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, 124 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/GraphViz/draw_dot.m b/sourcecodes/bnt-master/GraphViz/draw_dot.m
new file mode 100644
index 00000000..9624172c
--- /dev/null
+++ b/sourcecodes/bnt-master/GraphViz/draw_dot.m
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+function draw_dot(adj,varargin);
+%DRAW_DOT   Draw a graph.
+% DRAW_DOT(ADJ) plots the graph ADJ in the current figure window, using 
+% 'neato' to optimize the layout.
+%
+% Optional arguments can be passed as name/value pairs: [default]
+%
+% 'isbox'     - a vector specifying which nodes should be boxed [0]
+% 'rotate'    - rotate the graph so that nodes are vertically aligned [1]
+% 'tolerance' - alignment tolerance for 'rotate' [0.001]
+% 'start'     - a random seed (to select different solutions)
+% 'options'   - a string of command-line options for 'neato' ['']
+% All of the optional arguments to graph_to_dot are also supported, such as
+% 'node_label'.
+%
+% See also GRAPH_TO_DOT.
+%
+% Example:
+% size=15; Adj = rand(size) > .8;
+% Adj2 = triu(Adj,1)+ triu(Adj,1)' + diag(zeros(size,1));
+% draw_dot(Adj2)
+
+% Original: Leon Peshkin  
+% Modified by Tom Minka
+
+% minka
+N = size(adj,1);
+unique_labels = cellstr(num2str((1:N)','%-1d'));
+labels = unique_labels;
+isbox = zeros(N,1);
+rotate_flag = 1;
+tolerance = 0.001;
+options = '';
+for i = 1:2:length(varargin)
+  switch varargin{i}
+    case 'node_label', labels = varargin{i+1}; 
+      % replace with unique labels
+      varargin{i+1} = unique_labels;
+    case 'isbox', isbox = varargin{i+1};
+    case 'rotate', rotate_flag = varargin{i+1};
+    case 'tolerance', tolerance = varargin{i+1};
+    case 'start', start = varargin{i+1}; 
+      options = [options ' -Gstart=' num2str(start)];
+    case 'options', options = [options ' ' varargin{i+1}];
+  end
+end
+
+if ispc, shell = 'dos'; else, shell = 'unix'; end  %  Which OS ?
+
+cmdline = strcat(shell,'(''neato -V'')');
+status = eval(cmdline);
+%[status, result] = dos('neato -V');  % request version to check NEATO
+if status == 1,  fprintf('Complaining \n'); exit, end
+
+tmpDOTfile = '_GtDout.dot';            % to be platform independant no use of directories
+tmpLAYOUT  = '_LAYout.dot'; 
+graph_to_dot(adj > 0, 'filename', tmpDOTfile, 'node_label', unique_labels, varargin{:});  % save in file
+
+cmdline = strcat([shell '(''neato -Tdot ' tmpDOTfile options ' -o ' tmpLAYOUT ''')']); % preserve trailing spaces 
+status = eval(cmdline);         %  get NEATO todo layout
+
+[adj, permuted_labels, x, y] = dot_to_graph(tmpLAYOUT);  %  load layout 
+delete(tmpLAYOUT); delete(tmpDOTfile);     % clean up temporary files
+
+% permute the original arguments to match permuted_labels.
+order = [];
+for i = 1:length(permuted_labels)
+  j = strmatch(permuted_labels{i},unique_labels,'exact');
+  order(i) = j(1);
+end
+labels = labels(order);
+isbox = isbox(order);
+if rotate_flag
+  [x,y] = best_rotation(x,y,tolerance);
+end
+
+figure(1); clf; axis square      %  now plot 
+[x, y, h] = draw_graph(adj>0, labels, isbox, x, y, varargin{:});
+
+
+function [x,y] = best_rotation(x,y,h)
+% Rotate the points to maximize the horizontal and vertical alignment.
+% Written by Tom Minka.
+
+xm = mean(x);
+ym = mean(y);
+xr = max(x)-min(x);
+yr = max(y)-min(y);
+x = (x-xm)/xr;
+y = (y-ym)/yr;
+
+xy = [x(:) y(:)];
+if 1
+  angle = fminbnd(@rotation_cost,-pi/4,pi/4,[],xy,h);
+else
+  angles = linspace(-pi/4,pi/4,40);
+  e = [];
+  for i = 1:length(angles)
+    e(i) = rotation_cost(angles(i),xy,h);
+  end
+  %figure(2)
+  %plot(angles*180/pi,e)
+  angle = angles(argmin(e));
+end
+%angle*180/pi
+c = cos(angle); s = sin(angle);
+xy = xy*[c s; -s c];
+
+x = xy(:,1)*xr+xm;
+y = xy(:,2)*yr+ym;
+
+
+function e = rotation_cost(angle,xy,h)
+% xy is 2-column matrix.
+% e is small if many x's and y's are aligned.
+
+c = cos(angle); s = sin(angle);
+xy = xy*[c s; -s c];
+dx = sqdist(xy(:,1)',xy(:,1)');
+dy = sqdist(xy(:,2)',xy(:,2)');
+dx = setdiag(dx,Inf);
+dy = setdiag(dy,Inf);
+e = sum(exp(-dx(:)/h))+sum(exp(-dy(:)/h));
+e = -e;