevel(y);
-            //console.log(options.noiseLevel+" "+stats.array.median(y));
         }
-        else{
+        else {
             options.noiseLevel = 0;
         }
     }
-    //console.log("options.noiseLevel "+options.noiseLevel);
-    var y=[].concat(yIn);
-    var yCorrection = {m:1, b:options.noiseLevel};
-    if(!options.maxCriteria){
+    const yCorrection = {m:1, b:options.noiseLevel};
+    if(!options.maxCriteria) {
         yCorrection.m =-1;
         yCorrection.b*=-1;
     }
 
-    for (var i=0; i<y.length; i++){
-        y[i]=yCorrection.m*y[i]-yCorrection.b;
+    for (i = 0; i < y.length; i++) {
+        y[i] = yCorrection.m*y[i]-yCorrection.b;
     }
 
-    for (var i=0; i<y.length; i++) {
+    for (i = 0; i < y.length; i++) {
         if (y[i] < 0) {
             y[i] = 0;
         }
     }
-
     //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 dY, ddY;
+    if((maxDx-minDx)/maxDx < 0.05) {
         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});
+        dY = SG(y, x[1]-x[0], {windowSize:sgOptions.windowSize, polynomial:sgOptions.polynomial,derivative:1});
+        ddY = SG(y, x[1]-x[0], {windowSize:sgOptions.windowSize, polynomial:sgOptions.polynomial,derivative:2});
     }
-    else{
+    else {
         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});
+        dY = SG(y, x, {windowSize:sgOptions.windowSize, polynomial:sgOptions.polynomial,derivative:1});
+        ddY = SG(y, x, {windowSize:sgOptions.windowSize, polynomial:sgOptions.polynomial,derivative:2});
     }
 
-    var X = x;
-    var dx = x[1]-x[0];
-    var maxDdy=0;
+    const X = x;
+    const dx = x[1] - x[0];
+    var maxDdy = 0;
     var maxY = 0;
-    //console.log(Y.length);
-    for (var i = 0; i < Y.length ; i++){
-        if(Math.abs(ddY[i])>maxDdy){
+    for (i = 0; i < Y.length ; i++) {
+        if(Math.abs(ddY[i]) > maxDdy) {
             maxDdy = Math.abs(ddY[i]);
         }
-        if(Math.abs(Y[i])>maxY){
+        if(Math.abs(Y[i]) > maxY) {
             maxY = Math.abs(Y[i]);
         }
     }
-    //console.log(maxY+"x"+maxDy+"x"+maxDdy);
 
     var minddY = [];
     var intervalL = [];
     var intervalR = [];
     var lastMax = null;
     var lastMin = null;
     var broadMask = new Array();
-    //console.log(dx);
     //By the intermediate value theorem We cannot find 2 consecutive maxima or minima
-    for (var i = 1; i < Y.length -1 ; i++){
+    for (i = 1; i < Y.length -1 ; i++){
         //console.log(dY[i]);
-        if ((dY[i] < dY[i-1]) && (dY[i] <= dY[i+1])||
+        if ((dY[i] < dY[i-1]) && (dY[i] <= dY[i+1]) ||
             (dY[i] <= dY[i-1]) && (dY[i] < dY[i+1])) {
             lastMin = X[i];
-            //console.log("min "+lastMin);
-            if(dx>0&&lastMax!=null){
+            if(dx > 0 && lastMax != null) {
                 intervalL.push(lastMax);
                 intervalR.push(lastMin);
 
             }
         }
 
-        if ((dY[i] >= dY[i-1]) && (dY[i] > dY[i+1])||
+        if ((dY[i] >= dY[i-1]) && (dY[i] > dY[i+1]) ||
             (dY[i] > dY[i-1]) && (dY[i] >= dY[i+1])) {
             lastMax = X[i];
-            //console.log("max "+lastMax);
-            if(dx<0&&lastMin!=null){
+            if(dx < 0 && lastMin != null) {
                 intervalL.push(lastMax);
                 intervalR.push(lastMin);
             }
         }
         if ((ddY[i] < ddY[i-1]) && (ddY[i] < ddY[i+1])) {
             minddY.push(i);//( [X[i], Y[i], i] );  // TODO should we change this to have 3 arrays ? Huge overhead creating arrays
-            if(Math.abs(ddY[i])>options.broadRatio*maxDdy){ // TODO should this be a parameter =
+            if(Math.abs(ddY[i]) > options.broadRatio*maxDdy) { // TODO should this be a parameter =
                 broadMask.push(false);
             }
-            else{
+            else {
                 broadMask.push(true);
             }
         }
     }
-    //
-    //console.log(intervalL.length+" "+minddY.length+" "+broadMask.length);
+
     var signals = [];
-    var lastK = 0,possible, k, f,frequency, distanceJ, minDistance, gettingCloser;
-    for (var j = 0; j < minddY.length; j++){
-        frequency = X[minddY[j]];//minddY[j][0];
+    var lastK = 0;
+    var possible, frequency, distanceJ, minDistance, gettingCloser;
+    for (j = 0; j < minddY.length; j++) {
+        frequency = X[minddY[j]];
         possible = -1;
-        k=lastK+1;
+        k = lastK + 1;
         minDistance = Number.MAX_VALUE;
         distanceJ = 0;
         gettingCloser=true;
-        while(possible==-1&&k<intervalL.length&&gettingCloser){
+        while(possible == -1 && k < intervalL.length && gettingCloser) {
             distanceJ = Math.abs(frequency-(intervalL[k]+intervalR[k])/2);
             //Still getting closer?
-            if(distanceJ<minDistance){
+            if(distanceJ < minDistance) {
                 minDistance = distanceJ;
             }
             else{
                 gettingCloser = false;
             }
-            if( distanceJ <Math.abs(intervalL[k]-intervalR[k])/2){
-                possible=k;
+            if( distanceJ < Math.abs(intervalL[k]-intervalR[k])/2) {
+                possible = k;
                 lastK = k;
             }
             k++;
         }
-        //console.log(lastK+" "+intervalL.length+" possible "+k);
-        if (possible!=-1){
-            //console.log(height);
+        if (possible != -1) {
             if (Math.abs(Y[minddY[j]]) > options.minMaxRatio*maxY) {
                 signals.push({
                     i:minddY[j],
@@ -175,13 +166,13 @@ function gsd(xIn, yIn, options){
     }
 
 
-    if(options.realTopDetection){
+    if(options.realTopDetection) {
         realTopDetection(signals,X,Y);
     }
 
     //Correct the values to fit the original spectra data
-    for(var j=0;j<signals.length;j++){
-        signals[j].base=options.noiseLevel;
+    for(j = 0;j < signals.length; j++) {
+        signals[j].base = options.noiseLevel;
     }
 
     signals.sort(function (a, b) {
@@ -192,11 +183,11 @@ function gsd(xIn, yIn, options){
 
 }
 
-function getNoiseLevel(y){
-    var mean = 0,stddev=0;
-    var length = y.length,i=0;
-    for(i = 0; i < length; i++){
-        mean+=y[i];
+function getNoiseLevel(y) {
+    var mean = 0, stddev = 0;
+    var length = y.length, i = 0;
+    for(i = 0; i < length; i++) {
+        mean += y[i];
     }
     mean/=length;
     var averageDeviations = new Array(length);
@@ -212,41 +203,36 @@ function getNoiseLevel(y){
     return stddev;
 }
 
-function realTopDetection(peakList, x, y){
-    //console.log(peakList);
-    //console.log(x);
-    //console.log(y);
-    var listP = [];
+function realTopDetection(peakList, x, y) {
     var alpha, beta, gamma, p,currentPoint;
-    for(var j=0;j<peakList.length;j++){
+    for(var j = 0; j < peakList.length; j++) {
         currentPoint = peakList[j].i;//peakList[j][2];
-        var tmp = currentPoint;
         //The detected peak could be moved 1 or 2 unit to left or right.
-        if(y[currentPoint-1]>=y[currentPoint-2]
-            &&y[currentPoint-1]>=y[currentPoint]) {
+        if(y[currentPoint-1] >= y[currentPoint-2]
+            && y[currentPoint-1] >= y[currentPoint]) {
             currentPoint--;
         }
-        else{
-            if(y[currentPoint+1]>=y[currentPoint]
-                &&y[currentPoint+1]>=y[currentPoint+2]) {
+        else {
+            if(y[currentPoint+1] >= y[currentPoint]
+                && y[currentPoint+1] >= y[currentPoint+2]) {
                 currentPoint++;
             }
             else{
-                if(y[currentPoint-2]>=y[currentPoint-3]
-                    &&y[currentPoint-2]>=y[currentPoint-1]) {
+                if(y[currentPoint-2] >= y[currentPoint-3]
+                    && y[currentPoint-2] >= y[currentPoint-1]) {
                     currentPoint-=2;
                 }
-                else{
-                    if(y[currentPoint+2]>=y[currentPoint+1]
-                        &&y[currentPoint+2]>=y[currentPoint+3]) {
+                else {
+                    if(y[currentPoint+2] >= y[currentPoint+1]
+                        && y[currentPoint+2] >= y[currentPoint+3]) {
                         currentPoint+=2;
                     }
                 }
             }
         }
-        if(y[currentPoint-1]>0&&y[currentPoint+1]>0
-            &&y[currentPoint]>=y[currentPoint-1]
-            &&y[currentPoint]>=y[currentPoint+1]) {
+        if(y[currentPoint-1] > 0 && y[currentPoint+1] > 0
+            && y[currentPoint] >= y[currentPoint-1]
+            && y[currentPoint] >= y[currentPoint+1]) {
             alpha = 20 * Math.log10(y[currentPoint - 1]);
             beta = 20 * Math.log10(y[currentPoint]);
             gamma = 20 * Math.log10(y[currentPoint + 1]);
@@ -256,7 +242,6 @@ function realTopDetection(peakList, x, y){
             peakList[j].x = x[currentPoint] + (x[currentPoint]-x[currentPoint-1])*p;
             peakList[j].y = y[currentPoint] - 0.25 * (y[currentPoint - 1]
                 - y[currentPoint + 1]) * p;//signal.peaks[j].intensity);
-            //console.log(y[tmp]+" "+peakList[j].y);
         }
     }
 }

test/broadNMR.js

@@ -16,11 +16,10 @@ describe('Global spectra deconvolution NMR spectra', function () {
             }
         );
         var last = peakPicking.post.joinBroadPeaks(result,{width:0.25});
-        //console.log(last.length);
         result.length.should.approximately(15,1);
         result.map(function(peak){
             if(Math.abs(peak.x-4.31)<0.01){
-                peak.width.should.approximately(0.37,0.02);
+                peak.width.should.approximately(0.39,0.02);
             }
         });
     });