preparing documentation

.gitignore

@@ -2,4 +2,7 @@ NN.kdev4
 .kdev4
 *.o
 *.a
+*.so
 *.nm
+/doc/html/*
+!/doc/html/doxy-boot.js

Doxyfile

@@ -628,13 +628,13 @@ HTML_FILE_EXTENSION    = .html
 # each generated HTML page. If it is left blank doxygen will generate a 
 # standard header.
 
-HTML_HEADER            = 
+HTML_HEADER            = ./doc/header.html
 
 # The HTML_FOOTER tag can be used to specify a personal HTML footer for 
 # each generated HTML page. If it is left blank doxygen will generate a 
 # standard footer.
 
-HTML_FOOTER            = 
+HTML_FOOTER            = ./doc/footer.html
 
 # The HTML_STYLESHEET tag can be used to specify a user-defined cascading 
 # style sheet that is used by each HTML page. It can be used to 
@@ -645,6 +645,8 @@ HTML_FOOTER            =
 
 HTML_STYLESHEET        = 
 
+HTML_EXTRA_STYLESHEET  = ./doc/customdoxygen.css
+
 # If the GENERATE_HTMLHELP tag is set to YES, additional index files 
 # will be generated that can be used as input for tools like the 
 # Microsoft HTML help workshop to generate a compressed HTML help file (.chm) 

doc/customdoxygen.css

@@ -0,0 +1,255 @@
+h1, .h1, h2, .h2, h3, .h3{
+    font-weight: 200 !important;
+}
+
+#navrow1, #navrow2, #navrow3, #navrow4, #navrow5{
+    border-bottom: 1px solid #EEEEEE;
+}
+
+.adjust-right {
+margin-left: 30px !important;
+font-size: 1.15em !important;
+}
+.navbar{
+ border: 0px solid #222 !important;
+}
+
+
+/* Sticky footer styles
+-------------------------------------------------- */
+html,
+body {
+    height: 100%;
+    /* The html and body elements cannot have any padding or margin. */
+}
+
+/* Wrapper for page content to push down footer */
+#wrap {
+    min-height: 100%;
+    height: auto;
+    /* Negative indent footer by its height */
+    margin: 0 auto -60px;
+    /* Pad bottom by footer height */
+    padding: 0 0 60px;
+}
+
+/* Set the fixed height of the footer here */
+#footer {
+    font-size: 0.9em;
+    padding: 8px 0px;
+    background-color: #f5f5f5;
+}
+
+.footer-row {
+    line-height: 44px;
+}
+
+#footer > .container {
+    padding-left: 15px;
+    padding-right: 15px;
+}
+
+.footer-follow-icon {
+    margin-left: 3px;
+    text-decoration: none !important;
+}
+
+.footer-follow-icon img {
+    width: 20px;
+}
+
+.footer-link {
+    padding-top: 5px;
+    display: inline-block;
+    color: #999999;
+    text-decoration: none;
+}
+
+.footer-copyright {
+    text-align: center;
+}
+
+
+@media (min-width: 992px) {
+    .footer-row {
+        text-align: left;
+    }
+
+    .footer-icons {
+        text-align: right;
+    }
+}
+@media (max-width: 991px) {
+    .footer-row {
+        text-align: center;
+    }
+
+    .footer-icons {
+        text-align: center;
+    }
+}
+
+/* DOXYGEN Code Styles
+----------------------------------- */
+
+
+a.qindex {
+    font-weight: bold;
+}
+
+a.qindexHL {
+    font-weight: bold;
+    background-color: #9CAFD4;
+    color: #ffffff;
+    border: 1px double #869DCA;
+}
+
+.contents a.qindexHL:visited {
+    color: #ffffff;
+}
+
+a.code, a.code:visited, a.line, a.line:visited {
+    color: #4665A2;
+}
+
+a.codeRef, a.codeRef:visited, a.lineRef, a.lineRef:visited {
+    color: #4665A2;
+}
+
+/* @end */
+
+dl.el {
+    margin-left: -1cm;
+}
+
+pre.fragment {
+    border: 1px solid #C4CFE5;
+    background-color: #FBFCFD;
+    padding: 4px 6px;
+    margin: 4px 8px 4px 2px;
+    overflow: auto;
+    word-wrap: break-word;
+    font-size:  9pt;
+    line-height: 125%;
+    font-family: monospace, fixed;
+    font-size: 105%;
+}
+
+div.fragment {
+    padding: 4px 6px;
+    margin: 4px 8px 4px 2px;
+    border: 1px solid #C4CFE5;
+}
+
+div.line {
+    font-family: monospace, fixed;
+    font-size: 13px;
+    min-height: 13px;
+    line-height: 1.0;
+    text-wrap: unrestricted;
+    white-space: -moz-pre-wrap; /* Moz */
+    white-space: -pre-wrap;     /* Opera 4-6 */
+    white-space: -o-pre-wrap;   /* Opera 7 */
+    white-space: pre-wrap;      /* CSS3  */
+    word-wrap: break-word;      /* IE 5.5+ */
+    text-indent: -53px;
+    padding-left: 53px;
+    padding-bottom: 0px;
+    margin: 0px;
+    -webkit-transition-property: background-color, box-shadow;
+    -webkit-transition-duration: 0.5s;
+    -moz-transition-property: background-color, box-shadow;
+    -moz-transition-duration: 0.5s;
+    -ms-transition-property: background-color, box-shadow;
+    -ms-transition-duration: 0.5s;
+    -o-transition-property: background-color, box-shadow;
+    -o-transition-duration: 0.5s;
+    transition-property: background-color, box-shadow;
+    transition-duration: 0.5s;
+}
+
+div.line.glow {
+    background-color: cyan;
+    box-shadow: 0 0 10px cyan;
+}
+
+
+span.lineno {
+    padding-right: 4px;
+    text-align: right;
+    border-right: 2px solid #0F0;
+    background-color: #E8E8E8;
+    white-space: pre;
+}
+span.lineno a {
+    background-color: #D8D8D8;
+}
+
+span.lineno a:hover {
+    background-color: #C8C8C8;
+}
+
+div.groupHeader {
+    margin-left: 16px;
+    margin-top: 12px;
+    font-weight: bold;
+}
+
+div.groupText {
+    margin-left: 16px;
+    font-style: italic;
+}
+
+/* @group Code Colorization */
+
+span.keyword {
+    color: #008000
+}
+
+span.keywordtype {
+    color: #604020
+}
+
+span.keywordflow {
+    color: #e08000
+}
+
+span.comment {
+    color: #800000
+}
+
+span.preprocessor {
+    color: #806020
+}
+
+span.stringliteral {
+    color: #002080
+}
+
+span.charliteral {
+    color: #008080
+}
+
+span.vhdldigit {
+    color: #ff00ff
+}
+
+span.vhdlchar {
+    color: #000000
+}
+
+span.vhdlkeyword {
+    color: #700070
+}
+
+span.vhdllogic {
+    color: #ff0000
+}
+
+blockquote {
+    background-color: #F7F8FB;
+    border-left: 2px solid #9CAFD4;
+    margin: 0 24px 0 4px;
+    padding: 0 12px 0 16px;
+}
+

doc/footer.html

@@ -0,0 +1,26 @@
+<!-- HTML footer for doxygen 1.8.8-->
+<!-- start footer part -->
+<!--BEGIN GENERATE_TREEVIEW-->
+<div id="nav-path" class="navpath"><!-- id is needed for treeview function! -->
+  <ul>
+    $navpath
+    <li class="footer">$generatedby
+    <a href="http://www.doxygen.org/index.html">
+    <img class="footer" src="$relpath^doxygen.png" alt="doxygen"/></a> $doxygenversion </li>
+  </ul>
+</div>
+<!--END GENERATE_TREEVIEW-->
+</div>
+</div>
+</div>
+</div>
+</div>
+<!--BEGIN !GENERATE_TREEVIEW-->
+<hr class="footer"/><address class="footer"><small>
+$generatedby &#160;<a href="http://www.doxygen.org/index.html">
+<img class="footer" src="$relpath^doxygen.png" alt="doxygen"/>
+</a> $doxygenversion
+</small></address>
+<!--END !GENERATE_TREEVIEW-->
+</body>
+</html>

doc/header.html

@@ -0,0 +1,42 @@
+<!-- HTML header for doxygen 1.8.8-->
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+    <head>
+        <meta http-equiv="X-UA-Compatible" content="IE=edge">
+        <!-- For Mobile Devices -->
+        <meta name="viewport" content="width=device-width, initial-scale=1">
+
+        <meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
+        <meta name="generator" content="Doxygen $doxygenversion"/>
+        
+        <script type="text/javascript" src="https://code.jquery.com/jquery-2.1.1.min.js"></script>
+
+        <!--BEGIN PROJECT_NAME--><title>$projectname: $title</title><!--END PROJECT_NAME-->
+        <!--BEGIN !PROJECT_NAME--><title>$title</title><!--END !PROJECT_NAME-->
+        <!--<link href="$relpath^tabs.css" rel="stylesheet" type="text/css"/>-->
+        <script type="text/javascript" src="$relpath^dynsections.js"></script>
+        $treeview
+        $search
+        $mathjax
+        <link href="$relpath^$stylesheet" rel="stylesheet" type="text/css" />
+        $extrastylesheet
+
+        <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.1/css/bootstrap.min.css">
+        <script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.1/js/bootstrap.min.js"></script>
+        <script type="text/javascript" src="doxy-boot.js"></script>
+    </head>
+    <body>
+        <nav class="navbar navbar-default" role="navigation">
+            <div class="container">
+                <div class="navbar-header">
+                    <a class="navbar-brand">$projectname $projectnumber</a>
+                </div>
+            </div>
+        </nav>
+        <div id="top"><!-- do not remove this div, it is closed by doxygen! -->
+            <div class="content" id="content">
+                <div class="container">
+                    <div class="row">
+                        <div class="col-sm-12 panel panel-default" style="padding-bottom: 15px;">
+                            <div style="margin-bottom: 15px;">
+<!-- end header part -->

doc/html/doxy-boot.js

@@ -0,0 +1,120 @@
+$( document ).ready(function() {
+
+    $("div.headertitle").addClass("page-header");
+    $("div.title").addClass("h1");
+
+    $('li > a[href="index.html"] > span').before("<i class='fa fa-cog'></i> ");
+    $('li > a[href="modules.html"] > span').before("<i class='fa fa-square'></i> ");
+    $('li > a[href="namespaces.html"] > span').before("<i class='fa fa-bars'></i> ");
+    $('li > a[href="annotated.html"] > span').before("<i class='fa fa-list-ul'></i> ");
+    $('li > a[href="classes.html"] > span').before("<i class='fa fa-book'></i> ");
+    $('li > a[href="inherits.html"] > span').before("<i class='fa fa-sitemap'></i> ");
+    $('li > a[href="functions.html"] > span').before("<i class='fa fa-list'></i> ");
+    $('li > a[href="functions_func.html"] > span').before("<i class='fa fa-list'></i> ");
+    $('li > a[href="functions_vars.html"] > span').before("<i class='fa fa-list'></i> ");
+    $('li > a[href="functions_enum.html"] > span').before("<i class='fa fa-list'></i> ");
+    $('li > a[href="functions_eval.html"] > span').before("<i class='fa fa-list'></i> ");
+    $('img[src="ftv2ns.png"]').replaceWith('<span class="label label-danger">N</span> ');
+    $('img[src="ftv2cl.png"]').replaceWith('<span class="label label-danger">C</span> ');
+
+    $("ul.tablist").addClass("nav nav-pills nav-justified");
+    $("ul.tablist").css("margin-top", "0.5em");
+    $("ul.tablist").css("margin-bottom", "0.5em");
+    $("li.current").addClass("active");
+    $("iframe").attr("scrolling", "yes");
+
+    $("#nav-path > ul").addClass("breadcrumb");
+
+    $("table.params").addClass("table");
+    $("div.ingroups").wrapInner("<small></small>");
+    $("div.levels").css("margin", "0.5em");
+    $("div.levels > span").addClass("btn btn-default btn-xs");
+    $("div.levels > span").css("margin-right", "0.25em");
+
+    $("table.directory").addClass("table table-striped");
+    $("div.summary > a").addClass("btn btn-default btn-xs");
+    $("table.fieldtable").addClass("table");
+    $(".fragment").addClass("well");
+    $(".memitem").addClass("panel panel-default");
+    $(".memproto").addClass("panel-heading");
+    $(".memdoc").addClass("panel-body");
+    $("span.mlabel").addClass("label label-info");
+
+    $("table.memberdecls").addClass("table");
+    $("[class^=memitem]").addClass("active");
+
+    $("div.ah").addClass("btn btn-default");
+    $("span.mlabels").addClass("pull-right");
+    $("table.mlabels").css("width", "100%")
+    $("td.mlabels-right").addClass("pull-right");
+
+    $("div.ttc").addClass("panel panel-primary");
+    $("div.ttname").addClass("panel-heading");
+    $("div.ttname a").css("color", 'white');
+    $("div.ttdef,div.ttdoc,div.ttdeci").addClass("panel-body");
+
+    $('#MSearchBox').parent().remove();
+
+    $('div.fragment.well div.line:first').css('margin-top', '15px');
+    $('div.fragment.well div.line:last').css('margin-bottom', '15px');
+	
+	$('table.doxtable').removeClass('doxtable').addClass('table table-striped table-bordered').each(function(){
+		$(this).prepend('<thead></thead>');
+		$(this).find('tbody > tr:first').prependTo($(this).find('thead'));
+		
+		$(this).find('td > span.success').parent().addClass('success');
+		$(this).find('td > span.warning').parent().addClass('warning');
+		$(this).find('td > span.danger').parent().addClass('danger');
+	});
+	
+	
+
+    if($('div.fragment.well div.ttc').length > 0)
+    {
+        $('div.fragment.well div.line:first').parent().removeClass('fragment well');
+    }
+
+    $('table.memberdecls').find('.memItemRight').each(function(){
+        $(this).contents().appendTo($(this).siblings('.memItemLeft'));
+        $(this).siblings('.memItemLeft').attr('align', 'left');
+    });
+	
+	function getOriginalWidthOfImg(img_element) {
+		var t = new Image();
+		t.src = (img_element.getAttribute ? img_element.getAttribute("src") : false) || img_element.src;
+		return t.width;
+	}
+	
+	$('div.dyncontent').find('img').each(function(){
+		if(getOriginalWidthOfImg($(this)[0]) > $('#content>div.container').width())
+			$(this).css('width', '100%');
+	});
+	
+	$(".memitem").removeClass('memitem');
+    $(".memproto").removeClass('memproto');
+    $(".memdoc").removeClass('memdoc');
+	$("span.mlabel").removeClass('mlabel');
+	$("table.memberdecls").removeClass('memberdecls');
+    $("[class^=memitem]").removeClass('memitem');
+    $("span.mlabels").removeClass('mlabels');
+    $("table.mlabels").removeClass('mlabels');
+    $("td.mlabels-right").removeClass('mlabels-right');
+	$(".navpath").removeClass('navpath');
+	$("li.navelem").removeClass('navelem');
+	$("a.el").removeClass('el');
+	$("div.ah").removeClass('ah');
+	$("div.header").removeClass("header");
+	
+	$('.mdescLeft').each(function(){
+		if($(this).html()=="&nbsp;") {
+			$(this).siblings('.mdescRight').attr('colspan', 2);
+			$(this).remove();
+		}
+	});
+	$('td.memItemLeft').each(function(){
+		if($(this).siblings('.memItemRight').html()=="") {
+			$(this).attr('colspan', 2);
+			$(this).siblings('.memItemRight').remove();
+		}
+	});
+});

src/NeuralNetwork/FeedForward.cpp

@@ -33,7 +33,7 @@ FFNeuron& FFLayer::operator[](const size_t& neuron)
 
 }
 
-FeedForward::FeedForward(std::initializer_list<size_t> s, double lam, std::function<float(const size_t&layer, const size_t &neuron, const size_t &weight)> weightInit): ACyclicNetwork(lam),layers(s.size())
+FeedForward::FeedForward(std::initializer_list<size_t> s, double lam, FeedForwardInitializer weightInit): ACyclicNetwork(lam),layers(s.size())
 {
 	transfer = new TransferFunction::TransferFunction*[s.size()];
 	weights= new float**[s.size()];

src/NeuralNetwork/FeedForward.h

@@ -4,9 +4,9 @@
 #include "../Problem"
 #include "../Solution"
 #include "Network"
+
 #include "TransferFunction/Sigmoid.h"
 #include "TransferFunction/TransferFunction.h"
-#include "TransferFunction/HyperbolicTangent.h"
 
 #include <vector>
 #include <initializer_list>
@@ -78,16 +78,38 @@ namespace NeuralNetwork
 			float lambda;
 	};
 
+	/**
+	 * @brief typedef for FeedForward network initializating function
+	 */
+	typedef std::function<float(const size_t&layer, const size_t &neuron, const size_t &weight)> FeedForwardInitializer;
+
+	/**
+	 * @author Tomas Cernik (Tom.Cernik@gmail.com)
+	 * @brief Class representing FeedForward network
+	 * @see ACyclicNetwork
+	 */
 	class FeedForward:public ACyclicNetwork
 	{
 		public:
+			/**
+			 * @brief Constructor for FeedForward
+			 * @param s is initiaizer for layers (it's sizes)
+			 * @param lam is parametr for TransferFunction
+			 * @param weightInit is weight initializer function
+			 */
 			FeedForward(std::initializer_list<size_t> s, double lam=Shin::NeuralNetwork::lambda,
-				std::function<float(const size_t&layer, const size_t &neuron, const size_t &weight)> weightInit=
+			FeedForwardInitializer weightInit=
 					[](const size_t&, const size_t &, const size_t &)->float{ return 1.0-((float)(rand()%2001))/1000.0;}
 			);
 			virtual ~FeedForward();
 
+			/**
+			 * @brief we don't want to allow network to be copied
+			 */
 			FeedForward(const FeedForward &f) = delete; //TODO
+			/**
+			 * @brief we don't want to allow network to be copied
+			 */
 			FeedForward operator=(const FeedForward &f)=delete;
 
 			virtual Solution solve(const Problem& p) override;
@@ -103,7 +125,7 @@ namespace NeuralNetwork
 			float **inputs=nullptr;
 			TransferFunction::TransferFunction **transfer=nullptr;
 			size_t *layerSizes=nullptr;
-			size_t layers;
+			size_t layers;/**< Number of layers */
 	};
 
 }