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Release v1.1.5
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5 files changed

+172
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‎bower.json‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
{
22
"name": "ml-gsd",
3-
"version": "1.1.4",
3+
"version": "1.1.5",
44
"description": "Global Spectra Deconvolution",
55
"keywords": [
66
"optimization",

‎dist/ml-gsd.js‎

Lines changed: 167 additions & 47 deletions
Original file line numberDiff line numberDiff line change
@@ -262,7 +262,6 @@ return /******/ (function(modules) { // webpackBootstrap
262262
if(count>2){
263263
var fitted = Opt.optimizeSingleLorentzian(candidates,
264264
{x: broadLines[maxI].x, y:max, width: Math.abs(candidates[0][0]-candidates[candidates.length-1][0])});
265-
//console.log(fitted)
266265
peakList.push({x:fitted[0][0],y:fitted[1][0],width:fitted[2][0],soft:false});
267266

268267
}
@@ -430,15 +429,21 @@ return /******/ (function(modules) { // webpackBootstrap
430429
* @returns {*[]}
431430
*/
432431
function optimizeSingleLorentzian(xy, peak, opts) {
433-
var xy2 = parseData(xy);
432+
opts = opts || {};
433+
var xy2 = parseData(xy, opts.percentage||0);
434+
435+
if(xy2===null||xy2[0].rows<3){
436+
return null; //Cannot run an optimization with less than 3 points
437+
}
438+
434439
var t = xy2[0];
435440
var y_data = xy2[1];
436441
var maxY = xy2[2];
437-
var nbPoints = t.columns, i;
442+
var nbPoints = t.rows, i;
438443

439444
var weight = [nbPoints / Math.sqrt(y_data.dot(y_data))];
440445

441-
var opts=Object.create(opts || [ 3, 100, 1e-3, 1e-3, 1e-3, 1e-2, 1e-2, 11, 9, 1 ]);
446+
var opts=Object.create(opts.LMOptions || [ 3, 100, 1e-3, 1e-3, 1e-3, 1e-2, 1e-2, 11, 9, 1 ]);
442447
//var opts = [ 3, 100, 1e-3, 1e-3, 1e-3, 1e-2, 1e-2, 11, 9, 1 ];
443448
var consts = [ ];
444449
var dt = Math.abs(t[0][0]-t[1][0]);// optional vector of constants
@@ -461,16 +466,24 @@ return /******/ (function(modules) { // webpackBootstrap
461466
* @returns {*[]}
462467
*/
463468
function optimizeSingleGaussian(xy, peak, opts) {
464-
var xy2 = parseData(xy);
469+
opts = opts || {};
470+
var xy2 = parseData(xy, opts.percentage||0);
471+
472+
if(xy2===null||xy2[0].rows<3){
473+
return null; //Cannot run an optimization with less than 3 points
474+
}
475+
465476
var t = xy2[0];
466477
var y_data = xy2[1];
467478
var maxY = xy2[2];
468479

469-
var nbPoints = t.columns, i;
480+
var nbPoints = t.rows, i;
481+
482+
470483

471484
var weight = [nbPoints / Math.sqrt(y_data.dot(y_data))];
472485

473-
var opts=Object.create(opts || [ 3, 100, 1e-3, 1e-3, 1e-3, 1e-2, 1e-2, 11, 9, 1 ]);
486+
var opts=Object.create(opts.LMOptions || [ 3, 100, 1e-3, 1e-3, 1e-3, 1e-2, 1e-2, 11, 9, 1 ]);
474487
//var opts = [ 3, 100, 1e-3, 1e-3, 1e-3, 1e-2, 1e-2, 11, 9, 1 ];
475488
var consts = [ ]; // optional vector of constants
476489
var dt = Math.abs(t[0][0]-t[1][0]);
@@ -488,6 +501,91 @@ return /******/ (function(modules) { // webpackBootstrap
488501
return [p_fit[0],[p_fit[1][0]*maxY],p_fit[2]];
489502
}
490503

504+
/*
505+
peaks on group should sorted
506+
*/
507+
function optimizeLorentzianTrain(xy, group, opts){
508+
var xy2 = parseData(xy);
509+
//console.log(xy2[0].rows);
510+
if(xy2===null||xy2[0].rows<3){
511+
return null; //Cannot run an optimization with less than 3 points
512+
}
513+
514+
var t = xy2[0];
515+
var y_data = xy2[1];
516+
var maxY = xy2[2];
517+
var currentIndex = 0;
518+
var nbPoints = t.length;
519+
var nextX;
520+
var tI, yI, maxY;
521+
var result=[], current;
522+
for(var i=0; i<group.length;i++){
523+
nextX = group[i].x-group[i].width*4;
524+
//console.log(group[i]);
525+
while(t[currentIndex++]<nextX&&currentIndex<nbPoints);
526+
nextX = group[i].x+group[i].width*4;
527+
tI = [];
528+
yI = [];
529+
while(t[currentIndex]<=nextX&&currentIndex<nbPoints){
530+
tI.push(t[currentIndex][0]);
531+
yI.push(y_data[currentIndex][0]*maxY);
532+
currentIndex++;
533+
}
534+
535+
current=optimizeSingleLorentzian([tI, yI], group[i], opts);
536+
if(current){
537+
result.push({"x":current[0][0],"y":current[1][0],"width":current[2][0],"opt":true});
538+
}
539+
else{
540+
result.push({"x":group[i].x,"y":group[i].y,"width":group[i].width,"opt":false});
541+
}
542+
}
543+
544+
return result;
545+
546+
}
547+
548+
function optimizeGaussianTrain(xy, group, opts){
549+
var xy2 = parseData(xy);
550+
//console.log(xy2[0].rows);
551+
if(xy2===null||xy2[0].rows<3){
552+
return null; //Cannot run an optimization with less than 3 points
553+
}
554+
555+
var t = xy2[0];
556+
var y_data = xy2[1];
557+
var maxY = xy2[2];
558+
var currentIndex = 0;
559+
var nbPoints = t.length;
560+
var nextX;
561+
var tI, yI, maxY;
562+
var result=[], current;
563+
for(var i=0; i<group.length;i++){
564+
nextX = group[i].x-group[i].width*4;
565+
//console.log(group[i]);
566+
while(t[currentIndex++]<nextX&&currentIndex<nbPoints);
567+
nextX = group[i].x+group[i].width*4;
568+
tI = [];
569+
yI = [];
570+
while(t[currentIndex]<=nextX&&currentIndex<nbPoints){
571+
tI.push(t[currentIndex][0]);
572+
yI.push(y_data[currentIndex][0]*maxY);
573+
currentIndex++;
574+
}
575+
576+
current=optimizeSingleGaussian([tI, yI], group[i], opts);
577+
if(current){
578+
result.push({"x":current[0][0],"y":current[1][0],"width":current[2][0],"opt":true});
579+
}
580+
else{
581+
result.push({"x":group[i].x,"y":group[i].y,"width":group[i].width,"opt":false});
582+
}
583+
}
584+
585+
return result;
586+
}
587+
588+
491589

492590
/**
493591
*
@@ -497,13 +595,18 @@ return /******/ (function(modules) { // webpackBootstrap
497595
*/
498596
function optimizeLorentzianSum(xy, group, opts){
499597
var xy2 = parseData(xy);
598+
599+
if(xy2===null||xy2[0].rows<3){
600+
return null; //Cannot run an optimization with less than 3 points
601+
}
602+
500603
var t = xy2[0];
501604
var y_data = xy2[1];
502605
var maxY = xy2[2];
503-
var nbPoints = t.columns, i;
606+
var nbPoints = t.rows, i;
504607

505608
var weight = [nbPoints / math.sqrt(y_data.dot(y_data))];
506-
var opts=Object.create(opts || [ 3, 100, 1e-3, 1e-3, 1e-3, 1e-2, 1e-2, 11, 9, 1 ]);
609+
var opts=Object.create(opts || [ 3, 100, 1e-3, 1e-3, 1e-3, 1e-2, 1e-2, 11, 9, 1 ]);
507610
var consts = [ ];// optional vector of constants
508611

509612
var nL = group.length;
@@ -551,6 +654,11 @@ return /******/ (function(modules) { // webpackBootstrap
551654
*/
552655
function optimizeGaussianSum(xy, group, opts){
553656
var xy2 = parseData(xy);
657+
658+
if(xy2===null||xy2[0].rows<3){
659+
return null; //Cannot run an optimization with less than 3 points
660+
}
661+
554662
var t = xy2[0];
555663
var y_data = xy2[1];
556664
var maxY = xy2[2];
@@ -608,7 +716,7 @@ return /******/ (function(modules) { // webpackBootstrap
608716
* @param xy
609717
* @returns {*[]}
610718
*/
611-
function parseData(xy){
719+
function parseData(xy, threshold){
612720
var nbSeries = xy.length;
613721
var t = null;
614722
var y_data = null, x,y;
@@ -617,56 +725,66 @@ return /******/ (function(modules) { // webpackBootstrap
617725
if(nbSeries==2){
618726
//Looks like row wise matrix [x,y]
619727
var nbPoints = xy[0].length;
620-
if(nbPoints<3)
621-
throw new SizeException(nbPoints);
728+
//if(nbPoints<3)
729+
// throw new Exception(nbPoints);
730+
//else{
731+
t = new Array(nbPoints);//new Matrix(nbPoints,1);
732+
y_data = new Array(nbPoints);//new Matrix(nbPoints,1);
733+
x = xy[0];
734+
y = xy[1];
735+
if(typeof x[0] === "number"){
736+
for(i=0;i<nbPoints;i++){
737+
t[i]=x[i];
738+
y_data[i]=y[i];
739+
if(y[i]>maxY)
740+
maxY = y[i];
741+
}
742+
}
622743
else{
623-
t = new Matrix(nbPoints,1);
624-
y_data = new Matrix(nbPoints,1);
625-
x = xy[0];
626-
y = xy[1];
627-
if(typeof x[0] === "number"){
744+
//It is a colum matrix
745+
if(typeof x[0] === "object"){
628746
for(i=0;i<nbPoints;i++){
629-
t[i][0]=x[i];
630-
y_data[i][0]=y[i];
631-
if(y[i]>maxY)
632-
maxY = y[i];
633-
}
634-
}
635-
else{
636-
//It is a colum matrix
637-
if(typeof x[0] === "object"){
638-
for(i=0;i<nbPoints;i++){
639-
t[i][0]=x[i][0];
640-
y_data[i][0]=y[i][0];
641-
if(y[i][0]>maxY)
642-
maxY = y[i][0];
643-
}
747+
t[i]=x[i][0];
748+
y_data[i]=y[i][0];
749+
if(y[i][0]>maxY)
750+
maxY = y[i][0];
644751
}
645-
646752
}
647753

648754
}
755+
756+
//}
649757
}
650758
else{
651759
//Looks like a column wise matrix [[x],[y]]
652760
var nbPoints = nbSeries;
653-
if(nbPoints<3)
654-
throw new SizeException(nbPoints);
655-
else {
656-
t = new Matrix(nbPoints, 1);
657-
y_data = new Matrix(nbPoints, 1);
658-
for (i = 0; i < nbPoints; i++) {
659-
t[i][0] = xy[i][0];
660-
y_data[i][0] = xy[i][1];
661-
if(y_data[i][0]>maxY)
662-
maxY = y_data[i][0];
663-
}
664-
}
761+
//if(nbPoints<3)
762+
// throw new SizeException(nbPoints);
763+
//else {
764+
t = new Array(nbPoints);//new Matrix(nbPoints, 1);
765+
y_data = new Array(nbPoints);//new Matrix(nbPoints, 1);
766+
for (i = 0; i < nbPoints; i++) {
767+
t[i] = xy[i][0];
768+
y_data[i] = xy[i][1];
769+
if(y_data[i]>maxY)
770+
maxY = y_data[i];
771+
}
772+
//}
665773
}
666774
for (i = 0; i < nbPoints; i++) {
667-
y_data[i][0]/=maxY;
775+
y_data[i]/=maxY;
776+
}
777+
if(threshold){
778+
for (i = nbPoints-1; i >=0; i--) {
779+
if(y_data[i]<threshold) {
780+
y_data.splice(i,1);
781+
t.splice(i,1);
782+
}
783+
}
668784
}
669-
return [t,y_data,maxY];
785+
if(t.length>0)
786+
return [(new Matrix([t])).transpose(),(new Matrix([y_data])).transpose(),maxY];
787+
return null;
670788
}
671789

672790
function sizeException(nbPoints) {
@@ -679,6 +797,8 @@ return /******/ (function(modules) { // webpackBootstrap
679797
module.exports.optimizeGaussianSum = optimizeGaussianSum;
680798
module.exports.singleGaussian = singleGaussian;
681799
module.exports.singleLorentzian = singleLorentzian;
800+
module.exports.optimizeGaussianTrain = optimizeGaussianTrain;
801+
module.exports.optimizeLorentzianTrain = optimizeLorentzianTrain;
682802

683803
/***/ },
684804
/* 3 */

‎dist/ml-gsd.min.js‎

Lines changed: 2 additions & 2 deletions
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‎dist/ml-gsd.min.js.map‎

Lines changed: 1 addition & 1 deletion
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‎package.json‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
{
22
"name": "ml-gsd",
3-
"version": "1.1.4",
3+
"version": "1.1.5",
44
"description": "Global Spectra Deconvolution",
55
"main": "src/index.js",
66
"directories": {

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