diff toolboxes/FullBNT-1.0.7/GraphViz/draw_dot.m @ 0:e9a9cd732c1e tip

first hg version after svn

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/toolboxes/FullBNT-1.0.7/GraphViz/draw_dot.m	Tue Feb 10 15:05:51 2015 +0000
@@ -0,0 +1,124 @@
+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;