cheminfo-tools version up to 1.3

Author: andcastillo

dist/ml-gsd.js

@@ -4859,7 +4859,7 @@ return /******/ (function(modules) { // webpackBootstrap
 	};
 
 
-	function gsd(x, y, options){
+	function gsd(x, yIn, options){
 	    //options = extend({}, defaultOptions, options);
 	    var options=Object.create(options || {});
 	    if (options.minMaxRatio===undefined) options.minMaxRatio=0.00025;
@@ -4871,152 +4871,143 @@ return /******/ (function(modules) { // webpackBootstrap
 	    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);
-	    y=[].concat(y);
-	    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],
 	                    x: frequency,
-	                    y: (Y[minddY[j]]-yCorrection.b)/yCorrection.m,
+	                    y: (Y[minddY[j]]+yCorrection.b)/yCorrection.m,
 	                    width:Math.abs(intervalR[possible] - intervalL[possible]),//widthCorrection
 	                    soft:broadMask[j]
 	                })
@@ -5025,13 +5016,13 @@ return /******/ (function(modules) { // webpackBootstrap
 	    }
 
 
-	    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) {
@@ -5042,11 +5033,11 @@ return /******/ (function(modules) { // webpackBootstrap
 
 	}
 
-	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);
@@ -5062,41 +5053,36 @@ return /******/ (function(modules) { // webpackBootstrap
 	    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]);
@@ -5106,7 +5092,6 @@ return /******/ (function(modules) { // webpackBootstrap
 	            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);
 	        }
 	    }
 	}

dist/ml-gsd.min.js

@@ -29,7 +29,7 @@
   },
   "homepage": "https://github.com/mljs/global-spectral-deconvolution",
   "devDependencies": {
-    "cheminfo-tools": "^1.0.2",
+    "cheminfo-tools": "^1.3.1",
     "mocha": "^2.2.5",
     "mocha-better-spec-reporter": "^2.1.1",
     "should": "^7.0.2",