BNW using Octave instead of Matlab.

This version of BNW should perform the same as the original version. The only difference is that it uses Octave instead of Matlab when running BayesNet Toolbox during parameter learning.

I am calling this BNW_1.02. It can be accessed at:
compbio.uthsc.edu/BNW_1.02

1 files changed, 667 insertions, 0 deletions

diff --git a/sourcecodes/network_layout_evd.php~ b/sourcecodes/network_layout_evd.php~
new file mode 100644
index 00000000..a5909436
--- /dev/null
+++ b/sourcecodes/network_layout_evd.php~
@@ -0,0 +1,667 @@
+<?php 
+include("structuremap.php");
+
+function levelmap($inx,$name,$mapdata)
+{
+
+$leve_l=array();
+$leve_l=explode("\n",$mapdata);
+$leve_d=array();
+
+foreach($leve_l as $l)
+{ 
+  $l=trim($l);
+  $leve_d=explode("\t",$l);
+  $inxname=trim($leve_d[0]);
+  $name=trim($name);
+  if($inxname==$name)
+    return $leve_d[$inx];
+}
+           
+}
+
+
+////////////////////////////////////Read data from net_figure file///////////////////////Graphp Display/////////////////////////////////////////////
+$dir="./data/";
+
+
+$keyval=$_GET["My_key"];
+
+$matfile=$dir."$keyval"."net_figure.txt";
+
+$data_val="";
+
+$matrix=file("$matfile");
+$matrix1=file_get_contents("$matfile");   
+
+$lfile=$dir.$keyval."nlevels.txt";
+$levelmap=file_get_contents($lfile);   
+
+
+$str_arrmat=array();
+$str_arrmat=explode("\n",$matrix1);
+
+if($str_arrmat[2]=="" || $matrix1=="")
+{
+?>
+<h1><font color=blue>Error: Unable to display your network structure.</font></h1>
+<?php
+exit;
+}
+
+$datamat=array();
+$data_read=array();
+ 
+$node=trim($str_arrmat[0]);
+/*
+if($node<=5)
+{
+  $width=200;
+  $hieght=150;
+  $font=14;
+}
+else if($node>5 && $node<=7)
+{
+  $width=150;
+  $hieght=120;
+  $font=12;
+
+}
+else if($node>7 && $node<=10)
+{
+  $width=110;
+  $hieght=85;
+  $font=10;
+}
+else 
+{
+  $width=80;
+  $hieght=60;
+  $font=8;
+}
+*/
+  $width=150;
+  $hieght=150;
+  $font=12;
+
+$r_index=$node+2;
+
+for($i=0;$i<$node;$i++)
+{
+$datamat=explode("\t",$str_arrmat[$r_index]);
+$data_read[$i][0]=trim($datamat[0]);  //name
+$data_read[$i][1]=trim($datamat[1]);  //datatype
+$col_in=2;
+$r_index+=4;
+	if($datamat[1]==1)  //type=coninuous
+	{
+         for($j=1;$j<=101;$j++)
+         {
+           $datamat=explode("\t",$str_arrmat[$r_index]);
+           $data_read[$i][$col_in]=trim($datamat[0]);  //x data
+         //  echo $data_read[$i][$col_in];
+          // echo '&nbsp';
+
+           $col_in++;
+           $data_read[$i][$col_in]=trim($datamat[1]);  //y data
+          // echo $data_read[$i][$col_in];
+	   // echo '&nbsp';
+
+           $col_in++;
+           $r_index++; // increment to point next data
+           // echo "<br />"; 
+         } 
+	}
+	if($datamat[1]>1)  //type=descrete
+	{
+         $iter=$datamat[1];
+         for($j=1;$j<=$iter;$j++)
+         {
+           $datamat=explode("\t",$str_arrmat[$r_index]);
+           $data_read[$i][$col_in]=trim($datamat[0]);  //x data
+           //use level mapping
+           $data_read[$i][$col_in]=levelmap($data_read[$i][$col_in],$data_read[$i][0],$levelmap);
+ 
+           $col_in++;
+           $data_read[$i][$col_in]=trim($datamat[1]);  //y data
+         
+           $col_in++;
+           $r_index++; // increment to point next data
+           //echo "<br />"; 
+         } 
+	}
+
+}
+
+
+
+
+////////////////////////////////////////////////Graphviz data read////////////////////////////////////////////////////////////////////////////////
+
+$grv=$dir.$keyval."graphviz.txt";
+$line=shell_exec('/usr/bin/dot -Tplain -y '.$grv);
+
+
+$grviz_name_list=array();
+$g_file_name="./data/".$keyval."grviz_name_file.txt";
+$grviz_name=file_get_contents("$g_file_name");
+$grviz_name_list=explode("\n",$grviz_name);
+
+
+
+//$foutnew=fopen("contentofgraphviz.txt","w");
+//fwrite($foutnew,"$line");
+
+
+//$grfilename=$keyval."graphviz.txt";
+//$cmd="/usr/bin/dot -Tplain -y  $grfilename";
+//$line=system($cmd);
+
+
+
+
+$str_arrname=array();
+$str_arrname=explode("\n",$line);
+$data=array();
+$ID_data=array();
+$i=0;
+$ii=0;
+foreach($str_arrname as $row)
+{
+  $i++;
+  if($i>1)
+  {
+       
+  	$data=explode(" ",$row);
+       $j=0;
+       $k=0;
+       $flag=0;
+  	foreach($data as $cell)
+	{
+             
+             $j++;
+             
+             $cell=trim($cell);
+             //echo $cell;
+             //echo '&nbsp';
+             if($j==1 && $cell=="node")
+             {
+                $flag=1;
+             }  
+               
+             if($j>1 && $j<5 && $flag==1)
+             {
+    		  //echo $cell;
+   		  //echo '&nbsp';
+                if($j==2)
+                {
+                    
+                   $ID_data[$ii][$k]=$grviz_name_list[$cell];
+                } 
+                else
+                   $ID_data[$ii][$k]=round($cell/10*900);
+               // echo $ID_data[$ii][$k];
+                //echo '&nbsp';
+
+                $k++; 
+             }
+       } 
+  
+       if($flag==1)
+       {
+          $ID_data[$ii][3]=$ID_data[$ii][1]+100;
+          $ID_data[$ii][4]=$ID_data[$ii][2]+150; 
+          $ID_data[$ii][5]=$ID_data[$ii][1]+100;
+          $ID_data[$ii][6]=$ID_data[$ii][2]; 
+          $ii++;
+          //echo "<br />"; 
+       } 
+     // echo "<br />"; 
+	
+  }
+}
+
+$nnode=$ii;
+$edge_data=array();
+
+$i=0;
+$ii=0;
+
+foreach($str_arrname as $row)
+{
+  $i++;
+  if($i>1)
+  {
+       
+  	$data=explode(" ",$row);
+       $j=0;
+       
+       $flag=0;
+       $number_of_point=0;
+       $index=0; 
+  	foreach($data as $cell)
+	{
+             $j++;
+             $cell=trim($cell);
+         
+             if($j==1 && $cell=="edge")
+             {
+                $flag=1;
+             }  
+               
+             if($j==2 && $flag==1)
+             {
+                
+                for($k=0;$k<$nnode;$k++)
+                {     
+                      $cell=$grviz_name_list[$cell];
+                      if($cell==$ID_data[$k][0])
+                      {
+                          $edge_data[$ii][0]=$ID_data[$k][3];
+                          $edge_data[$ii][1]=$ID_data[$k][4];
+                      }                     
+
+                }
+               
+             }
+             else if($j==3 && $flag==1)
+             {
+               for($k=0;$k<$nnode;$k++)
+                {
+                      if($cell==$ID_data[$k][0])
+                      {
+                          $edge_data[$ii][2]=$ID_data[$k][5];
+                          $edge_data[$ii][3]=$ID_data[$k][6];
+                      }                     
+
+                }
+
+             }
+             else if($j==4 && $flag==1)
+             {
+                  $edge_data[$ii][4]=$cell;
+                  $number_of_point=$cell*2;
+                  $index=5;
+             }
+             else if($j>4 && $number_of_point>0 && $flag==1)
+             {
+                if(($j%2)!=0)
+                  $edge_data[$ii][$index]=round($cell/10*900)+60;//+30+30;
+                else
+                  $edge_data[$ii][$index]=round($cell/10*900)+48;//+18+30;
+
+                $number_of_point--;
+                $index++;
+             }
+
+
+             
+       } 
+       if($flag==1)
+       {
+          $ii++;
+          //echo "<br />"; 
+       } 
+ 	
+  }
+}
+
+
+$nedges=$ii;
+
+?>
+
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<html xmlns="http://www.w3.org/1999/xhtml">
+<head>
+<meta http-equiv="content-type" content="text/html; charset=utf-8"/>
+<script type="text/javascript" src="http://www.google.com/jsapi"></script>
+ <script type="text/javascript">
+  google.load('visualization', '1', {packages: ['corechart']});
+ </script>
+ 
+
+<?php 
+$data_val="";
+
+for($i=0;$i<$nnode;$i++)
+ {
+////////////////////////////select node //////////////////////////////////////
+ $name=$ID_data[$i][0];
+ $fname="draw_".$name."()";
+ $data_val.=$name;
+ for($j=0;$j<$node;$j++)
+ {
+    if($data_read[$j][0]==$name)
+    {
+       $s_i=$j;
+       break;
+    } 
+ }
+ 
+/////////////////////////////////Display nodes//////////////////////////////////////////////////////////
+?>    
+ <script type="text/javascript">
+
+
+<?php
+  $node_type=$data_read[$s_i][1];
+  if($node_type>1) //discrete node
+  { 
+?>
+  
+ 
+  function <?php print($fname);?> {
+  // Create and populate the data table.
+ 
+  var data = google.visualization.arrayToDataTable([
+   ['<?php print($name);?>', ''],
+  <?php
+  $c_i=2; 
+
+  for($j=0;$j<$node_type-1;$j++) 
+  {     
+       $val1=trim($data_read[$s_i][$c_i]);
+
+
+       $c_i++;
+       $val2=trim($data_read[$s_i][$c_i]);
+       $c_i++;
+       $data_val.="\t".$val2;
+        
+  ?>
+   ['<?php print($val1);?>', <?php print($val2);?>],
+
+  <?php
+  }
+  if($j==$node_type-1)
+  {
+        $val1=trim($data_read[$s_i][$c_i]);
+
+
+       $c_i++;
+       $val2=trim($data_read[$s_i][$c_i]);
+       $c_i++;
+       $data_val.="\t".$val2."\n";
+  ?> 
+    ['<?php print($val1);?>', <?php print($val2);?>]
+<?php
+  }
+?>
+  ]);
+      
+        // Create and draw the visualization.
+      
+      var cnode="<?php print($name); ?>";
+      var keyv="<?php print($keyval);?>";  
+
+        var chart = new google.visualization.BarChart(document.getElementById('<?php print($name);?>'));
+        function selectHandler() {
+          var selectedItem = chart.getSelection()[0];
+          if (selectedItem) {
+            var topping = data.getValue(selectedItem.row, 0);
+            
+            var s = window.prompt('Selected evidence ' + topping + ' for ' + cnode + '. Enter new evidence ', topping );
+           
+            window.location.href = "add_evd.php?name=" + cnode + "&evidence=" + s + "&My_key="  + keyv;
+           
+
+  
+              //alert('The user selected ' + topping + topname);
+          }
+        } 
+         chart.draw(data,
+                 {title:"<?php print($name);?>", titleTextStyle: {fontSize: <?php print($font);?>},
+                  width:<?php print($width);?>, height:<?php print($hieght);?>,
+                  vAxis: {title: "State", textStyle: {fontSize:<?php print($font);?>}},
+		    hAxis: {title: "Fraction", minValue: 0, maxValue: 1, gridlines: {count: 3}}, legend: {position: 'none'},
+                  backgroundColor: {stroke: 'black', strokeWidth: 5}}
+            );
+        google.visualization.events.addListener(chart, 'select', selectHandler);  
+
+  }
+<?php
+ }
+ else //continuous node
+ {
+?>
+  function <?php print($fname);?> {
+  // Create and populate the data table.
+  var data = google.visualization.arrayToDataTable([
+   ['<?php print($name);?>', ''],
+  <?php
+  $c_i=2;
+  for($j=0;$j<100;$j++) 
+  {
+       $val1=trim($data_read[$s_i][$c_i]);
+       $val1=map($name,$val1,$keyval);
+
+       $c_i++;
+       $val2=trim($data_read[$s_i][$c_i]);
+       $c_i++;         
+       $data_val.="\t".$val2;
+  ?>
+   ['<?php print($val1);?>', <?php print($val2);?>],
+
+  <?php
+  }
+  if($j==100)
+  {
+       $val1=trim($data_read[$s_i][$c_i]);
+       $val1=map($name,$val1,$keyval);
+
+       $c_i++;
+       $val2=trim($data_read[$s_i][$c_i]);
+       $c_i++;
+       $data_val.="\t".$val2."\n";
+  ?> 
+    ['<?php print($val1);?>', <?php print($val2);?>]
+<?php
+  }
+?>
+  ]);
+      
+        // Create and draw the visualization.
+      var cnode="<?php print($name); ?>";
+      var keyv="<?php print($keyval);?>";  
+        var chart = new google.visualization.LineChart(document.getElementById('<?php print($name);?>'));
+
+        function selectHandler() {
+          var selectedItem = chart.getSelection()[0];
+          if (selectedItem) {
+           
+            var topping = data.getValue(selectedItem.row, 0);
+            var s = window.prompt('Selected evidence ' + topping + ' for ' + cnode + '. Enter new evidence ', topping );
+            window.location.href = "add_evd.php?name=" + cnode + "&evidence=" + s + "&My_key=" + keyv;  
+
+          }
+        }
+            chart.draw(data, {curveType: "function",
+                  title:"<?php print($name);?>", titleTextStyle: {fontSize: <?php print($font);?>},
+			legend: {position: 'none'},
+                  width:<?php print($width);?>, height:<?php print($hieght);?>,
+                  hAxis: {maxValue: 1, minValue: 0},
+			vAxis: {maxValue: 1, minValue: 0},
+                  backgroundColor: {stroke: 'black', strokeWidth: 5}}
+            );
+           google.visualization.events.addListener(chart, 'select', selectHandler); 
+       }
+
+<?php
+ }
+?>
+</script>
+<?php
+///////////////////////////end of display nodes////////////////////////////////////////////////
+}
+
+///////////////////////////////////write data to file///////////////////////////////////////////////////////////
+$fl=$dir.$keyval."structure_old.txt";
+$fp = fopen("$fl","w");
+fwrite($fp,"$data_val");
+?>
+
+
+
+<script type="text/javascript">
+function canvas_arrow(context, fromx, fromy, tox, toy){
+    var headlen = 15;
+    var dx = tox-fromx;
+    var dy = toy-fromy;
+    var angle = Math.atan2(dy,dx);
+    context.moveTo(fromx,fromy);
+    context.lineTo(tox,toy);
+    context.lineTo(tox-headlen*Math.cos(angle-Math.PI/6),toy-headlen*Math.sin(angle-Math.PI/6));
+    context.moveTo(tox,toy);
+    context.lineTo(tox-headlen*Math.cos(angle+Math.PI/6),toy-headlen*Math.sin(angle+Math.PI/6));
+}
+</script>
+
+<script type="text/javascript">
+function canvas_arrow_head(context, fromx, fromy, tox, toy){
+    var headlen = 15;
+    var dx = tox-fromx;
+    var dy = toy-fromy;
+    var angle = Math.atan2(dy,dx);
+    context.moveTo(tox,toy);
+    context.lineTo(tox-headlen*Math.cos(angle-Math.PI/6),toy-headlen*Math.sin(angle-Math.PI/6));
+    context.moveTo(tox,toy);
+    context.lineTo(tox-headlen*Math.cos(angle+Math.PI/6),toy-headlen*Math.sin(angle+Math.PI/6));
+}
+</script>
+
+
+</head>
+
+<body>
+<canvas id="test" width="3000" height="3000" style="position:absolute">
+<script>
+function canvas_arrow_draw(n, polypts,context){
+
+//Create jsGraphics object
+var headlen = 10;
+/*
+var hexno=new String;
+arr=new Array("0","1","2","3","4","5","6","7","8","9","a","b","c","d","e","f");
+var n1=Math.round(Math.random()*15);
+var n2=Math.round(Math.random()*15);
+var n3=Math.round(Math.random()*15);
+var n4=Math.round(Math.random()*15);
+var n5=Math.round(Math.random()*15);
+var n6=Math.round(Math.random()*15);
+hexno="#"+arr[n1]+""+arr[n2]+""+arr[n3]+""+arr[n4]+""+arr[n5]+""+arr[n6];
+*/
+hexno="black";
+var polypoints = new Array();
+var n2=n*2;
+
+
+var sx=polypts[0];
+var sy=polypts[1];
+ 
+var sx1=polypts[n2-4];
+var sy1=polypts[n2-3];
+var ex1=polypts[n2-2];
+var ey1=polypts[n2-1];
+
+context.beginPath();
+canvas_arrow_head(context,sx1,sy1,ex1,ey1);
+
+context.moveTo(polypts[0],polypts[1]);
+nm=n%3;
+ni=(n-nm)/3;
+
+for(i=0;i<ni;i++)
+{
+  i11=i*6+2;
+  i12=i*6+3;
+  i21=i*6+4;
+  i22=i*6+5;
+  i31=i*6+6;
+  i32=i*6+7;
+
+  context.bezierCurveTo(polypts[i11],polypts[i12],polypts[i21],polypts[i22],polypts[i31],polypts[i32]);
+  context.moveTo(polypts[i31],polypts[i32]);
+
+ // polypoints[i] = new jxPoint(polypts[i1], polypts[i2]);
+}
+
+
+if(nm==2)
+{
+  context.moveTo(polypts[i21],polypts[i22]);
+  context.bezierCurveTo(polypts[i31],polypts[i32],sx1,sy1,ex1,ey1);
+  context.moveTo(ex1,ey1);
+
+}
+
+ context.strokeStyle = hexno;
+ context.stroke();
+
+}
+
+
+var canvas=document.getElementById("test");
+var context = canvas.getContext("2d");
+context.lineWidth = 3;
+
+<?php
+for($i=0;$i<$nedges;$i++)
+{
+
+   $n=$edge_data[$i][4]; 
+   $n2=$n*2;
+   
+?>
+var polypoints = new Array();
+var j=0;
+var n="<?php print($n);?>";
+<?php
+for($j=0;$j<$n2;$j++)
+{
+$inx=$j+5;
+$data=$edge_data[$i][$inx];
+
+?>
+	polypoints[j] = "<?php print($data);?>";
+
+       j++;
+<?php
+}
+?>
+canvas_arrow_draw(n,polypoints,context);
+<?php
+}
+?>
+
+
+
+</script>
+</canvas>
+
+
+<?php 
+for($i=0;$i<$nnode;$i++)
+{
+  $x=$ID_data[$i][1]-8; $y=$ID_data[$i][2]-20; 
+
+  $name=$ID_data[$i][0];
+?>
+
+<script type="text/javascript">
+   google.setOnLoadCallback(draw_<?php print($name)?>);
+</script>
+<div id="<?php print($name)?>" style="left: <?php print($x)?>px; top: <?php print($y)?>px; width:<?php print($width);?>; height:<?php print($hieght);?>; position: absolute"></div>
+
+<?php 
+}
+?>
+
+
+</body>
+
+
+
+</html>
+
+