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

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first hg version after svn
author wolffd
date Tue, 10 Feb 2015 15:05:51 +0000
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wolffd@0 1 function draw_dot(adj,varargin);
wolffd@0 2 %DRAW_DOT Draw a graph.
wolffd@0 3 % DRAW_DOT(ADJ) plots the graph ADJ in the current figure window, using
wolffd@0 4 % 'neato' to optimize the layout.
wolffd@0 5 %
wolffd@0 6 % Optional arguments can be passed as name/value pairs: [default]
wolffd@0 7 %
wolffd@0 8 % 'isbox' - a vector specifying which nodes should be boxed [0]
wolffd@0 9 % 'rotate' - rotate the graph so that nodes are vertically aligned [1]
wolffd@0 10 % 'tolerance' - alignment tolerance for 'rotate' [0.001]
wolffd@0 11 % 'start' - a random seed (to select different solutions)
wolffd@0 12 % 'options' - a string of command-line options for 'neato' ['']
wolffd@0 13 % All of the optional arguments to graph_to_dot are also supported, such as
wolffd@0 14 % 'node_label'.
wolffd@0 15 %
wolffd@0 16 % See also GRAPH_TO_DOT.
wolffd@0 17 %
wolffd@0 18 % Example:
wolffd@0 19 % size=15; Adj = rand(size) > .8;
wolffd@0 20 % Adj2 = triu(Adj,1)+ triu(Adj,1)' + diag(zeros(size,1));
wolffd@0 21 % draw_dot(Adj2)
wolffd@0 22
wolffd@0 23 % Original: Leon Peshkin
wolffd@0 24 % Modified by Tom Minka
wolffd@0 25
wolffd@0 26 % minka
wolffd@0 27 N = size(adj,1);
wolffd@0 28 unique_labels = cellstr(num2str((1:N)','%-1d'));
wolffd@0 29 labels = unique_labels;
wolffd@0 30 isbox = zeros(N,1);
wolffd@0 31 rotate_flag = 1;
wolffd@0 32 tolerance = 0.001;
wolffd@0 33 options = '';
wolffd@0 34 for i = 1:2:length(varargin)
wolffd@0 35 switch varargin{i}
wolffd@0 36 case 'node_label', labels = varargin{i+1};
wolffd@0 37 % replace with unique labels
wolffd@0 38 varargin{i+1} = unique_labels;
wolffd@0 39 case 'isbox', isbox = varargin{i+1};
wolffd@0 40 case 'rotate', rotate_flag = varargin{i+1};
wolffd@0 41 case 'tolerance', tolerance = varargin{i+1};
wolffd@0 42 case 'start', start = varargin{i+1};
wolffd@0 43 options = [options ' -Gstart=' num2str(start)];
wolffd@0 44 case 'options', options = [options ' ' varargin{i+1}];
wolffd@0 45 end
wolffd@0 46 end
wolffd@0 47
wolffd@0 48 if ispc, shell = 'dos'; else, shell = 'unix'; end % Which OS ?
wolffd@0 49
wolffd@0 50 cmdline = strcat(shell,'(''neato -V'')');
wolffd@0 51 status = eval(cmdline);
wolffd@0 52 %[status, result] = dos('neato -V'); % request version to check NEATO
wolffd@0 53 if status == 1, fprintf('Complaining \n'); exit, end
wolffd@0 54
wolffd@0 55 tmpDOTfile = '_GtDout.dot'; % to be platform independant no use of directories
wolffd@0 56 tmpLAYOUT = '_LAYout.dot';
wolffd@0 57 graph_to_dot(adj > 0, 'filename', tmpDOTfile, 'node_label', unique_labels, varargin{:}); % save in file
wolffd@0 58
wolffd@0 59 cmdline = strcat([shell '(''neato -Tdot ' tmpDOTfile options ' -o ' tmpLAYOUT ''')']); % preserve trailing spaces
wolffd@0 60 status = eval(cmdline); % get NEATO todo layout
wolffd@0 61
wolffd@0 62 [adj, permuted_labels, x, y] = dot_to_graph(tmpLAYOUT); % load layout
wolffd@0 63 delete(tmpLAYOUT); delete(tmpDOTfile); % clean up temporary files
wolffd@0 64
wolffd@0 65 % permute the original arguments to match permuted_labels.
wolffd@0 66 order = [];
wolffd@0 67 for i = 1:length(permuted_labels)
wolffd@0 68 j = strmatch(permuted_labels{i},unique_labels,'exact');
wolffd@0 69 order(i) = j(1);
wolffd@0 70 end
wolffd@0 71 labels = labels(order);
wolffd@0 72 isbox = isbox(order);
wolffd@0 73 if rotate_flag
wolffd@0 74 [x,y] = best_rotation(x,y,tolerance);
wolffd@0 75 end
wolffd@0 76
wolffd@0 77 figure(1); clf; axis square % now plot
wolffd@0 78 [x, y, h] = draw_graph(adj>0, labels, isbox, x, y, varargin{:});
wolffd@0 79
wolffd@0 80
wolffd@0 81 function [x,y] = best_rotation(x,y,h)
wolffd@0 82 % Rotate the points to maximize the horizontal and vertical alignment.
wolffd@0 83 % Written by Tom Minka.
wolffd@0 84
wolffd@0 85 xm = mean(x);
wolffd@0 86 ym = mean(y);
wolffd@0 87 xr = max(x)-min(x);
wolffd@0 88 yr = max(y)-min(y);
wolffd@0 89 x = (x-xm)/xr;
wolffd@0 90 y = (y-ym)/yr;
wolffd@0 91
wolffd@0 92 xy = [x(:) y(:)];
wolffd@0 93 if 1
wolffd@0 94 angle = fminbnd(@rotation_cost,-pi/4,pi/4,[],xy,h);
wolffd@0 95 else
wolffd@0 96 angles = linspace(-pi/4,pi/4,40);
wolffd@0 97 e = [];
wolffd@0 98 for i = 1:length(angles)
wolffd@0 99 e(i) = rotation_cost(angles(i),xy,h);
wolffd@0 100 end
wolffd@0 101 %figure(2)
wolffd@0 102 %plot(angles*180/pi,e)
wolffd@0 103 angle = angles(argmin(e));
wolffd@0 104 end
wolffd@0 105 %angle*180/pi
wolffd@0 106 c = cos(angle); s = sin(angle);
wolffd@0 107 xy = xy*[c s; -s c];
wolffd@0 108
wolffd@0 109 x = xy(:,1)*xr+xm;
wolffd@0 110 y = xy(:,2)*yr+ym;
wolffd@0 111
wolffd@0 112
wolffd@0 113 function e = rotation_cost(angle,xy,h)
wolffd@0 114 % xy is 2-column matrix.
wolffd@0 115 % e is small if many x's and y's are aligned.
wolffd@0 116
wolffd@0 117 c = cos(angle); s = sin(angle);
wolffd@0 118 xy = xy*[c s; -s c];
wolffd@0 119 dx = sqdist(xy(:,1)',xy(:,1)');
wolffd@0 120 dy = sqdist(xy(:,2)',xy(:,2)');
wolffd@0 121 dx = setdiag(dx,Inf);
wolffd@0 122 dy = setdiag(dy,Inf);
wolffd@0 123 e = sum(exp(-dx(:)/h))+sum(exp(-dy(:)/h));
wolffd@0 124 e = -e;