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| author | ziejd2 | 2017-09-28 15:04:40 -0500 |
|---|---|---|
| committer | ziejd2 | 2017-09-28 15:04:40 -0500 |
| commit | 8070dc963753142bb86c4ed698d91fd623ed28e7 (patch) | |
| tree | d0f6dd8fc46a49b819aa55c1a90faa14d8448883 /sourcecodes/bnt-master/GraphViz | |
| parent | 7cc31810d53176e805532b2789955f4eedbce6bb (diff) | |
| download | BNW-8070dc963753142bb86c4ed698d91fd623ed28e7.tar.gz | |
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
Diffstat (limited to 'sourcecodes/bnt-master/GraphViz')
27 files changed, 3540 insertions, 0 deletions
diff --git a/sourcecodes/bnt-master/GraphViz/CVS/Entries b/sourcecodes/bnt-master/GraphViz/CVS/Entries new file mode 100644 index 00000000..5af96cda --- /dev/null +++ b/sourcecodes/bnt-master/GraphViz/CVS/Entries @@ -0,0 +1,16 @@ +/README.txt/1.1.1.1/Mon Jun 7 14:33:20 2004// +/approxeq.m/1.1.1.1/Mon Jul 28 22:44:46 2003// +/arrow.m/1.1.1.1/Fri Mar 28 16:35:06 2003// +/dot_to_graph.m/1.1.1.1/Fri Mar 12 23:21:08 2004// +/draw_dbn.m/1.1.1.1/Wed May 29 15:59:54 2002// +/draw_dbn_test.m/1.1.1.1/Sat Jan 18 21:17:18 2003// +/draw_dot.m/1.1.1.1/Wed May 5 13:32:32 2004// +/draw_graph.m/1.1.1.1/Mon Mar 22 22:32:04 2004// +/draw_graph_test.m/1.1.1.1/Mon Jan 20 16:56:02 2003// +/draw_hmm.m/1.1.1.1/Thu Feb 6 03:16:32 2003// +/editGraphGUI.m/1.1.1.1/Tue Jan 27 21:08:48 2004// +/graph_to_dot.m/1.1.1.1/Tue Jun 15 17:50:40 2004// +/make_layout.m/1.1.1.1/Wed May 29 15:59:54 2002// +/my_call.m/1.1.1.1/Tue Jan 27 21:08:38 2004// +/process_options.m/1.1.1.1/Mon Jul 28 22:44:46 2003// +D diff --git a/sourcecodes/bnt-master/GraphViz/CVS/Entries.Log b/sourcecodes/bnt-master/GraphViz/CVS/Entries.Log new file mode 100644 index 00000000..24f16336 --- /dev/null +++ b/sourcecodes/bnt-master/GraphViz/CVS/Entries.Log @@ -0,0 +1 @@ +A D/Old//// diff --git a/sourcecodes/bnt-master/GraphViz/CVS/Repository b/sourcecodes/bnt-master/GraphViz/CVS/Repository new file mode 100644 index 00000000..ba3ef5c8 --- /dev/null +++ b/sourcecodes/bnt-master/GraphViz/CVS/Repository @@ -0,0 +1 @@ +FullBNT/GraphViz diff --git a/sourcecodes/bnt-master/GraphViz/CVS/Root b/sourcecodes/bnt-master/GraphViz/CVS/Root new file mode 100644 index 00000000..f3bd14a6 --- /dev/null +++ b/sourcecodes/bnt-master/GraphViz/CVS/Root @@ -0,0 +1 @@ +:ext:nsaunier@bnt.cvs.sourceforge.net:/cvsroot/bnt diff --git a/sourcecodes/bnt-master/GraphViz/Old/CVS/Entries b/sourcecodes/bnt-master/GraphViz/Old/CVS/Entries new file mode 100644 index 00000000..50af46f1 --- /dev/null +++ b/sourcecodes/bnt-master/GraphViz/Old/CVS/Entries @@ -0,0 +1,6 @@ +/dot_to_graph.m/1.1.1.1/Tue Jan 27 21:01:54 2004// +/draw_dot.m/1.1.1.1/Tue Jan 27 20:42:50 2004// +/draw_graph.m/1.1.1.1/Tue Jan 27 21:03:56 2004// +/graphToDot.m/1.1.1.1/Tue Feb 3 17:15:18 2004// +/pre_pesha_graph_to_dot.m/1.1.1.1/Tue Jan 27 20:47:40 2004// +D diff --git a/sourcecodes/bnt-master/GraphViz/Old/CVS/Repository b/sourcecodes/bnt-master/GraphViz/Old/CVS/Repository new file mode 100644 index 00000000..83ba7005 --- /dev/null +++ b/sourcecodes/bnt-master/GraphViz/Old/CVS/Repository @@ -0,0 +1 @@ +FullBNT/GraphViz/Old diff --git a/sourcecodes/bnt-master/GraphViz/Old/CVS/Root b/sourcecodes/bnt-master/GraphViz/Old/CVS/Root new file mode 100644 index 00000000..f3bd14a6 --- /dev/null +++ b/sourcecodes/bnt-master/GraphViz/Old/CVS/Root @@ -0,0 +1 @@ +:ext:nsaunier@bnt.cvs.sourceforge.net:/cvsroot/bnt diff --git a/sourcecodes/bnt-master/GraphViz/Old/dot_to_graph.m b/sourcecodes/bnt-master/GraphViz/Old/dot_to_graph.m new file mode 100644 index 00000000..59beb8fc --- /dev/null +++ b/sourcecodes/bnt-master/GraphViz/Old/dot_to_graph.m @@ -0,0 +1,107 @@ +function [Adj, labels, x, y] = dot_to_graph(filename) + +% [Adj, labels, x, y] = dot_to_graph(filename) +% Extract a matrix representation, node labels, and node position coordinates +% from a file in GraphViz format http://www.research.att.com/sw/tools/graphviz +% +% INPUTS: +% 'filename' - the file in DOT format containing the graph layout. +% OUTPUT: +% 'Adj' - an adjacency matrix representation of the graph in 'filename'; +% 'labels' - a character array with the names of the nodes of the graph; +% 'x' - a row vector with the x-coordinates of the nodes in 'filename'; +% 'y' - a row vector with the y-coordinates of the nodes in 'filename'. +% +% WARNINGS: not guaranted to parse ANY GraphViz file. Debugged on undirected +% sample graphs from GraphViz(Heawood, Petersen, ER, ngk10_4, process). +% Complaines about RecursionLimit set only to 500 on huge graphs. +% Ignores singletons (disjoint nodes). +% Sample DOT code "ABC.dot", read by [Adj, labels, x, y] = dot_to_graph('ABC.dot') +% digraph G { +% A [pos="28,31"]; +% B [pos="74,87"]; +% A -- B [pos="e,61,71 41,47 46,53 50,58 55,64"]; +% } +% last modified: Jan 2004 +% by Alexi Savov: asavov @wustl.edu | http://artsci.wustl.edu/~azsavov +% Leon Peshkin: pesha @ai.mit.edu | http://www.ai.mit.edu/~pesha + +if ~exist(filename) % Checks whether the specified file exists. + error('* * * File does not exist or could not be found. * * *'); return; +end; + +lines = textread(filename,'%s','delimiter','\n','commentstyle','c'); % Read file into cell array +dot_lines = strvcat(lines); % of lines, ignoring C-style comments + +if findstr(dot_lines(1,:), 'graph ') == [] % Is this a DOT file ? + error('* * * File does not appear to be in valid DOT format. * * *'); return; +end; + +Nlns = size(dot_lines,1); % The number of lines; +labels = {}; +unread = 1:Nlns; % 'unread' list of lines which has not been examined yet +edge_id = 1; +for line_ndx = 1:Nlns % This section sets the adjacency matrix A(Lnode,Rnode) = edge_id. + line = dot_lines(line_ndx,:); + Ddash_pos = strfind(line, ' -- ') + 1; % double dash positions + arrow_pos = strfind(line, ' -> ') + 1; % arrow dash positions + tokens = strread(line,'%s','delimiter',' "'); + left_bound = 1; + for dash_pos = [Ddash_pos arrow_pos]; % if empty - not a POS line + Lnode = sscanf(line(left_bound:dash_pos -2), '%s'); + Rnode = sscanf(line(dash_pos +3 : length(line)-1),'%s',1); + Lndx = strmatch(Lnode, labels, 'exact'); + Rndx = strmatch(Rnode, labels, 'exact'); + if isempty(Lndx) % extend our list of labels + labels{end+1} = Lnode; + Lndx = length(labels); + end + if isempty(Rndx) + labels{end+1} = Rnode; + Rndx = length(labels); + end + Adj(Lndx, Rndx) = edge_id;; + if ismember(dash_pos, Ddash_pos) % The edge is undirected, A(Rndx,LndxL) is also set to 1; + Adj(Rndx, Lndx) = edge_id; + end + edge_id = edge_id + 1; + left_bound = dash_pos + 3; + unread = setdiff(unread, line_ndx); + end +end +Nvrt = length(labels); % number of vertices we found [Do we ever have singleton vertices ???] +% labels = strvcat(labels); % convert to the searchable array +x = zeros(1, Nvrt); +y = zeros(1, Nvrt); +lst_node = 0; + % Find node's position coordinates if they are contained in 'filename'. +for line_ndx = unread % Look for node's coordiantes among the 'unread' lines. + line = dot_lines(line_ndx,:); + bra_pos = strfind(line, '['); % has to have "[" if it has the lable + pos_pos = strfind(line, 'pos'); % position of the "pos" + for node = 1:Nvrt % look through the list of labels + % THE NEXT STATEMENT we assume no label is substring of any other label + lbl_pos = strfind(line, labels{node}); + if (~isempty(lbl_pos) & ~isempty(bra_pos) & (x(node) == 0)) % make sure we have not seen it + if (lbl_pos(1) < bra_pos(1)) % label has to be to the left of braket + lst_node = node; + end + end + end + if (~isempty(pos_pos) & lst_node) % this line contains SOME position + [node_pos] = sscanf(line(pos_pos:length(line)), ' pos = "%d,%d"')'; + x(lst_node) = node_pos(1); + y(lst_node) = node_pos(2); + lst_node = 0; % not to assign position several times + end +end + +if (isempty(find(x)) & (nargout > 2)) % If coordinates were requested, but not found in 'filename'. + warning('File does not contain node coordinates.'); +end; +if ~(size(Adj,1)==size(Adj,2)) % Make sure Adj is a square matrix. ? + Adj = eye(max(size(Adj)),size(Adj,1))*Adj*eye(size(Adj,2),max(size(Adj))); +end; +x = .9*(x-min(x))/range(x)+.05; % normalise and push off margins +y = .9*(y-min(y))/range(y)+.05; + diff --git a/sourcecodes/bnt-master/GraphViz/Old/draw_dot.m b/sourcecodes/bnt-master/GraphViz/Old/draw_dot.m new file mode 100644 index 00000000..d6f37f81 --- /dev/null +++ b/sourcecodes/bnt-master/GraphViz/Old/draw_dot.m @@ -0,0 +1,26 @@ +function draw_dot(adj); +% +% draw_dot(name) +% +% Sample code illustrating use of dot_to_graph.m function +% Leon Peshkin +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'; +directed = 0; % assume UN-directed graph +graph_to_dot(adj > 0, 'directed', directed, 'filename', tmpDOTfile); % save in file + +cmdline = strcat([shell '(''neato -Tdot ' tmpDOTfile ' -o ' tmpLAYOUT ''')']); % preserve trailing spaces +status = eval(cmdline); % get NEATO todo layout + +[adj, labels, x, y] = dot_to_graph(tmpLAYOUT); % load layout +delete(tmpLAYOUT); delete(tmpDOTfile); % clean up temporary files + +figure(1); clf; axis square % now plot +[x, y, h] = draw_graph(adj>0, labels, zeros(size(x,2),1), x, y); \ No newline at end of file diff --git a/sourcecodes/bnt-master/GraphViz/Old/draw_graph.m b/sourcecodes/bnt-master/GraphViz/Old/draw_graph.m new file mode 100644 index 00000000..06e3d7a1 --- /dev/null +++ b/sourcecodes/bnt-master/GraphViz/Old/draw_graph.m @@ -0,0 +1,310 @@ +function [x, y, h] = draw_graph(adj, labels, node_t, x, y) +% DRAW_LAYOUT Draws a layout for a graph +% +% [<X, Y>] = DRAW_LAYOUT(ADJ, <LABELS, ISBOX, X, Y>) +% +% Inputs : +% ADJ : Adjacency matrix (source, sink) +% LABELS : Cell array containing labels <Default : '1':'N'> +% ISBOX : 1 if node is a box, 0 if oval <Default : zeros> +% X, Y, : Coordinates of nodes on the unit square <Default : calls make_layout> +% +% Outputs : +% X, Y : Coordinates of nodes on the unit square +% H : Object handles +% +% Usage Example : [x, y] = draw_layout([0 1;0 0], {'Hidden','Visible'}, [1 0]'); +% +% h(i,1) is the text handle - color +% h(i,2) is the circle handle - facecolor +% +% Note : +% See also MAKE_LAYOUT + +% Uses : + +% Change History : +% Date Time Prog Note +% 13-Apr-2000 9:06 PM ATC Created under MATLAB 5.3.1.29215a (R11.1) + +% ATC = Ali Taylan Cemgil, +% SNN - University of Nijmegen, Department of Medical Physics and Biophysics +% e-mail : cemgil@mbfys.kun.nl +adj = double(adj); +N = size(adj,1); +if nargin<2, +% labels = cellstr(char(zeros(N,1)+double('+'))); + labels = cellstr(int2str((1:N)')); +end; + +if nargin<3, + node_t = zeros(N,1); +% node_t = rand(N,1) > 0.5; +else + node_t = node_t(:); +end; + +axis([0 1 0 1]); +set(gca,'XTick',[],'YTick',[],'box','on'); +% axis('square'); +%colormap(flipud(gray)); + +if nargin<4, + [x y] = make_layout(adj); +end; + +idx1 = find(node_t==0); wd1=[]; +if ~isempty(idx1), +[h1 wd1] = textoval(x(idx1), y(idx1), labels(idx1)); +end; + +idx2 = find(node_t~=0); wd2 = []; +if ~isempty(idx2), +[h2 wd2] = textbox(x(idx2), y(idx2), labels(idx2)); +end; + +wd = zeros(size(wd1,1)+size(wd2,1),2); +if ~isempty(idx1), wd(idx1, :) = wd1; end; +if ~isempty(idx2), wd(idx2, :) = wd2; end; + +for i=1:N, + j = find(adj(i,:)==1); + for k=j, + if x(k)-x(i)==0, + sign = 1; + if y(i)>y(k), alpha = -pi/2; else alpha = pi/2; end; + else + alpha = atan((y(k)-y(i))/(x(k)-x(i))); + if x(i)<x(k), sign = 1; else sign = -1; end; + end; + dy1 = sign.*wd(i,2).*sin(alpha); dx1 = sign.*wd(i,1).*cos(alpha); + dy2 = sign.*wd(k,2).*sin(alpha); dx2 = sign.*wd(k,1).*cos(alpha); + if adj(k,i)==0, % if directed edge + arrow([x(i)+dx1 y(i)+dy1],[x(k)-dx2 y(k)-dy2]); + else + line([x(i)+dx1 x(k)-dx2],[y(i)+dy1 y(k)-dy2],'color','k'); + adj(k,i)=-1; % Prevent drawing lines twice + end; + end; +end; + +if nargout>2, + h = zeros(length(wd),2); + if ~isempty(idx1), + h(idx1,:) = h1; + end; + if ~isempty(idx2), + h(idx2,:) = h2; + end; +end; + +%%%%% + +function [t, wd] = textoval(x, y, str) +% TEXTOVAL Draws an oval around text objects +% +% [T, WIDTH] = TEXTOVAL(X, Y, STR) +% [..] = TEXTOVAL(STR) % Interactive +% +% Inputs : +% X, Y : Coordinates +% TXT : Strings +% +% Outputs : +% T : Object Handles +% WIDTH : x and y Width of ovals +% +% Usage Example : [t] = textoval('Visit to Asia?'); +% +% +% Note : +% See also TEXTBOX + +% Uses : + +% Change History : +% Date Time Prog Note +% 15-Jun-1998 10:36 AM ATC Created under MATLAB 5.1.0.421 + +% ATC = Ali Taylan Cemgil, +% SNN - University of Nijmegen, Department of Medical Physics and Biophysics +% e-mail : cemgil@mbfys.kun.nl + +temp = []; + +switch nargin, + case 1, + str = x; + if ~isa(str,'cell') str=cellstr(str); end; + N = length(str); + wd = zeros(N,2); + for i=1:N, + [x, y] = ginput(1); + tx = text(x,y,str{i},'HorizontalAlignment','center','VerticalAlign','middle'); + [ptc wx wy] = draw_oval(tx, x, y); + wd(i,:) = [wx wy]; + delete(tx); + tx = text(x,y,str{i},'HorizontalAlignment','center','VerticalAlign','middle'); + temp = [temp ; tx ptc]; + end; + case 3, + if ~isa(str,'cell') str=cellstr(str); end; + N = length(str); + wd = zeros(N,2); + for i=1:N, + tx = text(x(i),y(i),str{i},'HorizontalAlignment','center','VerticalAlign','middle'); + [ptc wx wy] = draw_oval(tx, x(i), y(i)); + wd(i,:) = [wx wy]; + delete(tx); + tx = text(x(i),y(i),str{i},'HorizontalAlignment','center','VerticalAlign','middle'); + temp = [temp; tx ptc]; + end; + otherwise, +end; + +if nargout>0, t = temp; end; + +%%%%%%%%% + + +function [ptc, wx, wy] = draw_oval(tx, x, y) +% Draws an oval box around a tex object +sz = get(tx,'Extent'); +wy = sz(4); +wx = max(2/3*sz(3), wy); +wx = 0.5*wx; % KPM +wy = 0.5*wy; +ptc = ellipse(x, y, wx, wy); +set(ptc, 'FaceColor','w'); + + +%%%%%%%%%%%%% + +function [p] = ellipse(x, y, rx, ry, c) +% ELLIPSE Draws Ellipse shaped patch objects +% +% [<P>] = ELLIPSE(X, Y, Rx, Ry, C) +% +% Inputs : +% X : N x 1 vector of x coordinates +% Y : N x 1 vector of y coordinates +% Rx, Ry : Radii +% C : Color index +% +% +% Outputs : +% P = Handles of Ellipse shaped path objects +% +% Usage Example : [] = ellipse(); +% +% +% Note : +% See also + +% Uses : + +% Change History : +% Date Time Prog Note +% 27-May-1998 9:55 AM ATC Created under MATLAB 5.1.0.421 + +% ATC = Ali Taylan Cemgil, +% SNN - University of Nijmegen, Department of Medical Physics and Biophysics +% e-mail : cemgil@mbfys.kun.nl + +if (nargin < 2) error('Usage Example : e = ellipse([0 1],[0 -1],[1 0.5],[2 0.5]); '); end; +if (nargin < 3) rx = 0.1; end; +if (nargin < 4) ry = rx; end; +if (nargin < 5) c = 1; end; + +if length(c)==1, c = ones(size(x)).*c; end; +if length(rx)==1, rx = ones(size(x)).*rx; end; +if length(ry)==1, ry = ones(size(x)).*ry; end; + +n = length(x); +p = zeros(size(x)); +t = 0:pi/30:2*pi; +for i=1:n, + px = rx(i)*cos(t)+x(i); + py = ry(i)*sin(t)+y(i); + p(i) = patch(px,py,c(i)); +end; + +if nargout>0, pp = p; end; + +%%%%% + +function [t, wd] = textbox(x,y,str) +% TEXTBOX Draws A Box around the text +% +% [T, WIDTH] = TEXTBOX(X, Y, STR) +% [..] = TEXTBOX(STR) +% +% Inputs : +% X, Y : Coordinates +% TXT : Strings +% +% Outputs : +% T : Object Handles +% WIDTH : x and y Width of boxes +%% +% Usage Example : t = textbox({'Ali','Veli','49','50'}); +% +% +% Note : +% See also TEXTOVAL + +% Uses : + +% Change History : +% Date Time Prog Note +% 09-Jun-1998 11:43 AM ATC Created under MATLAB 5.1.0.421 + +% ATC = Ali Taylan Cemgil, +% SNN - University of Nijmegen, Department of Medical Physics and Biophysics +% e-mail : cemgil@mbfys.kun.nl + +% See +temp = []; + +switch nargin, + case 1, + str = x; + if ~isa(str,'cell') str=cellstr(str); end; + N = length(str); + wd = zeros(N,2); + for i=1:N, + [x, y] = ginput(1); + tx = text(x,y,str{i},'HorizontalAlignment','center','VerticalAlign','middle'); + [ptc wx wy] = draw_box(tx, x, y); + wd(i,:) = [wx wy]; + delete(tx); + tx = text(x,y,str{i},'HorizontalAlignment','center','VerticalAlign','middle'); + temp = [temp; tx ptc]; + end; + case 3, + if ~isa(str,'cell') str=cellstr(str); end; + N = length(str); + for i=1:N, + tx = text(x(i),y(i),str{i},'HorizontalAlignment','center','VerticalAlign','middle'); + [ptc wx wy] = draw_box(tx, x(i), y(i)); + wd(i,:) = [wx wy]; + delete(tx); + tx = text(x(i),y(i),str{i},'HorizontalAlignment','center','VerticalAlign','middle'); + temp = [temp; tx ptc]; + end; + + otherwise, + +end; + +if nargout>0, t = temp; end; + + +function [ptc, wx, wy] = draw_box(tx, x, y) +% Draws a box around a tex object + sz = get(tx,'Extent'); + wy = 2/3*sz(4); + wx = max(2/3*sz(3), wy); + ptc = patch([x-wx x+wx x+wx x-wx], [y+wy y+wy y-wy y-wy],'w'); + set(ptc, 'FaceColor','w'); + diff --git a/sourcecodes/bnt-master/GraphViz/Old/graphToDot.m b/sourcecodes/bnt-master/GraphViz/Old/graphToDot.m new file mode 100644 index 00000000..1f3d232e --- /dev/null +++ b/sourcecodes/bnt-master/GraphViz/Old/graphToDot.m @@ -0,0 +1,84 @@ +function graphToDot(adj, varargin) +% GRAPHTODOT Makes a GraphViz (AT&T) ile representing an adjacency matrix +% function graphToDot(adj, ...) +% Optional arguments should be passed as name/value pairs [default] +% +% 'filename' - if omitted, writes to 'tmp.dot' +% 'arc_label' - arc_label{i,j} is a string attached to the i-j arc [""] +% 'node_label' - node_label{i} is a string attached to the node i ["i"] +% 'width' - width in inches [10] +% 'height' - height in inches [10] +% 'leftright' - 1 means layout left-to-right, 0 means top-to-bottom [0] +% 'directed' - 1 means use directed arcs, 0 means undirected [1] +% +% For details on graphviz, See http://www.research.att.com/sw/tools/graphviz +% +% See also dot_to_graph and draw_dot +% +% First version written by Kevin Murphy 2002. +% Modified by Leon Peshkin, Jan 2004. + +node_label = []; arc_label = []; % set default args +width = 10; height = 10; +leftright = 0; directed = 1; filename = 'tmp.dot'; + +for i = 1:2:nargin-1 % get optional args + switch varargin{i} + case 'filename', filename = varargin{i+1}; + case 'node_label', node_label = varargin{i+1}; + case 'arc_label', arc_label = varargin{i+1}; + case 'width', width = varargin{i+1}; + case 'height', height = varargin{i+1}; + case 'leftright', leftright = varargin{i+1}; + case 'directed', directed = varargin{i+1}; + end +end + +fid = fopen(filename, 'w'); +if directed + fprintf(fid, 'digraph G {\n'); + arctxt = '->'; + if isempty(arc_label) + labeltxt = ''; + else + labeltxt = '[label="%s"]'; + end +else + fprintf(fid, 'graph G {\n'); + arctxt = '--'; + if isempty(arc_label) + labeltxt = '[dir=none]'; + else + labeltext = '[label="%s",dir=none]'; + end +end +edgeformat = strcat(['%d ',arctxt,' %d ',labeltxt,';\n']); +fprintf(fid, 'center = 1;\n'); +fprintf(fid, 'size=\"%d,%d\";\n', width, height); +if leftright + fprintf(fid, 'rankdir=LR;\n'); +end +Nnds = length(adj); +for node = 1:Nnds % process nodes + if isempty(node_label) + fprintf(fid, '%d;\n', node); + else + fprintf(fid, '%d [ label = "%s" ];\n', node, +node_label{node}); + end +end +for node1 = 1:Nnds % process edges + if directed + arcs = find(adj(node1,:)); % children(adj, node); + else + arcs = find(adj(node1,node1+1:Nnds)); % remove duplicate arcs + end + for node2 = arcs + fprintf(fid, edgeformat, node1, node2); + end +end +fprintf(fid, '}'); +fclose(fid); + + + diff --git a/sourcecodes/bnt-master/GraphViz/Old/pre_pesha_graph_to_dot.m b/sourcecodes/bnt-master/GraphViz/Old/pre_pesha_graph_to_dot.m new file mode 100644 index 00000000..49f226f6 --- /dev/null +++ b/sourcecodes/bnt-master/GraphViz/Old/pre_pesha_graph_to_dot.m @@ -0,0 +1,166 @@ +function graph_to_dot(G, varargin) +% DAG_TO_DOT Make a file representing the directed graph in dotty format. +% dag_to_dot(G, ...) +% +% Optional arguments should be passed as name/value pairs [default] +% +% 'filename' - if omitted, we write to 'tmp.dot', convert this to 'tmp.ps', +% and then call ghostview automatically +% 'arc_label' - arc_label{i,j} is a string attached to the i->j arc. [""] +% 'node_label' - node_label{i} is a string attached to node i. ["i"] +% 'width' - width in inches [10] +% 'height' - height in inches [10] +% 'leftright' - 1 means layout left-to-right, 0 means top-to-bottom [0] +% 'directed' - 1 means use directed arcs, 0 means undirected [1] +% +% For details on dotty, See http://www.research.att.com/sw/tools/graphviz +% +% Example: +% G = rand(5,5); +% names = cell(5,5); +% names{1,2} = 'arc 1-2'; +% graph_to_dot(G, 'arc_label', names) +% or graph_to_dot(G, 'arc_label', 'numbers') % prints value of G(i,j) on i->j arc + +% Kevin Murphy, 1998 + +% set default args +filename = []; +node_label = []; +arc_label = []; +width = 10; +height = 10; +leftright = 0; +directed = 1; +% get optional args +args = varargin; +for i=1:2:length(args) + switch args{i} + case 'filename', filename = args{i+1}; + case 'node_label', node_label = args{i+1}; + case 'arc_label', arc_label = args{i+1}; + case 'width', width = args{i+1}; + case 'height', height = args{i+1}; + case 'leftright', leftright = args{i+1}; + case 'directed', directed = args{i+1}; + end +end + +if isstr(arc_label) & strcmp(arc_label, 'numbers') + N = length(G); + arc_label = cell(N,N); + for i=1:N + for j=1:N + arc_label{i,j} = sprintf('%4.2f', G(i,j)); + end + end +end + +if isempty(filename) + make_file(G, 'tmp.dot', node_label, arc_label, width, height, leftright, directed); + if isunix + !dot -Tps tmp.dot -o tmp.ps + + !gs tmp.ps & + else + dos('dot -Tps tmp.dot -o tmp.ps'); + dos('gsview32 tmp.ps &'); + end +else + + + make_file(G, filename, node_label, arc_label, width, height, leftright, directed); +end + + +%%%%%% + +function make_file(G, filename, node_label, arc_label, width, height, leftright, directed) + +n = length(G); +fid = fopen(filename, 'w'); +if directed + fprintf(fid, 'digraph G {\n'); +else + fprintf(fid, 'graph G {\n'); +end +fprintf(fid, 'center = 1;\n'); +fprintf(fid, 'size=\"%d,%d\";\n', width, height); +if leftright + fprintf(fid, 'rankdir=LR;\n'); +end +for i=1:n + if isempty(node_label) + fprintf(fid, '%d;\n', i); + else + fprintf(fid, '%d [ label = "%s" ];\n', i, node_label{i}); + end +end +if directed + for i=1:n + cs = children(G,i); + for j=1:length(cs) + c = cs(j); + if isempty(arc_label) + fprintf(fid, '%d -> %d;\n', i, c); + else + fprintf(fid, '%d -> %d [label="%s"];\n', i, c, arc_label{i,c}); + end + end + end +else + for i=1:n + ns = intersect(neighbors(G,i), i+1:n); % remove duplicate arcs + for j=1:length(ns) + c = ns(j); + if isempty(arc_label) + fprintf(fid, '%d -- %d [dir=none];\n', i, c); + else + fprintf(fid, '%d -- %d [label="%s",dir=none];\n', i, c, arc_label{i,c}); + end + end + end +end +fprintf(fid, '\n}'); +fclose(fid); + + + +%%%%%%%%%%%%%%% + +function cs = children(adj_mat, i, t) +% CHILDREN Return the indices of a node's children in sorted order +% c = children(adj_mat, i, t) +% +% t is an optional argument: if present, dag is assumed to be a 2-slice DBN + +if nargin < 3 + cs = find(adj_mat(i,:)); +else + if t==1 + cs = find(adj_mat(i,:)); + else + ss = length(adj_mat)/2; + j = i+ss; + cs = find(adj_mat(j,:)) + (t-2)*ss; + end +end + +%%%%%%%%%%%% + +function ps = parents(adj_mat, i) +% PARENTS Return the list of parents of node i +% ps = parents(adj_mat, i) + +ps = find(adj_mat(:,i))'; + +%%%%%%%%%%%%% + +function ns = neighbors(adj_mat, i) +% NEIGHBORS Find the parents and children of a node in a graph. +% ns = neighbors(adj_mat, i) + +ns = union(children(adj_mat, i), parents(adj_mat, i)); + + + diff --git a/sourcecodes/bnt-master/GraphViz/README.txt b/sourcecodes/bnt-master/GraphViz/README.txt new file mode 100644 index 00000000..4ae15fac --- /dev/null +++ b/sourcecodes/bnt-master/GraphViz/README.txt @@ -0,0 +1,16 @@ +Graph visualization (automatic layout) functions +------------------------------------------------ + +This directory contains code to automatically layout and visualize +graphs. It provides a matlab interface to the graphviz program: + http://www.research.att.com/sw/tools/graphviz +Written by Kevin Murphy, Leon Peshkin, Tom Minka. + +draw_graph was written by Ali Taylan Cemgil, and is entirely +self-contained matlab: it does not need graphviz, but produces lower +quality results. +http://www.mbfys.kun.nl/~cemgil/matlab/layout.html + +See also the following URLs for other graph layout programs: + http://www.ics.uci.edu/~eppstein/gina/gdraw.html + http://www.cwi.nl/InfoVisu/ diff --git a/sourcecodes/bnt-master/GraphViz/approxeq.m b/sourcecodes/bnt-master/GraphViz/approxeq.m new file mode 100644 index 00000000..559efc5e --- /dev/null +++ b/sourcecodes/bnt-master/GraphViz/approxeq.m @@ -0,0 +1,21 @@ +function p = approxeq(a, b, tol, rel) +% APPROXEQ Are a and b approximately equal (to within a specified tolerance)? +% p = approxeq(a, b, thresh) +% 'tol' defaults to 1e-3. +% p(i) = 1 iff abs(a(i) - b(i)) < thresh +% +% p = approxeq(a, b, thresh, 1) +% p(i) = 1 iff abs(a(i)-b(i))/abs(a(i)) < thresh + +if nargin < 3, tol = 1e-2; end +if nargin < 4, rel = 0; end + +a = a(:); +b = b(:); +d = abs(a-b); +if rel + p = ~any( (d ./ (abs(a)+eps)) > tol); +else + p = ~any(d > tol); +end + diff --git a/sourcecodes/bnt-master/GraphViz/arrow.m b/sourcecodes/bnt-master/GraphViz/arrow.m new file mode 100644 index 00000000..4c5c1852 --- /dev/null +++ b/sourcecodes/bnt-master/GraphViz/arrow.m @@ -0,0 +1,1460 @@ +function [h,yy,zz] = arrow(varargin) +% ARROW Draw a line with an arrowhead. +% +% ARROW(Start,Stop) draws a line with an arrow from Start to Stop (points +% should be vectors of length 2 or 3, or matrices with 2 or 3 +% columns), and returns the graphics handle of the arrow(s). +% +% ARROW uses the mouse (click-drag) to create an arrow. +% +% ARROW DEMO & ARROW DEMO2 show 3-D & 2-D demos of the capabilities of ARROW. +% +% ARROW may be called with a normal argument list or a property-based list. +% ARROW(Start,Stop,Length,BaseAngle,TipAngle,Width,Page,CrossDir) is +% the full normal argument list, where all but the Start and Stop +% points are optional. If you need to specify a later argument (e.g., +% Page) but want default values of earlier ones (e.g., TipAngle), +% pass an empty matrix for the earlier ones (e.g., TipAngle=[]). +% +% ARROW('Property1',PropVal1,'Property2',PropVal2,...) creates arrows with the +% given properties, using default values for any unspecified or given as +% 'default' or NaN. Some properties used for line and patch objects are +% used in a modified fashion, others are passed directly to LINE, PATCH, +% or SET. For a detailed properties explanation, call ARROW PROPERTIES. +% +% Start The starting points. B +% Stop The end points. /|\ ^ +% Length Length of the arrowhead in pixels. /|||\ | +% BaseAngle Base angle in degrees (ADE). //|||\\ L| +% TipAngle Tip angle in degrees (ABC). ///|||\\\ e| +% Width Width of the base in pixels. ////|||\\\\ n| +% Page Use hardcopy proportions. /////|D|\\\\\ g| +% CrossDir Vector || to arrowhead plane. //// ||| \\\\ t| +% NormalDir Vector out of arrowhead plane. /// ||| \\\ h| +% Ends Which end has an arrowhead. //<----->|| \\ | +% ObjectHandles Vector of handles to update. / base ||| \ V +% E angle||<-------->C +% ARROW(H,'Prop1',PropVal1,...), where H is a |||tipangle +% vector of handles to previously-created arrows ||| +% and/or line objects, will update the previously- ||| +% created arrows according to the current view -->|A|<-- width +% and any specified properties, and will convert +% two-point line objects to corresponding arrows. ARROW(H) will update +% the arrows if the current view has changed. Root, figure, or axes +% handles included in H are replaced by all descendant Arrow objects. +% +% A property list can follow any specified normal argument list, e.g., +% ARROW([1 2 3],[0 0 0],36,'BaseAngle',60) creates an arrow from (1,2,3) to +% the origin, with an arrowhead of length 36 pixels and 60-degree base angle. +% +% Normally, an ARROW is a PATCH object, so any valid PATCH property/value pairs +% can be passed, e.g., ARROW(Start,Stop,'EdgeColor','r','FaceColor','g'). +% ARROW will use LINE objects when requested by ARROW(...,'Type','line') or, +% using LINE property/value pairs, ARROW(Start,Stop,'Type','line','Color','b'). +% +% The basic arguments or properties can generally be vectorized to create +% multiple arrows with the same call. This is done by passing a property +% with one row per arrow, or, if all arrows are to have the same property +% value, just one row may be specified. +% +% You may want to execute AXIS(AXIS) before calling ARROW so it doesn't change +% the axes on you; ARROW determines the sizes of arrow components BEFORE the +% arrow is plotted, so if ARROW changes axis limits, arrows may be malformed. +% +% This version of ARROW uses features of MATLAB 6.x and is incompatible with +% earlier MATLAB versions (ARROW for MATLAB 4.2c is available separately); +% some problems with perspective plots still exist. + +% Copyright (c)1995-2016, Dr. Erik A. Johnson <JohnsonE@usc.edu>, 5/25/2016 +% http://www.usc.edu/civil_eng/johnsone/ + +% Revision history: +% 5/25/16 EAJ Add documentation of 'Type','line' +% Add documentation of how to set color +% Add 'Color' property (which sets both 'EdgeColor' and 'FaceColor' for patch objects) +% 5/24/16 EAJ Remove 'EraseMode' in HG2 +% 7/16/14 EAJ R2014b HandleGraphics2 compatibility +% 7/14/14 EAJ 5/20/13 patch extension didn't work right in HG2 +% so break the arrow along its length instead +% 5/20/13 EAJ Extend patch line one more segment so EPS/PDF printed versions +% have nice rounded tips when the LineWidth is wider +% 2/06/13 EAJ Add ShortenLength property to shorten length if arrow is short +% 1/24/13 EAJ Remove some old comments. +% 5/20/09 EAJ Fix view direction in (3D) demo. +% 6/26/08 EAJ Replace eval('trycmd','catchcmd') with try, trycmd; catch, +% catchcmd; end; -- break's MATLAB 5 compatibility. +% 8/26/03 EAJ Eliminate OpenGL attempted fix since it didn't fix anyway. +% 11/15/02 EAJ Accomodate how MATLAB 6.5 handles NaN and logicals +% 7/28/02 EAJ Tried (but failed) work-around for MATLAB 6.x / OpenGL bug +% if zero 'Width' or not double-ended +% 11/10/99 EAJ Add logical() to eliminate zero index problem in MATLAB 5.3. +% 11/10/99 EAJ Corrected warning if axis limits changed on multiple axes. +% 11/10/99 EAJ Update e-mail address. +% 2/10/99 EAJ Some documentation updating. +% 2/24/98 EAJ Fixed bug if Start~=Stop but both colinear with viewpoint. +% 8/14/97 EAJ Added workaround for MATLAB 5.1 scalar logical transpose bug. +% 7/21/97 EAJ Fixed a few misc bugs. +% 7/14/97 EAJ Make arrow([],'Prop',...) do nothing (no old handles) +% 6/23/97 EAJ MATLAB 5 compatible version, release. +% 5/27/97 EAJ Added Line Arrows back in. Corrected a few bugs. +% 5/26/97 EAJ Changed missing Start/Stop to mouse-selected arrows. +% 5/19/97 EAJ MATLAB 5 compatible version, beta. +% 4/13/97 EAJ MATLAB 5 compatible version, alpha. +% 1/31/97 EAJ Fixed bug with multiple arrows and unspecified Z coords. +% 12/05/96 EAJ Fixed one more bug with log plots and NormalDir specified +% 10/24/96 EAJ Fixed bug with log plots and NormalDir specified +% 11/13/95 EAJ Corrected handling for 'reverse' axis directions +% 10/06/95 EAJ Corrected occasional conflict with SUBPLOT +% 4/24/95 EAJ A major rewrite. +% Fall 94 EAJ Original code. + +% Things to be done: +% - in the arrow_clicks section, prompt by printing to the screen so that +% the user knows what's going on; also make sure the figure is brought +% to the front. +% - segment parsing, computing, and plotting into separate subfunctions +% - change computing from Xform to Camera paradigms +% + this will help especially with 3-D perspective plots +% + if the WarpToFill section works right, remove warning code +% + when perpsective works properly, remove perspective warning code +% - add cell property values and struct property name/values (like get/set) +% - get rid of NaN as the "default" data label +% + perhaps change userdata to a struct and don't include (or leave +% empty) the values specified as default; or use a cell containing +% an empty matrix for a default value +% - add functionality of GET to retrieve current values of ARROW properties +% +% New list of things to be done: +% - rewrite as a graphics or class object that updates itself in real time +% (but have a 'Static' or 'DoNotUpdate' property to avoid updating) + +% Permission is granted to distribute ARROW with the toolboxes for the book +% "Solving Solid Mechanics Problems with MATLAB 5", by F. Golnaraghi et al. +% (Prentice Hall, 1999). + +% Permission is granted to Dr. Josef Bigun to distribute ARROW with his +% software to reproduce the figures in his image analysis text. + +% global variable initialization +persistent ARROW_PERSP_WARN ARROW_STRETCH_WARN ARROW_AXLIMITS ARROW_AX +if isempty(ARROW_PERSP_WARN ), ARROW_PERSP_WARN =1; end; +if isempty(ARROW_STRETCH_WARN), ARROW_STRETCH_WARN=1; end; + +% Handle callbacks +if (nargin>0 & isstr(varargin{1}) & strcmp(lower(varargin{1}),'callback')), + arrow_callback(varargin{2:end}); return; +end; + +% Are we doing the demo? +c = sprintf('\n'); +if (nargin==1 & isstr(varargin{1})), + arg1 = lower(varargin{1}); + if strncmp(arg1,'prop',4), arrow_props; + elseif strncmp(arg1,'demo',4) + clf reset + demo_info = arrow_demo; + if ~strncmp(arg1,'demo2',5), + hh=arrow_demo3(demo_info); + else, + hh=arrow_demo2(demo_info); + end; + if (nargout>=1), h=hh; end; + elseif strncmp(arg1,'fixlimits',3), + arrow_fixlimits(ARROW_AX,ARROW_AXLIMITS); + ARROW_AXLIMITS=[]; ARROW_AX=[]; + elseif strncmp(arg1,'help',4), + disp(help(mfilename)); + else, + error([upper(mfilename) ' got an unknown single-argument string ''' deblank(arg1) '''.']); + end; + return; +end; + +% Check # of arguments +if (nargout>3), error([upper(mfilename) ' produces at most 3 output arguments.']); end; + +% find first property number +firstprop = nargin+1; +for k=1:length(varargin), if ~isnumeric(varargin{k}) && ~all(ishandle(varargin{k})), firstprop=k; break; end; end; %eaj 5/24/16 for k=1:length(varargin), if ~isnumeric(varargin{k}), firstprop=k; break; end; end; +lastnumeric = firstprop-1; + +% check property list +if (firstprop<=nargin), + for k=firstprop:2:nargin, + curarg = varargin{k}; + if ~isstr(curarg) | sum(size(curarg)>1)>1, + error([upper(mfilename) ' requires that a property name be a single string.']); + end; + end; + if (rem(nargin-firstprop,2)~=1), + error([upper(mfilename) ' requires that the property ''' ... + varargin{nargin} ''' be paired with a property value.']); + end; +end; + +% default output +if (nargout>0), h=[]; end; +if (nargout>1), yy=[]; end; +if (nargout>2), zz=[]; end; + +% set values to empty matrices +start = []; +stop = []; +len = []; +baseangle = []; +tipangle = []; +wid = []; +page = []; +crossdir = []; +ends = []; +shorten = []; +ax = []; +oldh = []; +ispatch = []; +defstart = [NaN NaN NaN]; +defstop = [NaN NaN NaN]; +deflen = 16; +defbaseangle = 90; +deftipangle = 16; +defwid = 0; +defpage = 0; +defcrossdir = [NaN NaN NaN]; +defends = 1; +defshorten = 0; +defoldh = []; +defispatch = 1; + +% The 'Tag' we'll put on our arrows +ArrowTag = 'Arrow'; + +% check for oldstyle arguments +if (firstprop==2), + % assume arg1 is a set of handles + oldh = varargin{1}(:); + if isempty(oldh), return; end; +elseif (firstprop>9), + error([upper(mfilename) ' takes at most 8 non-property arguments.']); +elseif (firstprop>2), + {start,stop,len,baseangle,tipangle,wid,page,crossdir}; + args = [varargin(1:firstprop-1) cell(1,length(ans)-(firstprop-1))]; + [start,stop,len,baseangle,tipangle,wid,page,crossdir] = deal(args{:}); +end; + +% parse property pairs +extraprops={}; +for k=firstprop:2:nargin, + prop = varargin{k}; + val = varargin{k+1}; + prop = [lower(prop(:)') ' ']; + if strncmp(prop,'start' ,5), start = val; + elseif strncmp(prop,'stop' ,4), stop = val; + elseif strncmp(prop,'len' ,3), len = val(:); + elseif strncmp(prop,'base' ,4), baseangle = val(:); + elseif strncmp(prop,'tip' ,3), tipangle = val(:); + elseif strncmp(prop,'wid' ,3), wid = val(:); + elseif strncmp(prop,'page' ,4), page = val; + elseif strncmp(prop,'cross' ,5), crossdir = val; + elseif strncmp(prop,'norm' ,4), if (isstr(val)), crossdir=val; else, crossdir=val*sqrt(-1); end; + elseif strncmp(prop,'end' ,3), ends = val; + elseif strncmp(prop,'shorten',5), shorten = val; + elseif strncmp(prop,'object' ,6), oldh = val(:); + elseif strncmp(prop,'handle' ,6), oldh = val(:); + elseif strncmp(prop,'type' ,4), ispatch = val; + elseif strncmp(prop,'userd' ,5), %ignore it + else, + % make sure it is a valid patch or line property + try + get(0,['DefaultPatch' varargin{k}]); + catch + errstr = lasterr; + try + get(0,['DefaultLine' varargin{k}]); + catch + errstr(1:max(find(errstr==char(13)|errstr==char(10)))) = ''; + error([upper(mfilename) ' got ' errstr]); + end + end; + extraprops={extraprops{:},varargin{k},val}; + end; +end; + +% Check if we got 'default' values +start = arrow_defcheck(start ,defstart ,'Start' ); +stop = arrow_defcheck(stop ,defstop ,'Stop' ); +len = arrow_defcheck(len ,deflen ,'Length' ); +baseangle = arrow_defcheck(baseangle,defbaseangle,'BaseAngle' ); +tipangle = arrow_defcheck(tipangle ,deftipangle ,'TipAngle' ); +wid = arrow_defcheck(wid ,defwid ,'Width' ); +crossdir = arrow_defcheck(crossdir ,defcrossdir ,'CrossDir' ); +page = arrow_defcheck(page ,defpage ,'Page' ); +ends = arrow_defcheck(ends ,defends ,'' ); +shorten = arrow_defcheck(shorten ,defshorten ,'' ); +oldh = arrow_defcheck(oldh ,[] ,'ObjectHandles'); +ispatch = arrow_defcheck(ispatch ,defispatch ,'' ); + +% check transpose on arguments +[m,n]=size(start ); if any(m==[2 3])&(n==1|n>3), start = start'; end; +[m,n]=size(stop ); if any(m==[2 3])&(n==1|n>3), stop = stop'; end; +[m,n]=size(crossdir); if any(m==[2 3])&(n==1|n>3), crossdir = crossdir'; end; + +% convert strings to numbers +if ~isempty(ends) & isstr(ends), + endsorig = ends; + [m,n] = size(ends); + col = lower([ends(:,1:min(3,n)) ones(m,max(0,3-n))*' ']); + ends = NaN*ones(m,1); + oo = ones(1,m); + ii=find(all(col'==['non']'*oo)'); if ~isempty(ii), ends(ii)=ones(length(ii),1)*0; end; + ii=find(all(col'==['sto']'*oo)'); if ~isempty(ii), ends(ii)=ones(length(ii),1)*1; end; + ii=find(all(col'==['sta']'*oo)'); if ~isempty(ii), ends(ii)=ones(length(ii),1)*2; end; + ii=find(all(col'==['bot']'*oo)'); if ~isempty(ii), ends(ii)=ones(length(ii),1)*3; end; + if any(isnan(ends)), + ii = min(find(isnan(ends))); + error([upper(mfilename) ' does not recognize ''' deblank(endsorig(ii,:)) ''' as a valid ''Ends'' value.']); + end; +else, + ends = ends(:); +end; +if ~isempty(ispatch) & isstr(ispatch), + col = lower(ispatch(:,1)); + patchchar='p'; linechar='l'; defchar=' '; + mask = col~=patchchar & col~=linechar & col~=defchar; + if any(mask), + error([upper(mfilename) ' does not recognize ''' deblank(ispatch(min(find(mask)),:)) ''' as a valid ''Type'' value.']); + end; + ispatch = (col==patchchar)*1 + (col==linechar)*0 + (col==defchar)*defispatch; +else, + ispatch = ispatch(:); +end; +oldh = oldh(:); + +% check object handles +if ~all(ishandle(oldh)), error([upper(mfilename) ' got invalid object handles.']); end; + +% expand root, figure, and axes handles +if ~isempty(oldh), + ohtype = get(oldh,'Type'); + mask = strcmp(ohtype,'root') | strcmp(ohtype,'figure') | strcmp(ohtype,'axes'); + if any(mask), + oldh = num2cell(oldh); + for ii=find(mask)', + oldh(ii) = {findobj(oldh{ii},'Tag',ArrowTag)}; + end; + oldh = cat(1,oldh{:}); + if isempty(oldh), return; end; % no arrows to modify, so just leave + end; +end; + +% largest argument length +[mstart,junk]=size(start); [mstop,junk]=size(stop); [mcrossdir,junk]=size(crossdir); +argsizes = [length(oldh) mstart mstop ... + length(len) length(baseangle) length(tipangle) ... + length(wid) length(page) mcrossdir length(ends) length(shorten)]; +args=['length(ObjectHandle) '; ... + '#rows(Start) '; ... + '#rows(Stop) '; ... + 'length(Length) '; ... + 'length(BaseAngle) '; ... + 'length(TipAngle) '; ... + 'length(Width) '; ... + 'length(Page) '; ... + '#rows(CrossDir) '; ... + '#rows(Ends) '; ... + 'length(ShortenLength) ']; +if (any(imag(crossdir(:))~=0)), + args(9,:) = '#rows(NormalDir) '; +end; +if isempty(oldh), + narrows = max(argsizes); +else, + narrows = length(oldh); +end; +if (narrows<=0), narrows=1; end; + +% Check size of arguments +ii = find((argsizes~=0)&(argsizes~=1)&(argsizes~=narrows)); +if ~isempty(ii), + s = args(ii',:); + while ((size(s,2)>1)&((abs(s(:,size(s,2)))==0)|(abs(s(:,size(s,2)))==abs(' ')))), + s = s(:,1:size(s,2)-1); + end; + s = [ones(length(ii),1)*[upper(mfilename) ' requires that '] s ... + ones(length(ii),1)*[' equal the # of arrows (' num2str(narrows) ').' c]]; + s = s'; + s = s(:)'; + s = s(1:length(s)-1); + error(setstr(s)); +end; + +% check element length in Start, Stop, and CrossDir +if ~isempty(start), + [m,n] = size(start); + if (n==2), + start = [start NaN*ones(m,1)]; + elseif (n~=3), + error([upper(mfilename) ' requires 2- or 3-element Start points.']); + end; +end; +if ~isempty(stop), + [m,n] = size(stop); + if (n==2), + stop = [stop NaN*ones(m,1)]; + elseif (n~=3), + error([upper(mfilename) ' requires 2- or 3-element Stop points.']); + end; +end; +if ~isempty(crossdir), + [m,n] = size(crossdir); + if (n<3), + crossdir = [crossdir NaN*ones(m,3-n)]; + elseif (n~=3), + if (all(imag(crossdir(:))==0)), + error([upper(mfilename) ' requires 2- or 3-element CrossDir vectors.']); + else, + error([upper(mfilename) ' requires 2- or 3-element NormalDir vectors.']); + end; + end; +end; + +% fill empty arguments +if isempty(start ), start = [Inf Inf Inf]; end; +if isempty(stop ), stop = [Inf Inf Inf]; end; +if isempty(len ), len = Inf; end; +if isempty(baseangle ), baseangle = Inf; end; +if isempty(tipangle ), tipangle = Inf; end; +if isempty(wid ), wid = Inf; end; +if isempty(page ), page = Inf; end; +if isempty(crossdir ), crossdir = [Inf Inf Inf]; end; +if isempty(ends ), ends = Inf; end; +if isempty(shorten ), shorten = Inf; end; +if isempty(ispatch ), ispatch = Inf; end; + +% expand single-column arguments +o = ones(narrows,1); +if (size(start ,1)==1), start = o * start ; end; +if (size(stop ,1)==1), stop = o * stop ; end; +if (length(len )==1), len = o * len ; end; +if (length(baseangle )==1), baseangle = o * baseangle ; end; +if (length(tipangle )==1), tipangle = o * tipangle ; end; +if (length(wid )==1), wid = o * wid ; end; +if (length(page )==1), page = o * page ; end; +if (size(crossdir ,1)==1), crossdir = o * crossdir ; end; +if (length(ends )==1), ends = o * ends ; end; +if (length(shorten )==1), shorten = o * shorten ; end; +if (length(ispatch )==1), ispatch = o * ispatch ; end; +ax = repmat(gca,narrows,1); %eaj 7/16/14 ax=gca; if ~isnumeric(ax), ax=double(ax); end; ax=o*ax; + +% if we've got handles, get the defaults from the handles +if ~isempty(oldh), + for k=1:narrows, + oh = oldh(k); + ud = get(oh,'UserData'); + ax(k) = get(oh,'Parent'); %eaj 7/16/14 get(oh,'Parent'); if ~isnumeric(ans), double(ans); end; ax(k)=ans; + ohtype = get(oh,'Type'); + if strcmp(get(oh,'Tag'),ArrowTag), % if it's an arrow already + if isinf(ispatch(k)), ispatch(k)=strcmp(ohtype,'patch'); end; + % arrow UserData format: [start' stop' len base tip wid page crossdir' ends shorten] + start0 = ud(1:3); + stop0 = ud(4:6); + if (isinf(len(k))), len(k) = ud( 7); end; + if (isinf(baseangle(k))), baseangle(k) = ud( 8); end; + if (isinf(tipangle(k))), tipangle(k) = ud( 9); end; + if (isinf(wid(k))), wid(k) = ud(10); end; + if (isinf(page(k))), page(k) = ud(11); end; + if (isinf(crossdir(k,1))), crossdir(k,1) = ud(12); end; + if (isinf(crossdir(k,2))), crossdir(k,2) = ud(13); end; + if (isinf(crossdir(k,3))), crossdir(k,3) = ud(14); end; + if (isinf(ends(k))), ends(k) = ud(15); end; + if (isinf(shorten(k))), shorten(k) = ud(16); end; + elseif strcmp(ohtype,'line')|strcmp(ohtype,'patch'), % it's a non-arrow line or patch + convLineToPatch = 1; %set to make arrow patches when converting from lines. + if isinf(ispatch(k)), ispatch(k)=convLineToPatch|strcmp(ohtype,'patch'); end; + x=get(oh,'XData'); x=x(~isnan(x(:))); if isempty(x), x=NaN; end; + y=get(oh,'YData'); y=y(~isnan(y(:))); if isempty(y), y=NaN; end; + z=get(oh,'ZData'); z=z(~isnan(z(:))); if isempty(z), z=NaN; end; + start0 = [x(1) y(1) z(1) ]; + stop0 = [x(end) y(end) z(end)]; + else, + error([upper(mfilename) ' cannot convert ' ohtype ' objects.']); + end; + ii=find(isinf(start(k,:))); if ~isempty(ii), start(k,ii)=start0(ii); end; + ii=find(isinf(stop( k,:))); if ~isempty(ii), stop( k,ii)=stop0( ii); end; + end; +end; + +% convert Inf's to NaN's +start( isinf(start )) = NaN; +stop( isinf(stop )) = NaN; +len( isinf(len )) = NaN; +baseangle( isinf(baseangle)) = NaN; +tipangle( isinf(tipangle )) = NaN; +wid( isinf(wid )) = NaN; +page( isinf(page )) = NaN; +crossdir( isinf(crossdir )) = NaN; +ends( isinf(ends )) = NaN; +shorten( isinf(shorten )) = NaN; +ispatch( isinf(ispatch )) = NaN; + +% set up the UserData data (here so not corrupted by log10's and such) +ud = [start stop len baseangle tipangle wid page crossdir ends shorten]; + +% Set Page defaults +page = ~isnan(page) & trueornan(page); + +% Get axes limits, range, min; correct for aspect ratio and log scale +axm = zeros(3,narrows); +axr = zeros(3,narrows); +axrev = zeros(3,narrows); +ap = zeros(2,narrows); +xyzlog = zeros(3,narrows); +limmin = zeros(2,narrows); +limrange = zeros(2,narrows); +oldaxlims = zeros(6,narrows); +oneax = all(ax==ax(1)); +if (oneax), + T = zeros(4,4); + invT = zeros(4,4); +else, + T = zeros(16,narrows); + invT = zeros(16,narrows); +end; +axnotdone = true(size(ax)); +while (any(axnotdone)), + ii = find(axnotdone,1); + curax = ax(ii); + curpage = page(ii); + % get axes limits and aspect ratio + axl = [get(curax,'XLim'); get(curax,'YLim'); get(curax,'ZLim')]; + ax==curax; oldaxlims(:,ans)=repmat(reshape(axl',[],1),1,sum(ans)); + % get axes size in pixels (points) + u = get(curax,'Units'); + axposoldunits = get(curax,'Position'); + really_curpage = curpage & strcmp(u,'normalized'); + if (really_curpage), + curfig = get(curax,'Parent'); + pu = get(curfig,'PaperUnits'); + set(curfig,'PaperUnits','points'); + pp = get(curfig,'PaperPosition'); + set(curfig,'PaperUnits',pu); + set(curax,'Units','pixels'); + curapscreen = get(curax,'Position'); + set(curax,'Units','normalized'); + curap = pp.*get(curax,'Position'); + else, + set(curax,'Units','pixels'); + curapscreen = get(curax,'Position'); + curap = curapscreen; + end; + set(curax,'Units',u); + set(curax,'Position',axposoldunits); + % handle non-stretched axes position + str_stretch = { 'DataAspectRatioMode' ; ... + 'PlotBoxAspectRatioMode' ; ... + 'CameraViewAngleMode' }; + str_camera = { 'CameraPositionMode' ; ... + 'CameraTargetMode' ; ... + 'CameraViewAngleMode' ; ... + 'CameraUpVectorMode' }; + notstretched = strcmp(get(curax,str_stretch),'manual'); + manualcamera = strcmp(get(curax,str_camera),'manual'); + if ~arrow_WarpToFill(notstretched,manualcamera,curax), + % give a warning that this has not been thoroughly tested + if 0 & ARROW_STRETCH_WARN, + ARROW_STRETCH_WARN = 0; + strs = {str_stretch{1:2},str_camera{:}}; + strs = [char(ones(length(strs),1)*sprintf('\n ')) char(strs)]'; + warning([upper(mfilename) ' may not yet work quite right ' ... + 'if any of the following are ''manual'':' strs(:).']); + end; + % find the true pixel size of the actual axes + texttmp = text(axl(1,[1 2 2 1 1 2 2 1]), ... + axl(2,[1 1 2 2 1 1 2 2]), ... + axl(3,[1 1 1 1 2 2 2 2]),''); + set(texttmp,'Units','points'); + textpos = get(texttmp,'Position'); + delete(texttmp); + textpos = cat(1,textpos{:}); + textpos = max(textpos(:,1:2)) - min(textpos(:,1:2)); + % adjust the axes position + if (really_curpage), + % adjust to printed size + textpos = textpos * min(curap(3:4)./textpos); + curap = [curap(1:2)+(curap(3:4)-textpos)/2 textpos]; + else, + % adjust for pixel roundoff + textpos = textpos * min(curapscreen(3:4)./textpos); + curap = [curap(1:2)+(curap(3:4)-textpos)/2 textpos]; + end; + end; + if ARROW_PERSP_WARN & ~strcmp(get(curax,'Projection'),'orthographic'), + ARROW_PERSP_WARN = 0; + warning([upper(mfilename) ' does not yet work right for 3-D perspective projection.']); + end; + % adjust limits for log scale on axes + curxyzlog = strcmp(get(curax,{'XScale' 'YScale' 'ZScale'})','log'); + if (any(curxyzlog)), + ii = find([curxyzlog;curxyzlog]); + if (any(axl(ii)<=0)), + error([upper(mfilename) ' does not support non-positive limits on log-scaled axes.']); + else, + axl(ii) = log10(axl(ii)); + end; + end; + % correct for 'reverse' direction on axes; + curreverse = strcmp(get(curax,{'XDir' 'YDir' 'ZDir'})','reverse'); + ii = find(curreverse); + if ~isempty(ii), + axl(ii,[1 2])=-axl(ii,[2 1]); + end; + % compute the range of 2-D values + try, curT=get(curax,'Xform'); catch, num2cell(get(curax,'View')); curT=viewmtx(ans{:}); end; + lim = curT*[0 1 0 1 0 1 0 1;0 0 1 1 0 0 1 1;0 0 0 0 1 1 1 1;1 1 1 1 1 1 1 1]; + lim = lim(1:2,:)./([1;1]*lim(4,:)); + curlimmin = min(lim')'; + curlimrange = max(lim')' - curlimmin; + curinvT = inv(curT); + if (~oneax), + curT = curT.'; + curinvT = curinvT.'; + curT = curT(:); + curinvT = curinvT(:); + end; + % check which arrows to which cur corresponds + ii = find((ax==curax)&(page==curpage)); + oo = ones(1,length(ii)); + axr(:,ii) = diff(axl')' * oo; + axm(:,ii) = axl(:,1) * oo; + axrev(:,ii) = curreverse * oo; + ap(:,ii) = curap(3:4)' * oo; + xyzlog(:,ii) = curxyzlog * oo; + limmin(:,ii) = curlimmin * oo; + limrange(:,ii) = curlimrange * oo; + if (oneax), + T = curT; + invT = curinvT; + else, + T(:,ii) = curT * oo; + invT(:,ii) = curinvT * oo; + end; + axnotdone(ii) = zeros(1,length(ii)); +end; + +% correct for log scales +curxyzlog = xyzlog.'; +ii = find(curxyzlog(:)); +if ~isempty(ii), + start( ii) = real(log10(start( ii))); + stop( ii) = real(log10(stop( ii))); + if (all(imag(crossdir)==0)), % pulled (ii) subscript on crossdir, 12/5/96 eaj + crossdir(ii) = real(log10(crossdir(ii))); + end; +end; + +% correct for reverse directions +ii = find(axrev.'); +if ~isempty(ii), + start( ii) = -start( ii); + stop( ii) = -stop( ii); + crossdir(ii) = -crossdir(ii); +end; + +% transpose start/stop values +start = start.'; +stop = stop.'; + +% take care of defaults, page was done above +ii=find(isnan(start(:) )); if ~isempty(ii), start(ii) = axm(ii)+axr(ii)/2; end; +ii=find(isnan(stop(:) )); if ~isempty(ii), stop(ii) = axm(ii)+axr(ii)/2; end; +ii=find(isnan(crossdir(:) )); if ~isempty(ii), crossdir(ii) = zeros(length(ii),1); end; +ii=find(isnan(len )); if ~isempty(ii), len(ii) = ones(length(ii),1)*deflen; end; +ii=find(isnan(baseangle )); if ~isempty(ii), baseangle(ii) = ones(length(ii),1)*defbaseangle; end; +ii=find(isnan(tipangle )); if ~isempty(ii), tipangle(ii) = ones(length(ii),1)*deftipangle; end; +ii=find(isnan(wid )); if ~isempty(ii), wid(ii) = ones(length(ii),1)*defwid; end; +ii=find(isnan(ends )); if ~isempty(ii), ends(ii) = ones(length(ii),1)*defends; end; +ii=find(isnan(shorten )); if ~isempty(ii), shorten(ii) = ones(length(ii),1)*defshorten; end; + +% transpose rest of values +len = len.'; +baseangle = baseangle.'; +tipangle = tipangle.'; +wid = wid.'; +page = page.'; +crossdir = crossdir.'; +ends = ends.'; +shorten = shorten.'; +ax = ax.'; + +% given x, a 3xN matrix of points in 3-space; +% want to convert to X, the corresponding 4xN 2-space matrix +% +% tmp1=[(x-axm)./axr; ones(1,size(x,1))]; +% if (oneax), X=T*tmp1; +% else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=T.*tmp1; +% tmp2=zeros(4,4*N); tmp2(:)=tmp1(:); +% X=zeros(4,N); X(:)=sum(tmp2)'; end; +% X = X ./ (ones(4,1)*X(4,:)); + +% for all points with start==stop, start=stop-(verysmallvalue)*(up-direction); +ii = find(all(start==stop)); +if ~isempty(ii), + % find an arrowdir vertical on screen and perpendicular to viewer + % transform to 2-D + tmp1 = [(stop(:,ii)-axm(:,ii))./axr(:,ii);ones(1,length(ii))]; + if (oneax), twoD=T*tmp1; + else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=T(:,ii).*tmp1; + tmp2=zeros(4,4*length(ii)); tmp2(:)=tmp1(:); + twoD=zeros(4,length(ii)); twoD(:)=sum(tmp2)'; end; + twoD=twoD./(ones(4,1)*twoD(4,:)); + % move the start point down just slightly + tmp1 = twoD + [0;-1/1000;0;0]*(limrange(2,ii)./ap(2,ii)); + % transform back to 3-D + if (oneax), threeD=invT*tmp1; + else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=invT(:,ii).*tmp1; + tmp2=zeros(4,4*length(ii)); tmp2(:)=tmp1(:); + threeD=zeros(4,length(ii)); threeD(:)=sum(tmp2)'; end; + start(:,ii) = (threeD(1:3,:)./(ones(3,1)*threeD(4,:))).*axr(:,ii)+axm(:,ii); +end; + +% compute along-arrow points +% transform Start points + tmp1=[(start-axm)./axr;ones(1,narrows)]; + if (oneax), X0=T*tmp1; + else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=T.*tmp1; + tmp2=zeros(4,4*narrows); tmp2(:)=tmp1(:); + X0=zeros(4,narrows); X0(:)=sum(tmp2)'; end; + X0=X0./(ones(4,1)*X0(4,:)); +% transform Stop points + tmp1=[(stop-axm)./axr;ones(1,narrows)]; + if (oneax), Xf=T*tmp1; + else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=T.*tmp1; + tmp2=zeros(4,4*narrows); tmp2(:)=tmp1(:); + Xf=zeros(4,narrows); Xf(:)=sum(tmp2)'; end; + Xf=Xf./(ones(4,1)*Xf(4,:)); +% compute pixel distance between points + D = sqrt(sum(((Xf(1:2,:)-X0(1:2,:)).*(ap./limrange)).^2)); + D = D + (D==0); %eaj new 2/24/98 +% shorten the length if requested % added 2/6/2013 + numends = (ends==1) + (ends==2) + 2*(ends==3); + mask = shorten & D<len.*numends; + len(mask) = D(mask) ./ numends(mask); +% compute and modify along-arrow distances + len1 = len; + len2 = len - (len.*tan(tipangle/180*pi)-wid/2).*tan((90-baseangle)/180*pi); + slen0 = zeros(1,narrows); + slen1 = len1 .* ((ends==2)|(ends==3)); + slen2 = len2 .* ((ends==2)|(ends==3)); + len0 = zeros(1,narrows); + len1 = len1 .* ((ends==1)|(ends==3)); + len2 = len2 .* ((ends==1)|(ends==3)); + % for no start arrowhead + ii=find((ends==1)&(D<len2)); + if ~isempty(ii), + slen0(ii) = D(ii)-len2(ii); + end; + % for no end arrowhead + ii=find((ends==2)&(D<slen2)); + if ~isempty(ii), + len0(ii) = D(ii)-slen2(ii); + end; + len1 = len1 + len0; + len2 = len2 + len0; + slen1 = slen1 + slen0; + slen2 = slen2 + slen0; + % note: the division by D below will probably not be accurate if both + % of the following are true: + % 1. the ratio of the line length to the arrowhead + % length is large + % 2. the view is highly perspective. +% compute stoppoints + tmp1=X0.*(ones(4,1)*(len0./D))+Xf.*(ones(4,1)*(1-len0./D)); + if (oneax), tmp3=invT*tmp1; + else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=invT.*tmp1; + tmp2=zeros(4,4*narrows); tmp2(:)=tmp1(:); + tmp3=zeros(4,narrows); tmp3(:)=sum(tmp2)'; end; + stoppoint = tmp3(1:3,:)./(ones(3,1)*tmp3(4,:)).*axr+axm; +% compute tippoints + tmp1=X0.*(ones(4,1)*(len1./D))+Xf.*(ones(4,1)*(1-len1./D)); + if (oneax), tmp3=invT*tmp1; + else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=invT.*tmp1; + tmp2=zeros(4,4*narrows); tmp2(:)=tmp1(:); + tmp3=zeros(4,narrows); tmp3(:)=sum(tmp2)'; end; + tippoint = tmp3(1:3,:)./(ones(3,1)*tmp3(4,:)).*axr+axm; +% compute basepoints + tmp1=X0.*(ones(4,1)*(len2./D))+Xf.*(ones(4,1)*(1-len2./D)); + if (oneax), tmp3=invT*tmp1; + else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=invT.*tmp1; + tmp2=zeros(4,4*narrows); tmp2(:)=tmp1(:); + tmp3=zeros(4,narrows); tmp3(:)=sum(tmp2)'; end; + basepoint = tmp3(1:3,:)./(ones(3,1)*tmp3(4,:)).*axr+axm; +% compute startpoints + tmp1=X0.*(ones(4,1)*(1-slen0./D))+Xf.*(ones(4,1)*(slen0./D)); + if (oneax), tmp3=invT*tmp1; + else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=invT.*tmp1; + tmp2=zeros(4,4*narrows); tmp2(:)=tmp1(:); + tmp3=zeros(4,narrows); tmp3(:)=sum(tmp2)'; end; + startpoint = tmp3(1:3,:)./(ones(3,1)*tmp3(4,:)).*axr+axm; +% compute stippoints + tmp1=X0.*(ones(4,1)*(1-slen1./D))+Xf.*(ones(4,1)*(slen1./D)); + if (oneax), tmp3=invT*tmp1; + else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=invT.*tmp1; + tmp2=zeros(4,4*narrows); tmp2(:)=tmp1(:); + tmp3=zeros(4,narrows); tmp3(:)=sum(tmp2)'; end; + stippoint = tmp3(1:3,:)./(ones(3,1)*tmp3(4,:)).*axr+axm; +% compute sbasepoints + tmp1=X0.*(ones(4,1)*(1-slen2./D))+Xf.*(ones(4,1)*(slen2./D)); + if (oneax), tmp3=invT*tmp1; + else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=invT.*tmp1; + tmp2=zeros(4,4*narrows); tmp2(:)=tmp1(:); + tmp3=zeros(4,narrows); tmp3(:)=sum(tmp2)'; end; + sbasepoint = tmp3(1:3,:)./(ones(3,1)*tmp3(4,:)).*axr+axm; + +% compute cross-arrow directions for arrows with NormalDir specified +if (any(imag(crossdir(:))~=0)), + ii = find(any(imag(crossdir)~=0)); + crossdir(:,ii) = cross((stop(:,ii)-start(:,ii))./axr(:,ii), ... + imag(crossdir(:,ii))).*axr(:,ii); +end; + +% compute cross-arrow directions +basecross = crossdir + basepoint; +tipcross = crossdir + tippoint; +sbasecross = crossdir + sbasepoint; +stipcross = crossdir + stippoint; +ii = find(all(crossdir==0)|any(isnan(crossdir))); +if ~isempty(ii), + numii = length(ii); + % transform start points + tmp1 = [basepoint(:,ii) tippoint(:,ii) sbasepoint(:,ii) stippoint(:,ii)]; + tmp1 = (tmp1-axm(:,[ii ii ii ii])) ./ axr(:,[ii ii ii ii]); + tmp1 = [tmp1; ones(1,4*numii)]; + if (oneax), X0=T*tmp1; + else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=T(:,[ii ii ii ii]).*tmp1; + tmp2=zeros(4,16*numii); tmp2(:)=tmp1(:); + X0=zeros(4,4*numii); X0(:)=sum(tmp2)'; end; + X0=X0./(ones(4,1)*X0(4,:)); + % transform stop points + tmp1 = [(2*stop(:,ii)-start(:,ii)-axm(:,ii))./axr(:,ii);ones(1,numii)]; + tmp1 = [tmp1 tmp1 tmp1 tmp1]; + if (oneax), Xf=T*tmp1; + else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=T(:,[ii ii ii ii]).*tmp1; + tmp2=zeros(4,16*numii); tmp2(:)=tmp1(:); + Xf=zeros(4,4*numii); Xf(:)=sum(tmp2)'; end; + Xf=Xf./(ones(4,1)*Xf(4,:)); + % compute perpendicular directions + pixfact = ((limrange(1,ii)./limrange(2,ii)).*(ap(2,ii)./ap(1,ii))).^2; + pixfact = [pixfact pixfact pixfact pixfact]; + pixfact = [pixfact;1./pixfact]; + [dummyval,jj] = max(abs(Xf(1:2,:)-X0(1:2,:))); + jj1 = ((1:4)'*ones(1,length(jj))==ones(4,1)*jj); + jj2 = ((1:4)'*ones(1,length(jj))==ones(4,1)*(3-jj)); + jj3 = jj1(1:2,:); + Xf(jj1)=Xf(jj1)+(Xf(jj1)-X0(jj1)==0); %eaj new 2/24/98 + Xp = X0; + Xp(jj2) = X0(jj2) + ones(sum(jj2(:)),1); + Xp(jj1) = X0(jj1) - (Xf(jj2)-X0(jj2))./(Xf(jj1)-X0(jj1)) .* pixfact(jj3); + % inverse transform the cross points + if (oneax), Xp=invT*Xp; + else, tmp1=[Xp;Xp;Xp;Xp]; tmp1=invT(:,[ii ii ii ii]).*tmp1; + tmp2=zeros(4,16*numii); tmp2(:)=tmp1(:); + Xp=zeros(4,4*numii); Xp(:)=sum(tmp2)'; end; + Xp=(Xp(1:3,:)./(ones(3,1)*Xp(4,:))).*axr(:,[ii ii ii ii])+axm(:,[ii ii ii ii]); + basecross(:,ii) = Xp(:,0*numii+(1:numii)); + tipcross(:,ii) = Xp(:,1*numii+(1:numii)); + sbasecross(:,ii) = Xp(:,2*numii+(1:numii)); + stipcross(:,ii) = Xp(:,3*numii+(1:numii)); +end; + +% compute all points +% compute start points + axm11 = [axm axm axm axm axm axm axm axm axm axm axm]; + axr11 = [axr axr axr axr axr axr axr axr axr axr axr]; + st = [stoppoint tippoint basepoint sbasepoint stippoint startpoint stippoint sbasepoint basepoint tippoint stoppoint]; + tmp1 = (st - axm11) ./ axr11; + tmp1 = [tmp1; ones(1,size(tmp1,2))]; + if (oneax), X0=T*tmp1; + else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=[T T T T T T T T T T T].*tmp1; + tmp2=zeros(4,44*narrows); tmp2(:)=tmp1(:); + X0=zeros(4,11*narrows); X0(:)=sum(tmp2)'; end; + X0=X0./(ones(4,1)*X0(4,:)); +% compute stop points + tmp1 = ([start tipcross basecross sbasecross stipcross stop stipcross sbasecross basecross tipcross start] ... + - axm11) ./ axr11; + tmp1 = [tmp1; ones(1,size(tmp1,2))]; + if (oneax), Xf=T*tmp1; + else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=[T T T T T T T T T T T].*tmp1; + tmp2=zeros(4,44*narrows); tmp2(:)=tmp1(:); + Xf=zeros(4,11*narrows); Xf(:)=sum(tmp2)'; end; + Xf=Xf./(ones(4,1)*Xf(4,:)); +% compute lengths + len0 = len.*((ends==1)|(ends==3)).*tan(tipangle/180*pi); + slen0 = len.*((ends==2)|(ends==3)).*tan(tipangle/180*pi); + le = [zeros(1,narrows) len0 wid/2 wid/2 slen0 zeros(1,narrows) -slen0 -wid/2 -wid/2 -len0 zeros(1,narrows)]; + aprange = ap./limrange; + aprange = [aprange aprange aprange aprange aprange aprange aprange aprange aprange aprange aprange]; + D = sqrt(sum(((Xf(1:2,:)-X0(1:2,:)).*aprange).^2)); + Dii=find(D==0); if ~isempty(Dii), D=D+(D==0); le(Dii)=zeros(1,length(Dii)); end; %should fix DivideByZero warnings + tmp1 = X0.*(ones(4,1)*(1-le./D)) + Xf.*(ones(4,1)*(le./D)); +% inverse transform + if (oneax), tmp3=invT*tmp1; + else, tmp1=[tmp1;tmp1;tmp1;tmp1]; tmp1=[invT invT invT invT invT invT invT invT invT invT invT].*tmp1; + tmp2=zeros(4,44*narrows); tmp2(:)=tmp1(:); + tmp3=zeros(4,11*narrows); tmp3(:)=sum(tmp2)'; end; + pts = tmp3(1:3,:)./(ones(3,1)*tmp3(4,:)) .* axr11 + axm11; + +% correct for ones where the crossdir was specified +ii = find(~(all(crossdir==0)|any(isnan(crossdir)))); +if ~isempty(ii), + D1 = [pts(:,1*narrows+ii)-pts(:,9*narrows+ii) ... + pts(:,2*narrows+ii)-pts(:,8*narrows+ii) ... + pts(:,3*narrows+ii)-pts(:,7*narrows+ii) ... + pts(:,4*narrows+ii)-pts(:,6*narrows+ii) ... + pts(:,6*narrows+ii)-pts(:,4*narrows+ii) ... + pts(:,7*narrows+ii)-pts(:,3*narrows+ii) ... + pts(:,8*narrows+ii)-pts(:,2*narrows+ii) ... + pts(:,9*narrows+ii)-pts(:,1*narrows+ii)]/2; + ii = ii'*ones(1,8) + ones(length(ii),1)*[1:4 6:9]*narrows; + ii = ii(:)'; + pts(:,ii) = st(:,ii) + D1; +end; + + +% readjust for reverse directions +iicols=(1:narrows)'; iicols=iicols(:,ones(1,11)); iicols=iicols(:).'; +tmp1=axrev(:,iicols); +ii = find(tmp1(:)); if ~isempty(ii), pts(ii)=-pts(ii); end; + +% change from starting/ending at the stop point to doing it at the midpoint %eaj 7/14/2014 +(pts(:,2*narrows+1:3*narrows)+pts(:,3*narrows+1:4*narrows))/2; %eaj 7/14/2014 +pts = [ans pts(:,[3*narrows+1:end narrows+1:3*narrows]) ans]; %eaj 7/14/2014 + +% readjust for log scale on axes +tmp1=xyzlog(:,iicols); +ii = find(tmp1(:)); if ~isempty(ii), pts(ii)=10.^pts(ii); end; + +% compute the x,y,z coordinates of the patches; +ii = narrows*(0:size(pts,2)/narrows-1)'*ones(1,narrows) + ones(size(pts,2)/narrows,1)*(1:narrows); +ii = ii(:)'; +x = zeros(size(pts,2)/narrows,narrows); +y = zeros(size(pts,2)/narrows,narrows); +z = zeros(size(pts,2)/narrows,narrows); +x(:) = pts(1,ii)'; +y(:) = pts(2,ii)'; +z(:) = pts(3,ii)'; + +% do the output +if (nargout<=1), +% % create or modify the patches + newpatch = trueornan(ispatch) & (isempty(oldh)|~strcmp(get(oldh,'Type'),'patch')); + newline = ~trueornan(ispatch) & (isempty(oldh)|~strcmp(get(oldh,'Type'),'line')); + if isempty(oldh), H=zeros(narrows,1); else, H=oldh; end; +% % make or modify the arrows + for k=1:narrows, + if all(isnan(ud(k,[3 6])))&arrow_is2DXY(ax(k)), zz=[]; else, zz=z(:,k); end; + xx=x(:,k); yy=y(:,k); + if (0), % this fix didn't work, so let's not use it -- 8/26/03 + % try to work around a MATLAB 6.x OpenGL bug -- 7/28/02 + mask=any([ones(1,2+size(zz,2));diff([xx yy zz],[],1)],2); + xx=xx(mask); yy=yy(mask); if ~isempty(zz), zz=zz(mask); end; + end; + % plot the patch or line + if newpatch(k) || trueornan(ispatch(k)) %eaj 7/14/2014, 5/25/2016 + % patch is closed so don't need endpoints %eaj 7/14/2014 + if ~isempty(xx), xx(end)=[]; end; %eaj 7/14/2014 + if ~isempty(yy), yy(end)=[]; end; %eaj 7/14/2014 + if ~isempty(zz), zz(end)=[]; end; %eaj 7/14/2014 + end %eaj 7/14/2014 + xyz = {'XData',xx,'YData',yy,'ZData',zz,'Tag',ArrowTag}; + if newpatch(k)|newline(k), + if newpatch(k), + H(k) = patch(xyz{:}); + else, + H(k) = line(xyz{:}); + end; + if ~isempty(oldh), arrow_copyprops(oldh(k),H(k)); end; + else, + if strcmp(get(H(k),'Type'),'patch') %eaj 5/25/16 if ispatch(k) + xyz = {xyz{:},'CData',[]}; + end; + set(H(k),xyz{:}); + end; + end; + if ~isempty(oldh), delete(oldh(oldh~=H)); end; +% % additional properties + set(H,'Clipping','off'); + set(H,{'UserData'},num2cell(ud,2)); + if length(extraprops)>0 + ii = find(strcmpi(extraprops(1:2:end),'color')); %eaj 5/25/16 + ispatch = strcmp(get(H,'Type'),'patch'); + %eaj start 5/25/16 + while ~isempty(ii) && any(ispatch) + if ii>1, set(H,extraprops{1:2*ii-2}); end; + c = extraprops{2*ii}; + extraprops(1:2*ii) = []; + ii(1) = []; + if all(ispatch) || ischar(c)&&size(c,1)==1 || isnumeric(c)&&isequal(size(c),[1 3]) + set(H,'EdgeColor',c,'FaceColor',c) + elseif iscell(c) && numel(c)~=numel(H) + set(H(ispatch),'EdgeColor',c(ispatch),'FaceColor',c(ispatch)); + set(H(~ispatch),'Color',c(~ispatch)); + elseif isnumeric(c) && isequal(size(c),[numel(H) 3]) + set(H(ispatch),'EdgeColor',num2cell(c(ispatch,:),2),'FaceColor',num2cell(c(ispatch,:),2)); + set(H(~ispatch),'Color',num2cell(c(~ispatch,:),2)); + else + warning('ignoring unknown or invalid ''Color'' specification'); + end + end + if ~isempty(extraprops) + %eaj end 5/25/16 + set(H,extraprops{:}); + end %eaj 5/25/16 + end + % handle choosing arrow Start and/or Stop locations if unspecified + [H,oldaxlims,errstr] = arrow_clicks(H,ud,x,y,z,ax,oldaxlims); + if ~isempty(errstr), error([upper(mfilename) ' got ' errstr]); end; + % set the output + if (nargout>0), h=H; end; + % make sure the axis limits did not change + if isempty(oldaxlims), + ARROW_AXLIMITS = []; + ARROW_AX = []; + else, + lims = get(ax(:),{'XLim','YLim','ZLim'})'; + lims = reshape(cat(2,lims{:}),6,size(lims,2)); + mask = arrow_is2DXY(ax(:)); + oldaxlims(5:6,mask) = lims(5:6,mask); + % store them for possible restoring + mask = any(oldaxlims~=lims,1); ARROW_AX=ax(mask); ARROW_AXLIMITS=oldaxlims(:,mask); + if any(mask), + warning(arrow_warnlimits(ARROW_AX,narrows)); + end; + end; +else, + % don't create the patch, just return the data + h=x; + yy=y; + zz=z; +end; + + + +function out = arrow_defcheck(in,def,prop) +% check if we got 'default' values + out = in; + if ~isstr(in), return; end; + if size(in,1)==1 & strncmp(lower(in),'def',3), + out = def; + elseif ~isempty(prop), + error([upper(mfilename) ' does not recognize ''' in(:)' ''' as a valid ''' prop ''' string.']); + end; + + + +function [H,oldaxlims,errstr] = arrow_clicks(H,ud,x,y,z,ax,oldaxlims) +% handle choosing arrow Start and/or Stop locations if necessary + errstr = ''; + if isempty(H)|isempty(ud)|isempty(x), return; end; + % determine which (if any) need Start and/or Stop + needStart = all(isnan(ud(:,1:3)'))'; + needStop = all(isnan(ud(:,4:6)'))'; + mask = any(needStart|needStop); + if ~any(mask), return; end; + ud(~mask,:)=[]; ax(:,~mask)=[]; + x(:,~mask)=[]; y(:,~mask)=[]; z(:,~mask)=[]; + % make them invisible for the time being + set(H,'Visible','off'); + % save the current axes and limits modes; set to manual for the time being + oldAx = gca; + limModes=get(ax(:),{'XLimMode','YLimMode','ZLimMode'}); + set(ax(:),{'XLimMode','YLimMode','ZLimMode'},{'manual','manual','manual'}); + % loop over each arrow that requires attention + jj = find(mask); + for ii=1:length(jj), + h = H(jj(ii)); + axes(ax(ii)); + % figure out correct call + if needStart(ii), prop='Start'; else, prop='Stop'; end; + [wasInterrupted,errstr] = arrow_click(needStart(ii)&needStop(ii),h,prop,ax(ii)); + % handle errors and control-C + if wasInterrupted, + delete(H(jj(ii:end))); + H(jj(ii:end))=[]; + oldaxlims(jj(ii:end),:)=[]; + break; + end; + end; + % restore the axes and limit modes + axes(oldAx); + set(ax(:),{'XLimMode','YLimMode','ZLimMode'},limModes); + +function [wasInterrupted,errstr] = arrow_click(lockStart,H,prop,ax) +% handle the clicks for one arrow + fig = get(ax,'Parent'); + % save some things + oldFigProps = {'Pointer','WindowButtonMotionFcn','WindowButtonUpFcn'}; + oldFigValue = get(fig,oldFigProps); + oldArrowProps = {'EraseMode'}; + if ~isnumeric(fig), oldArrowProps={}; end %eaj 5/24/16 % only use in HG2 + oldArrowValue = get(H,oldArrowProps); + if isnumeric(fig), %eaj 5/24/16 + set(H,'EraseMode','background'); %because 'xor' makes shaft invisible unless Width>1 -- only use in HG2 + end %eaj 5/24/16 + global ARROW_CLICK_H ARROW_CLICK_PROP ARROW_CLICK_AX ARROW_CLICK_USE_Z + ARROW_CLICK_H=H; ARROW_CLICK_PROP=prop; ARROW_CLICK_AX=ax; + ARROW_CLICK_USE_Z=~arrow_is2DXY(ax)|~arrow_planarkids(ax); + set(fig,'Pointer','crosshair'); + % set up the WindowButtonMotion so we can see the arrow while moving around + set(fig,'WindowButtonUpFcn','set(gcf,''WindowButtonUpFcn'','''')', ... + 'WindowButtonMotionFcn',''); + if ~lockStart, + set(H,'Visible','on'); + set(fig,'WindowButtonMotionFcn',[mfilename '(''callback'',''motion'');']); + end; + % wait for the button to be pressed + [wasKeyPress,wasInterrupted,errstr] = arrow_wfbdown(fig); + % if we wanted to click-drag, set the Start point + if lockStart & ~wasInterrupted, + pt = arrow_point(ARROW_CLICK_AX,ARROW_CLICK_USE_Z); + feval(mfilename,H,'Start',pt,'Stop',pt); + set(H,'Visible','on'); + ARROW_CLICK_PROP='Stop'; + set(fig,'WindowButtonMotionFcn',[mfilename '(''callback'',''motion'');']); + % wait for the mouse button to be released + try + waitfor(fig,'WindowButtonUpFcn',''); + catch + errstr = lasterr; + wasInterrupted = 1; + end; + end; + if ~wasInterrupted, feval(mfilename,'callback','motion'); end; + % restore some things + set(gcf,oldFigProps,oldFigValue); + set(H,oldArrowProps,oldArrowValue); + +function arrow_callback(varargin) +% handle redrawing callbacks + if nargin==0, return; end; + str = varargin{1}; + if ~isstr(str), error([upper(mfilename) ' got an invalid Callback command.']); end; + s = lower(str); + if strcmp(s,'motion'), + % motion callback + global ARROW_CLICK_H ARROW_CLICK_PROP ARROW_CLICK_AX ARROW_CLICK_USE_Z + feval(mfilename,ARROW_CLICK_H,ARROW_CLICK_PROP,arrow_point(ARROW_CLICK_AX,ARROW_CLICK_USE_Z)); + drawnow; + else, + error([upper(mfilename) ' does not recognize ''' str(:).' ''' as a valid Callback option.']); + end; + +function out = arrow_point(ax,use_z) +% return the point on the given axes + if nargin==0, ax=gca; end; + if nargin<2, use_z=~arrow_is2DXY(ax)|~arrow_planarkids(ax); end; + out = get(ax,'CurrentPoint'); + out = out(1,:); + if ~use_z, out=out(1:2); end; + +function [wasKeyPress,wasInterrupted,errstr] = arrow_wfbdown(fig) +% wait for button down ignoring object ButtonDownFcn's + if nargin==0, fig=gcf; end; + errstr = ''; + % save ButtonDownFcn values + objs = findobj(fig); + buttonDownFcns = get(objs,'ButtonDownFcn'); + mask=~strcmp(buttonDownFcns,''); objs=objs(mask); buttonDownFcns=buttonDownFcns(mask); + set(objs,'ButtonDownFcn',''); + % save other figure values + figProps = {'KeyPressFcn','WindowButtonDownFcn'}; + figValue = get(fig,figProps); + % do the real work + set(fig,'KeyPressFcn','set(gcf,''KeyPressFcn'','''',''WindowButtonDownFcn'','''');', ... + 'WindowButtonDownFcn','set(gcf,''WindowButtonDownFcn'','''')'); + lasterr(''); + try + waitfor(fig,'WindowButtonDownFcn',''); + wasInterrupted = 0; + catch + wasInterrupted = 1; + end + wasKeyPress = ~wasInterrupted & strcmp(get(fig,'KeyPressFcn'),''); + if wasInterrupted, errstr=lasterr; end; + % restore ButtonDownFcn and other figure values + set(objs,'ButtonDownFcn',buttonDownFcns); + set(fig,figProps,figValue); + + + +function [out,is2D] = arrow_is2DXY(ax) +% check if axes are 2-D X-Y plots + % may not work for modified camera angles, etc. + out = false(size(ax)); % 2-D X-Y plots + is2D = out; % any 2-D plots + views = get(ax(:),{'View'}); + views = cat(1,views{:}); + out(:) = abs(views(:,2))==90; + is2D(:) = out(:) | all(rem(views',90)==0)'; + +function out = arrow_planarkids(ax) +% check if axes descendents all have empty ZData (lines,patches,surfaces) + out = true(size(ax)); + allkids = get(ax(:),{'Children'}); + for k=1:length(allkids), + kids = get([findobj(allkids{k},'flat','Type','line') + findobj(allkids{k},'flat','Type','patch') + findobj(allkids{k},'flat','Type','surface')],{'ZData'}); + for j=1:length(kids), + if ~isempty(kids{j}), out(k)=logical(0); break; end; + end; + end; + + + +function arrow_fixlimits(ax,lims) +% reset the axis limits as necessary + if isempty(ax) || isempty(lims), disp([upper(mfilename) ' does not remember any axis limits to reset.']); end; + for k=1:numel(ax), + if any(get(ax(k),'XLim')~=lims(1:2,k)'), set(ax(k),'XLim',lims(1:2,k)'); end; + if any(get(ax(k),'YLim')~=lims(3:4,k)'), set(ax(k),'YLim',lims(3:4,k)'); end; + if any(get(ax(k),'ZLim')~=lims(5:6,k)'), set(ax(k),'ZLim',lims(5:6,k)'); end; + end; + + + +function out = arrow_WarpToFill(notstretched,manualcamera,curax) +% check if we are in "WarpToFill" mode. + out = strcmp(get(curax,'WarpToFill'),'on'); + % 'WarpToFill' is undocumented, so may need to replace this by + % out = ~( any(notstretched) & any(manualcamera) ); + + + +function out = arrow_warnlimits(ax,narrows) +% create a warning message if we've changed the axis limits + msg = ''; + switch (numel(ax)) + case 1, msg=''; + case 2, msg='on two axes '; + otherwise, msg='on several axes '; + end; + msg = [upper(mfilename) ' changed the axis limits ' msg ... + 'when adding the arrow']; + if (narrows>1), msg=[msg 's']; end; + out = [msg '.' sprintf('\n') ' Call ' upper(mfilename) ... + ' FIXLIMITS to reset them now.']; + + + +function arrow_copyprops(fm,to) +% copy line properties to patches + props = {'EraseMode','LineStyle','LineWidth','Marker','MarkerSize',... + 'MarkerEdgeColor','MarkerFaceColor','ButtonDownFcn', ... + 'Clipping','DeleteFcn','BusyAction','HandleVisibility', ... + 'Selected','SelectionHighlight','Visible'}; + if ~isnumeric(findobj('Type','root')), props(strcmp(props,'EraseMode'))=[]; end; %eaj 5/24/16 + lineprops = {'Color', props{:}}; + patchprops = {'EdgeColor',props{:}}; + patch2props = {'FaceColor',patchprops{:}}; + fmpatch = strcmp(get(fm,'Type'),'patch'); + topatch = strcmp(get(to,'Type'),'patch'); + set(to( fmpatch& topatch),patch2props,get(fm( fmpatch& topatch),patch2props)); %p->p + set(to(~fmpatch&~topatch),lineprops, get(fm(~fmpatch&~topatch),lineprops )); %l->l + set(to( fmpatch&~topatch),lineprops, get(fm( fmpatch&~topatch),patchprops )); %p->l + set(to(~fmpatch& topatch),patchprops, get(fm(~fmpatch& topatch),lineprops) ,'FaceColor','none'); %l->p + + + +function arrow_props +% display further help info about ARROW properties + c = sprintf('\n'); + disp([c ... + 'ARROW Properties: Default values are given in [square brackets], and other' c ... + ' acceptable equivalent property names are in (parenthesis).' c c ... + ' Start The starting points. For N arrows, B' c ... + ' this should be a Nx2 or Nx3 matrix. /|\ ^' c ... + ' Stop The end points. For N arrows, this /|||\ |' c ... + ' should be a Nx2 or Nx3 matrix. //|||\\ L|' c ... + ' Length Length of the arrowhead (in pixels on ///|||\\\ e|' c ... + ' screen, points on a page). [16] (Len) ////|||\\\\ n|' c ... + ' BaseAngle Angle (degrees) of the base angle /////|D|\\\\\ g|' c ... + ' ADE. For a simple stick arrow, use //// ||| \\\\ t|' c ... + ' BaseAngle=TipAngle. [90] (Base) /// ||| \\\ h|' c ... + ' TipAngle Angle (degrees) of tip angle ABC. //<----->|| \\ |' c ... + ' [16] (Tip) / base ||| \ V' c ... + ' Width Width of the base in pixels. Not E angle ||<-------->C' c ... + ' the ''LineWidth'' prop. [0] (Wid) |||tipangle' c ... + ' Page If provided, non-empty, and not NaN, |||' c ... + ' this causes ARROW to use hardcopy |||' c ... + ' rather than onscreen proportions. A' c ... + ' This is important if screen aspect --> <-- width' c ... + ' ratio and hardcopy aspect ratio are ----CrossDir---->' c ... + ' vastly different. []' c... + ' CrossDir A vector giving the direction towards which the fletches' c ... + ' on the arrow should go. [computed such that it is perpen-' c ... + ' dicular to both the arrow direction and the view direction' c ... + ' (i.e., as if it was pasted on a normal 2-D graph)] (Note' c ... + ' that CrossDir is a vector. Also note that if an axis is' c ... + ' plotted on a log scale, then the corresponding component' c ... + ' of CrossDir must also be set appropriately, i.e., to 1 for' c ... + ' no change in that direction, >1 for a positive change, >0' c ... + ' and <1 for negative change.)' c ... + ' NormalDir A vector normal to the fletch direction (CrossDir is then' c ... + ' computed by the vector cross product [Line]x[NormalDir]). []' c ... + ' (Note that NormalDir is a vector. Unlike CrossDir,' c ... + ' NormalDir is used as is regardless of log-scaled axes.)' c ... + ' Ends Set which end has an arrowhead. Valid values are ''none'',' c ... + ' ''stop'', ''start'', and ''both''. [''stop''] (End)' c... + ' ShortenLength Shorten length of arrowhead(s) if line is too short' c ... + ' ObjectHandles Vector of handles to previously-created arrows to be' c ... + ' updated or line objects to be converted to arrows.' c ... + ' [] (Object,Handle)' c ... + ' Type ''patch'' creates the arrow with a PATCH object (the default)' c ... + ' and ''line'' creates it with a LINE object [''patch''].' c ... + ' Color For patch arrows (the default), set both ''FaceColor'' and' c ... + ' ''EdgeColor'' to the given value. For line arrows, set' c ... + ' the ''Color'' property to the given value.' c ... + ]); + + + +function out = arrow_demo + % demo + % create the data + [x,y,z] = peaks; + [ddd,out.iii]=max(z(:)); + out.axlim = [min(x(:)) max(x(:)) min(y(:)) max(y(:)) min(z(:)) max(z(:))]; + + % modify it by inserting some NaN's + [m,n] = size(z); + m = floor(m/2); + n = floor(n/2); + z(1:m,1:n) = NaN*ones(m,n); + + % graph it + clf('reset'); + out.hs=surf(x,y,z); + out.x=x; out.y=y; out.z=z; + xlabel('x'); ylabel('y'); + +function h = arrow_demo3(in) + % set the view + axlim = in.axlim; + axis(axlim); + zlabel('z'); + %set(in.hs,'FaceColor','interp'); + view(3); % view(viewmtx(-37.5,30,20)); + title(['Demo of the capabilities of the ARROW function in 3-D']); + + % Normal blue arrow + h1 = feval(mfilename,[axlim(1) axlim(4) 4],[-.8 1.2 4], ... + 'EdgeColor','b','FaceColor','b'); + + % Normal white arrow, clipped by the surface + h2 = feval(mfilename,axlim([1 4 6]),[0 2 4]); + t=text(-2.4,2.7,7.7,'arrow clipped by surf'); + + % Baseangle<90 + h3 = feval(mfilename,[3 .125 3.5],[1.375 0.125 3.5],30,50); + t2=text(3.1,.125,3.5,'local maximum'); + + % Baseangle<90, fill and edge colors different + h4 = feval(mfilename,axlim(1:2:5)*.5,[0 0 0],36,60,25, ... + 'EdgeColor','b','FaceColor','c'); + t3=text(axlim(1)*.5,axlim(3)*.5,axlim(5)*.5-.75,'origin'); + set(t3,'HorizontalAlignment','center'); + + % Baseangle>90, black fill + h5 = feval(mfilename,[-2.9 2.9 3],[-1.3 .4 3.2],30,120,[],6, ... + 'EdgeColor','r','FaceColor','k','LineWidth',2); + + % Baseangle>90, no fill + h6 = feval(mfilename,[-2.9 2.9 1.3],[-1.3 .4 1.5],30,120,[],6, ... + 'EdgeColor','r','FaceColor','none','LineWidth',2); + + % Stick arrow + h7 = feval(mfilename,[-1.6 -1.65 -6.5],[0 -1.65 -6.5],[],16,16); + t4=text(-1.5,-1.65,-7.25,'global mininum'); + set(t4,'HorizontalAlignment','center'); + + % Normal, black fill + h8 = feval(mfilename,[-1.4 0 -7.2],[-1.4 0 -3],'FaceColor','k'); + t5=text(-1.5,0,-7.75,'local minimum'); + set(t5,'HorizontalAlignment','center'); + + % Gray fill, crossdir specified, 'LineStyle' -- + h9 = feval(mfilename,[-3 2.2 -6],[-3 2.2 -.05],36,[],27,6,[],[0 -1 0], ... + 'EdgeColor','k','FaceColor',.75*[1 1 1],'LineStyle','--'); + + % a series of normal arrows, linearly spaced, crossdir specified + h10y=(0:4)'/3; + h10 = feval(mfilename,[-3*ones(size(h10y)) h10y -6.5*ones(size(h10y))], ... + [-3*ones(size(h10y)) h10y -.05*ones(size(h10y))], ... + 12,[],[],[],[],[0 -1 0]); + + % a series of normal arrows, linearly spaced + h11x=(1:.33:2.8)'; + h11 = feval(mfilename,[h11x -3*ones(size(h11x)) 6.5*ones(size(h11x))], ... + [h11x -3*ones(size(h11x)) -.05*ones(size(h11x))]); + + % series of magenta arrows, radially oriented, crossdir specified + h12x=2; h12y=-3; h12z=axlim(5)/2; h12xr=1; h12zr=h12z; ir=.15;or=.81; + h12t=(0:11)'/6*pi; + h12 = feval(mfilename, ... + [h12x+h12xr*cos(h12t)*ir h12y*ones(size(h12t)) ... + h12z+h12zr*sin(h12t)*ir],[h12x+h12xr*cos(h12t)*or ... + h12y*ones(size(h12t)) h12z+h12zr*sin(h12t)*or], ... + 10,[],[],[],[], ... + [-h12xr*sin(h12t) zeros(size(h12t)) h12zr*cos(h12t)],... + 'FaceColor','none','EdgeColor','m'); + + % series of normal arrows, tangentially oriented, crossdir specified + or13=.91; h13t=(0:.5:12)'/6*pi; + locs = [h12x+h12xr*cos(h13t)*or13 h12y*ones(size(h13t)) h12z+h12zr*sin(h13t)*or13]; + h13 = feval(mfilename,locs(1:end-1,:),locs(2:end,:),6); + + % arrow with no line ==> oriented downwards + h14 = feval(mfilename,[3 3 .100001],[3 3 .1],30); + t6=text(3,3,3.6,'no line'); set(t6,'HorizontalAlignment','center'); + + % arrow with arrowheads at both ends + h15 = feval(mfilename,[-.5 -3 -3],[1 -3 -3],'Ends','both','FaceColor','g', ... + 'Length',20,'Width',3,'CrossDir',[0 0 1],'TipAngle',25); + + h=[h1;h2;h3;h4;h5;h6;h7;h8;h9;h10;h11;h12;h13;h14;h15]; + +function h = arrow_demo2(in) + axlim = in.axlim; + dolog = 1; + if (dolog), set(in.hs,'YData',10.^get(in.hs,'YData')); end; + shading('interp'); + view(2); + title(['Demo of the capabilities of the ARROW function in 2-D']); + hold on; [C,H]=contour(in.x,in.y,in.z,20,'-'); hold off; + for k=H', + set(k,'ZData',(axlim(6)+1)*ones(size(get(k,'XData'))),'Color','k'); + if (dolog), set(k,'YData',10.^get(k,'YData')); end; + end; + if (dolog), axis([axlim(1:2) 10.^axlim(3:4)]); set(gca,'YScale','log'); + else, axis(axlim(1:4)); end; + + % Normal blue arrow + start = [axlim(1) axlim(4) axlim(6)+2]; + stop = [in.x(in.iii) in.y(in.iii) axlim(6)+2]; + if (dolog), start(:,2)=10.^start(:,2); stop(:,2)=10.^stop(:,2); end; + h1 = feval(mfilename,start,stop,'EdgeColor','b','FaceColor','b'); + + % three arrows with varying fill, width, and baseangle + start = [-3 -3 10; -3 -1.5 10; -1.5 -3 10]; + stop = [-.03 -.03 10; -.03 -1.5 10; -1.5 -.03 10]; + if (dolog), start(:,2)=10.^start(:,2); stop(:,2)=10.^stop(:,2); end; + h2 = feval(mfilename,start,stop,24,[90;60;120],[],[0;0;4],'Ends',str2mat('both','stop','stop')); + set(h2(2),'EdgeColor',[0 .35 0],'FaceColor',[0 .85 .85]); + set(h2(3),'EdgeColor','r','FaceColor',[1 .5 1]); + h=[h1;h2]; + +function out = trueornan(x) +if isempty(x), + out=x; +else, + out = isnan(x); + out(~out) = x(~out); +end; diff --git a/sourcecodes/bnt-master/GraphViz/dot_to_graph.m b/sourcecodes/bnt-master/GraphViz/dot_to_graph.m new file mode 100644 index 00000000..05b47480 --- /dev/null +++ b/sourcecodes/bnt-master/GraphViz/dot_to_graph.m @@ -0,0 +1,121 @@ +function [Adj, labels, x, y] = dot_to_graph(filename) +% [Adj, labels, x, y] = dot_to_graph(filename) +% Extract a matrix representation, node labels, and node position coordinates +% from a file in GraphViz format http://www.research.att.com/sw/tools/graphviz +% +% INPUTS: +% 'filename' - the file in DOT format containing the graph layout. +% OUTPUT: +% 'Adj' - an adjacency matrix representation of the graph in 'filename'; +% 'labels' - a character array with the names of the nodes of the graph; +% 'x' - a row vector with the x-coordinates of the nodes in 'filename'; +% 'y' - a row vector with the y-coordinates of the nodes in 'filename'. +% +% WARNINGS: not guaranted to parse ANY GraphViz file. Debugged on undirected +% sample graphs from GraphViz(Heawood, Petersen, ER, ngk10_4, process). +% Complaines about RecursionLimit set only to 500 on huge graphs. +% Ignores singletons (disjoint nodes). +% Sample DOT code "ABC.dot", read by [Adj, labels, x, y] = dot_to_graph('ABC.dot') +% digraph G { +% A [pos="28,31"]; +% B [pos="74,87"]; +% A -- B [pos="e,61,71 41,47 46,53 50,58 55,64"]; +% } +% last modified: Jan 2004 +% by Alexi Savov: asavov @wustl.edu | http://artsci.wustl.edu/~azsavov +% Leon Peshkin: pesha @ai.mit.edu | http://www.ai.mit.edu/~pesha +% Tom Minka + +if ~exist(filename) % Checks whether the specified file exists. + error('* * * File does not exist or could not be found. * * *'); +end; + +lines = textread(filename,'%s','delimiter','\n','commentstyle','c'); % Read file into cell array +dot_lines = strvcat(lines); % of lines, ignoring C-style comments + +if findstr(dot_lines(1,:), 'graph ') == [] % Is this a DOT file ? + error('* * * File does not appear to be in valid DOT format. * * *'); +end; + +Nlns = size(dot_lines,1); % The number of lines; +nodes = {}; +unread = 1:Nlns; % 'unread' list of lines which has not been examined yet +edge_id = 1; +Adj = []; +for line_ndx = 1:Nlns % This section sets the adjacency matrix A(Lnode,Rnode) = edge_id. + line = dot_lines(line_ndx,:); + Ddash_pos = strfind(line, ' -- ') + 1; % double dash positions + arrow_pos = strfind(line, ' -> ') + 1; % arrow dash positions + tokens = strread(line,'%s','delimiter',' "'); + left_bound = 1; + for dash_pos = [Ddash_pos arrow_pos]; % if empty - not a POS line + Lnode = sscanf(line(left_bound:dash_pos -2), '%s'); + Rnode = sscanf(line(dash_pos +3 : length(line)-1),'%s',1); + Lndx = strmatch(Lnode, nodes, 'exact'); + Rndx = strmatch(Rnode, nodes, 'exact'); + if isempty(Lndx) % extend our list of nodes + nodes{end+1} = Lnode; + Lndx = length(nodes); + end + if isempty(Rndx) + nodes{end+1} = Rnode; + Rndx = length(nodes); + end + Adj(Lndx, Rndx) = edge_id; + if ismember(dash_pos, Ddash_pos) % The edge is undirected, A(Rndx,LndxL) is also set to 1; + Adj(Rndx, Lndx) = edge_id; + end + edge_id = edge_id + 1; + left_bound = dash_pos + 3; + unread = setdiff(unread, line_ndx); + end +end +Nvrt = length(nodes); % number of vertices we found [Do we ever have singleton vertices ???] +% nodes = strvcat(nodes); % convert to the searchable array +x = zeros(1, Nvrt); +y = zeros(1, Nvrt); +labels = nodes; +% Find node's position coordinates if they are contained in 'filename'. +for line_ndx = unread % Look for node's coordinates among the 'unread' lines. + line = dot_lines(line_ndx,:); + bra_pos = strfind(line, '['); % has to have "[" if it has the label + lst_node = 0; + for node = 1:Nvrt % look through the list of nodes + % THE NEXT STATEMENT we assume no node is substring of any other node + lbl_pos = strfind(line, nodes{node}); + if (~isempty(lbl_pos) & ~isempty(bra_pos) & (x(node) == 0)) % make sure we have not seen it + if (lbl_pos(1) < bra_pos(1)) % label has to be to the left of bracket + lst_node = node; + end + end + end + if lst_node + pos_pos = strfind(line, 'pos'); % position of the "pos" + if ~isempty(pos_pos) % this line contains SOME position + [node_pos] = sscanf(line(pos_pos:end), ' pos = "%d,%d"')'; + x(lst_node) = node_pos(1); + y(lst_node) = node_pos(2); + end + % minka + label_pos = strfind(line, 'label'); % position of the "label" + if ~isempty(label_pos) + label_end = strfind(line(label_pos:end),','); + labels{lst_node} = unquote(line(label_pos+(6:label_end(1)-2))); + end + end +end + +if (isempty(find(x)) & (nargout > 2)) % If coordinates were requested, but not found in 'filename'. + warning('File does not contain node coordinates.'); +end; +if ~(size(Adj,1)==size(Adj,2)) % Make sure Adj is a square matrix. ? + Adj = eye(max(size(Adj)),size(Adj,1))*Adj*eye(size(Adj,2),max(size(Adj))); +end; +x = .9*(x-min(x))/range(x)+.05; % normalise and push off margins +y = .9*(y-min(y))/range(y)+.05; + + + +function s = unquote(s) + +s = strrep(s,'"',''); diff --git a/sourcecodes/bnt-master/GraphViz/draw_dbn.m b/sourcecodes/bnt-master/GraphViz/draw_dbn.m new file mode 100644 index 00000000..89bf2b13 --- /dev/null +++ b/sourcecodes/bnt-master/GraphViz/draw_dbn.m @@ -0,0 +1,99 @@ +function [x, y, h] = draw_dbn(adj, inter, flip_intra, K, labels, node_t, x, y) +% DRAW_LAYOUT_DBN Draws a layout for a Dynamical Belief Network +% +% [<X1, Y1, X2, Y2>] = DRAW_LAYOUT_DBN(INTRA, INTER, <FLIP_FLAG, K, LABELS, ISBOX, X1, Y1>) +% +% Inputs : +% INTRA, INTER : Adjacency matrices +% FLIP_FLAG : Transposes the DAG layout obtained from INTRA connections +% If X1, Y1 are specified, FLIP_FLAG has no effect. +% K : Unfold K times <Default = 2> +% LABELS - if -1, we use 1:N*K +% Rest : See DRAW_LAYOUT +% +% Outputs : +% Xi, Yi : Coordinates of nodes (for i'th timeslice) on the unit square +% H : Object Handles +% +% Usage Example : draw_layout_dbn(intra, inter, 1); +% draw_layout_dbn(intra, inter); +% +% Note : +% See also DRAW_GRAPH + +% Uses : DRAW_GRAPH + +% Change History : +% Date Time Prog Note +% 17-Apr-2000 1:02 PM ATC Created under MATLAB 5.3.1.29215a (R11.1) + +% ATC = Ali Taylan Cemgil, +% SNN - University of Nijmegen, Department of Medical Physics and Biophysics +% e-mail : cemgil@mbfys.kun.nl + +N = size(adj,1); +if nargin<3, + flip_intra = 0; +end; + +if nargin<4, + K = 2; +end; + +if K<2 | K>7, error('2<=K<=7 must hold..'); end; + + +if nargin<5 +% labels = cellstr(char(zeros(N,1)+double('+'))); +% labels = cellstr(int2str((1:N)')); + labels = cellstr(char((0:N-1)'+double('a'))); +end; + +if nargin<6, + node_t = zeros(N,1); +% node_t = rand(N,1) > 0.5; +end; + +if nargin<7, + [x1 y1] = make_layout(adj); + if flip_intra, tmp = x1; x1 = y1; y1 = tmp; end; +end; + +mid = round(K/2); + + +xi = x1(:)-1; +x = []; +y = repmat(y1(:), [K 1]); +node_t2 = repmat(node_t(:), [K 1]); + +if isa(labels,'double') & labels==-1 % KPM + lb = num2strcell(1:N*K); +else + lb = {}; + for i=1:K, + labels1 = labels(:); + if i==mid, str = ''; else str = sprintf('%+d',i-mid); end; + for i=1:N, + labels1{i} = [labels1{i} '(t' str ')']; + end; + lb = [lb; labels1(:)]; + end; +end + +dag = zeros(N*K); + +for i=1:K, + xi = xi+1; + x = [x; xi]; + + idx = ((i-1)*N+1):i*N; + dag(idx,idx) = adj; + if i<K, + dag(idx,idx+N) = inter; + end; +end; + +[x, y, h] = draw_graph(dag, lb, node_t2, x/K, y); + + diff --git a/sourcecodes/bnt-master/GraphViz/draw_dbn_test.m b/sourcecodes/bnt-master/GraphViz/draw_dbn_test.m new file mode 100644 index 00000000..7d7c2367 --- /dev/null +++ b/sourcecodes/bnt-master/GraphViz/draw_dbn_test.m @@ -0,0 +1,68 @@ +% TEST_LAYOUT_DBN Script to test some DBN layouts +% + +% Change History : +% Date Time Prog Note +% 17-Apr-2000 2:40 PM ATC Created under MATLAB 5.3.1.29215a (R11.1) + +% ATC = Ali Taylan Cemgil, +% SNN - University of Nijmegen, Department of Medical Physics and Biophysics +% e-mail : cemgil@mbfys.kun.nl + +disp('draw mhmm1') +clf +set(gcf, 'pos', [0 0 1024 600]); + +intra = zeros(3); +intra(1,[2 3]) = 1; +intra(2,3) = 1; +inter = zeros(3); +inter(1,1) = 1; +n = 3; +dnodes = [1 2]; +isbox = zeros(n,1); isbox(dnodes) = 1; +unfold = 4; +draw_dbn(intra, inter, 0, unfold, {'Q', 'M', 'Y'}, isbox); + + +pause +clf +disp('draw water1') +bnet = mk_water_dbn; +unfold = 3; +flip = 1; +[dummyx, dummyy, h] = draw_dbn(bnet.intra, bnet.inter, flip, unfold); + +col = rand(size(h,1),3); +for i=1:length(h), + col = rand(1,3); + % patches + set(h(i,2),'facecolor', col); drawnow; + % text + set(h(i,1),'color', 1-col); drawnow; +end; + + +pause +clf +disp('draw BAT static') +% This requires BNT + +%sz = get(0, 'ScreenSize'); +%sv = get(gcf, 'pos'); +%set(gcf, 'units','pix','pos', sz); +[bnet, names] = mk_bat_dbn; +N = size(bnet.intra,1); +G = [bnet.intra bnet.inter; + zeros(N,N) bnet.intra]; +names2 = names; +for i=1:N + names2{i} = sprintf('%s(1)', names{i}); + names2{i+N} = sprintf('%s(2)', names{i}); +end +draw_graph(G, names2); + +pause +disp('draw bat dbn') +clf +draw_dbn(bnet.intra, bnet.inter, 0, 2, names2); 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 @@ -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; diff --git a/sourcecodes/bnt-master/GraphViz/draw_graph.m b/sourcecodes/bnt-master/GraphViz/draw_graph.m new file mode 100644 index 00000000..be9a5b5b --- /dev/null +++ b/sourcecodes/bnt-master/GraphViz/draw_graph.m @@ -0,0 +1,335 @@ +function [x, y, h] = draw_graph(adj, labels, node_t, x, y, varargin) +% DRAW_LAYOUT Draws a layout for a graph +% +% [X, Y, H] = DRAW_LAYOUT(ADJ, <LABELS, ISBOX, X, Y>) +% +% Inputs : +% ADJ : Adjacency matrix (source, sink) +% LABELS : Cell array containing labels <Default : '1':'N'> +% ISBOX : 1 if node is a box, 0 if oval <Default : zeros> +% X, Y, : Coordinates of nodes on the unit square <Default : calls make_layout> +% +% Outputs : +% X, Y : Coordinates of nodes on the unit square +% H : Object handles +% +% Usage Example : [x, y] = draw_layout([0 1;0 0], {'Hidden','Visible'}, [1 0]'); +% +% h(i,1) is the text handle - color +% h(i,2) is the circle handle - facecolor +% +% See also MAKE_LAYOUT + +% Change History : +% Date Time Prog Note +% 13-Apr-2000 9:06 PM ATC Created under MATLAB 5.3.1.29215a (R11.1) +% +% ATC = Ali Taylan Cemgil, +% SNN - University of Nijmegen, Department of Medical Physics and Biophysics +% e-mail : cemgil@mbfys.kun.nl + +adj = double(adj); +N = size(adj,1); +if nargin<2, + labels = cellstr(int2str((1:N)')); +end + +if nargin<3, + node_t = zeros(N,1); +else + node_t = node_t(:); +end; + +axis([0 1 0 1]); +set(gca,'XTick',[],'YTick',[],'box','on'); +% axis('square'); +%colormap(flipud(gray)); + +if nargin<4, + [x y] = make_layout(adj); +end; + +idx1 = find(node_t==0); h1 = []; wd1=[]; +if ~isempty(idx1) + [h1 wd1] = textoval(x(idx1), y(idx1), labels(idx1), varargin{:}); +end; + +idx2 = find(node_t~=0); h2 = []; wd2 = []; +if ~isempty(idx2) + [h2 wd2] = textbox(x(idx2), y(idx2), labels(idx2), varargin{:}); +end; + +wd = zeros(size(wd1,1)+size(wd2,1),2); +if ~isempty(idx1), wd(idx1, :) = wd1; end; +if ~isempty(idx2), wd(idx2, :) = wd2; end; + +% coloring +color.box = 'black'; +color.text = color.box; +color.edge = [1 1 1]*3/4; +%color.edge = 'green'; +if ~isempty(idx1) + set(h1(:,1),'Color',color.text) + set(h1(:,2),'EdgeColor',color.box) +end +if ~isempty(idx2) + set(h2(:,1),'Color',color.text) + set(h2(:,2),'EdgeColor',color.box) +end + +% bug: this code assumes [x y] is the center of each box and oval, which +% isn't exactly true. +h_edge = []; +for i=1:N, + j = find(adj(i,:)==1); + for k=j, + if x(k)-x(i)==0, + sign = 1; + if y(i)>y(k), alpha = -pi/2; else alpha = pi/2; end; + else + alpha = atan((y(k)-y(i))/(x(k)-x(i))); + if x(i)<x(k), sign = 1; else sign = -1; end; + end; + dy1 = sign.*wd(i,2).*sin(alpha); dx1 = sign.*wd(i,1).*cos(alpha); + dy2 = sign.*wd(k,2).*sin(alpha); dx2 = sign.*wd(k,1).*cos(alpha); + if adj(k,i)==0, % if directed edge + h = arrow([x(i)+dx1 y(i)+dy1],[x(k)-dx2 y(k)-dy2],'BaseAngle',30); + set(h, 'FaceColor', color.edge) + set(h, 'EdgeColor', color.edge) + else + h = line([x(i)+dx1 x(k)-dx2],[y(i)+dy1 y(k)-dy2]); + set(h, 'Color', color.edge) + adj(k,i)=-1; % Prevent drawing lines twice + end; + h_edge = [h_edge h]; + end; +end; + +if nargout>2, + h = zeros(length(wd),2); + if ~isempty(idx1), + h(idx1,:) = h1; + end; + if ~isempty(idx2), + h(idx2,:) = h2; + end; +end; + +%%%%% + +function [t, wd] = textoval(x, y, str, varargin) +% TEXTOVAL Draws an oval around text objects +% +% [T, WIDTH] = TEXTOVAL(X, Y, STR) +% [..] = TEXTOVAL(STR) % Interactive +% +% Inputs : +% X, Y : Coordinates +% TXT : Strings +% +% Outputs : +% T : Object Handles +% WIDTH : x and y Width of ovals +% +% Usage Example : [t] = textoval('Visit to Asia?'); +% +% +% Note : +% See also TEXTBOX + +% Uses : + +% Change History : +% Date Time Prog Note +% 15-Jun-1998 10:36 AM ATC Created under MATLAB 5.1.0.421 +% 12-Mar-2004 10:00 AM minka Changed placement/sizing. +% +% ATC = Ali Taylan Cemgil, +% SNN - University of Nijmegen, Department of Medical Physics and Biophysics +% e-mail : cemgil@mbfys.kun.nl + +temp = []; +textProperties = {'BackgroundColor','Color','FontAngle','FontName','FontSize','FontUnits','FontWeight','Rotation'}; +varargin = argfilter(varargin,textProperties); + +if nargin == 1 + str = x; +end +if ~isa(str,'cell') str=cellstr(str); end; +N = length(str); +wd = zeros(N,2); +for i=1:N, + if nargin == 1 + [x, y] = ginput(1); + end + tx = text(x(i),y(i),str{i},'HorizontalAlignment','center',varargin{:}); + % minka + [ptc wx wy] = draw_oval(tx); + wd(i,:) = [wx wy]; + % draw_oval will paint over the text, so need to redraw it + delete(tx); + tx = text(x(i),y(i),str{i},'HorizontalAlignment','center',varargin{:}); + temp = [temp; tx ptc]; +end +if nargout>0, t = temp; end; + +%%%%%%%%% + + +function [ptc, wx, wy] = draw_oval(tx, x, y) +% Draws an oval box around a tex object +sz = get(tx,'Extent'); +% minka +wy = 2/3*sz(4); +wx = 2/3*sz(3); +x = sz(1)+sz(3)/2; +y = sz(2)+sz(4)/2; +ptc = ellipse(x, y, wx, wy); +set(ptc, 'FaceColor','w'); + + +%%%%%%%%%%%%% + +function [p] = ellipse(x, y, rx, ry, c) +% ELLIPSE Draws Ellipse shaped patch objects +% +% [<P>] = ELLIPSE(X, Y, Rx, Ry, C) +% +% Inputs : +% X : N x 1 vector of x coordinates +% Y : N x 1 vector of y coordinates +% Rx, Ry : Radii +% C : Color index +% +% +% Outputs : +% P = Handles of Ellipse shaped path objects +% +% Usage Example : [] = ellipse(); +% +% +% Note : +% See also + +% Uses : + +% Change History : +% Date Time Prog Note +% 27-May-1998 9:55 AM ATC Created under MATLAB 5.1.0.421 + +% ATC = Ali Taylan Cemgil, +% SNN - University of Nijmegen, Department of Medical Physics and Biophysics +% e-mail : cemgil@mbfys.kun.nl + +if (nargin < 2) error('Usage Example : e = ellipse([0 1],[0 -1],[1 0.5],[2 0.5]); '); end; +if (nargin < 3) rx = 0.1; end; +if (nargin < 4) ry = rx; end; +if (nargin < 5) c = 1; end; + +if length(c)==1, c = ones(size(x)).*c; end; +if length(rx)==1, rx = ones(size(x)).*rx; end; +if length(ry)==1, ry = ones(size(x)).*ry; end; + +n = length(x); +p = zeros(size(x)); +t = 0:pi/30:2*pi; +for i=1:n, + px = rx(i)*cos(t)+x(i); + py = ry(i)*sin(t)+y(i); + p(i) = patch(px,py,c(i)); +end; + +if nargout>0, pp = p; end; + +%%%%% + +function [t, wd] = textbox(x,y,str,varargin) +% TEXTBOX Draws A Box around the text +% +% [T, WIDTH] = TEXTBOX(X, Y, STR) +% [..] = TEXTBOX(STR) +% +% Inputs : +% X, Y : Coordinates +% TXT : Strings +% +% Outputs : +% T : Object Handles +% WIDTH : x and y Width of boxes +%% +% Usage Example : t = textbox({'Ali','Veli','49','50'}); +% +% +% Note : +% See also TEXTOVAL + +% Uses : + +% Change History : +% Date Time Prog Note +% 09-Jun-1998 11:43 AM ATC Created under MATLAB 5.1.0.421 +% 12-Mar-2004 10:00 AM minka Changed placement/sizing. +% +% ATC = Ali Taylan Cemgil, +% SNN - University of Nijmegen, Department of Medical Physics and Biophysics +% e-mail : cemgil@mbfys.kun.nl + +temp = []; +textProperties = {'BackgroundColor','Color','FontAngle','FontName','FontSize','FontUnits','FontWeight','Rotation'}; +varargin = argfilter(varargin,textProperties); + +if nargin == 1 + str = x; +end +if ~isa(str,'cell') str=cellstr(str); end; +N = length(str); +wd = zeros(N,2); +for i=1:N, + if nargin == 1 + [x, y] = ginput(1); + end + tx = text(x(i),y(i),str{i},'HorizontalAlignment','center',varargin{:}); + % minka + [ptc wx wy] = draw_box(tx); + wd(i,:) = [wx wy]; + % draw_box will paint over the text, so need to redraw it + delete(tx); + tx = text(x(i),y(i),str{i},'HorizontalAlignment','center',varargin{:}); + temp = [temp; tx ptc]; +end; + +if nargout>0, t = temp; end; + + +function [ptc, wx, wy] = draw_box(tx) +% Draws a box around a text object +sz = get(tx,'Extent'); +% minka +wy = 1/2*sz(4); +wx = 1/2*sz(3); +x = sz(1)+sz(3)/2; +y = sz(2)+sz(4)/2; +ptc = patch([x-wx x+wx x+wx x-wx], [y+wy y+wy y-wy y-wy],'w'); +set(ptc, 'FaceColor','w'); + + + +function args = argfilter(args,keep) +%ARGFILTER Remove unwanted arguments. +% ARGFILTER(ARGS,KEEP), where ARGS = {'arg1',value1,'arg2',value2,...}, +% returns a new argument list where only the arguments named in KEEP are +% retained. KEEP is a character array or cell array of strings. + +% Written by Tom Minka + +if ischar(keep) + keep = cellstr(keep); +end +i = 1; +while i < length(args) + if ~ismember(args{i},keep) + args = args(setdiff(1:length(args),[i i+1])); + else + i = i + 2; + end +end diff --git a/sourcecodes/bnt-master/GraphViz/draw_graph_test.m b/sourcecodes/bnt-master/GraphViz/draw_graph_test.m new file mode 100644 index 00000000..0d3aa186 --- /dev/null +++ b/sourcecodes/bnt-master/GraphViz/draw_graph_test.m @@ -0,0 +1,50 @@ +% TEST_LAYOUT Script to test some bayesian net layouts +% + +% Change History : +% Date Time Prog Note +% 13-Apr-2000 10:40 PM ATC Created under MATLAB 5.3.1.29215a (R11.1) + +% ATC = Ali Taylan Cemgil, +% SNN - University of Nijmegen, Department of Medical Physics and Biophysics +% e-mail : cemgil@mbfys.kun.nl + +%bnet = mk_asia_bnet; +%draw_graph(bnet.dag); + +% Make the following network (from Jensen (1996) p84 fig 4.17) +% 1 +% / | \ +% 2 3 4 +% | | | +% 5 6 7 +% \/ \/ +% 8 9 +% where all arcs point downwards + +disp('plot directed') +clf; + +N = 9; +dag = zeros(N,N); +dag(1,2)=1; dag(1,3)=1; dag(1,4)=1; +dag(2,5)=1; dag(3,6)=1; dag(4,7)=1; +dag(5,8)=1; dag(6,8)=1; dag(6,9)=1; dag(7,9) = 1; + +draw_graph(dag); + +pause +clf +disp('plot undirected') +udag = [dag+dag']; +draw_graph(udag); + +pause +clf +disp('plot mixed') +mg = [dag]; +mg(2,1) = 1; mg(8,5) = 1; +draw_graph(mg); + + + diff --git a/sourcecodes/bnt-master/GraphViz/draw_hmm.m b/sourcecodes/bnt-master/GraphViz/draw_hmm.m new file mode 100644 index 00000000..e517789c --- /dev/null +++ b/sourcecodes/bnt-master/GraphViz/draw_hmm.m @@ -0,0 +1,117 @@ +function draw_hmm(A, varargin) +% DRAW_HMM Make a picture of the HMM using dotty +% function draw_hmm(A, ...) +% +% For details on dotty, see http://www.research.att.com/sw/tools/graphviz +% +% If A(i,j) > thresh, we draw and arc from state i to state j. +% +% Optional arguments (name/value pairs) [default] +% +% thresh - [1e-1] +% obsprob - If B(i,o) > 0, we include "o" in the name of state i. +% e.g., if state 5 emits 1,3,7, its label becomes "5: 1 3 7". +% startprob - ifstartprob(i) > 0, the state name will be prefixed with "+". +% endprob - if endprob(i) > 0, the state name will be appended with "-". +% filename - if [], we write to 'tmp.dot', convert this to 'tmp.ps' +% using 'dot -Tps tmp.dot -o tmp.ps', and then call ghostview to display the result. +% dot and gv must be on your system path. +% If filename ~= [], we just generate the dot file, and do not +% convert it to postscript or call ghostview. + +[thresh, B, startprob, endprob, filename] = ... + process_options(varargin, 'thresh', 1e-1, 'obsprob', [], 'startprob', [], 'endprob', [], ... + 'filename', []); + +Q = length(A); + +arclabel = cell(Q,Q); +G = zeros(Q,Q); +for i=1:Q + for j=1:Q + if A(i,j) < thresh + arclabel{i,j} = ''; + else + G(i,j) = 1; + arclabel{i,j} = sprintf('%5.3f', A(i,j)); + end + end +end + + +nodelabel = cell(1,Q); +for i=1:Q + % annotate start/stop states + if ~isempty(startprob) & ~approxeq(startprob(i), 0) + start = '+'; + else + start = ''; + end + if ~isempty(endprob) & ~approxeq(hmm.endprob(i), 0) + stop = '-'; + else + stop = ''; + end + label = sprintf('%s%d%s :', start, i, stop); + + if ~isempty(B) + output_label = mk_output_label(B); + label = strcat(label, output_label); + end + + nodelabel{i} = label; +end + + +if isempty(filename) + filename = 'tmp.dot'; + %mkdot(G, filename, arclabel, nodelabel) + graph_to_dot(G, 'filename', filename, 'arc_label', arclabel, 'node_label', nodelabel); + fprintf('converting from .ps to .dot\n') + !dot -Tps tmp.dot -o tmp.ps + !gv tmp.ps & +else + graph_to_dot(G, 'filename', filename, 'arc_label', arclabel, 'node_label', nodelabel); + %mkdot(G, filename, arclabel, nodelabel) +end + + +%%%%%%%%% + +function label = mk_output_label(B) + +[Q O] = size(B); +label = ''; + +if 0 + % print most probable symbols + for i=1:Q + m = max(B(i,:)); + ndx = find(abs(B(i,:) - repmat(m,1,O)) < 1e-2); + %ndx = find(B(i,:)==m); + %label = sprintf('%d,', ndx); + end +end + +if 0 + % print prob distrib over all symbols + for o=1:O + if approxeq(B(i,o), 0) + % + else + label = strcat(label, sprintf('%d(%3.2f),', o, B(i,o))); + end + end +end + +if 1 + % print all non-zero symbols + chars = ['a' 'b' 'c']; + for o=1:O + if approxeq(B(i,o), 0) + % + else + label = strcat(label, sprintf('%s', chars(o))); + end + end +end diff --git a/sourcecodes/bnt-master/GraphViz/editGraphGUI.m b/sourcecodes/bnt-master/GraphViz/editGraphGUI.m new file mode 100644 index 00000000..45de6497 --- /dev/null +++ b/sourcecodes/bnt-master/GraphViz/editGraphGUI.m @@ -0,0 +1,16 @@ +function g +%here is how one creates a function ("callback") which does something +%(prints the node label) when you click on the node's text in Matlab figure. +% +% Leon Peshkin http://www.ai.mit.edu/~pesha +% +%draw_graph(...) + + % "gca" is the current "axes" object, parent of all objects in figure + % "gcbo" is the handle of the object whose callback is being executed + % "findall" gives handles to all elements of a given type in the figure +text_elms = findall(gca,'Type','text'); +for ndx = 1:length(text_elms) + callbk = 'my_call(str2num(get(gcbo,''String'')))'; + set(text_elms(ndx), 'ButtonDownFcn', callbk); % assume the node label is a number +end diff --git a/sourcecodes/bnt-master/GraphViz/graph_to_dot.m b/sourcecodes/bnt-master/GraphViz/graph_to_dot.m new file mode 100644 index 00000000..c9f692d1 --- /dev/null +++ b/sourcecodes/bnt-master/GraphViz/graph_to_dot.m @@ -0,0 +1,86 @@ +function graph_to_dot(adj, varargin) +%GRAPH_TO_DOT Makes a GraphViz (AT&T) file representing an adjacency matrix +% graph_to_dot(adj, ...) writes to the specified filename. +% +% Optional arguments can be passed as name/value pairs: [default] +% +% 'filename' - if omitted, writes to 'tmp.dot' +% 'arc_label' - arc_label{i,j} is a string attached to the i-j arc [""] +% 'node_label' - node_label{i} is a string attached to the node i ["i"] +% 'width' - width in inches [10] +% 'height' - height in inches [10] +% 'leftright' - 1 means layout left-to-right, 0 means top-to-bottom [0] +% 'directed' - 1 means use directed arcs, 0 means undirected [1] +% +% For details on graphviz, See http://www.research.att.com/sw/tools/graphviz +% +% See also dot_to_graph and draw_dot. + +% First version written by Kevin Murphy 2002. +% Modified by Leon Peshkin, Jan 2004. +% Bugfix by Tom Minka, Mar 2004. + +node_label = []; arc_label = []; % set default args +width = 10; height = 10; +leftright = 0; directed = 1; filename = 'tmp.dot'; + +for i = 1:2:nargin-1 % get optional args + switch varargin{i} + case 'filename', filename = varargin{i+1}; + case 'node_label', node_label = varargin{i+1}; + case 'arc_label', arc_label = varargin{i+1}; + case 'width', width = varargin{i+1}; + case 'height', height = varargin{i+1}; + case 'leftright', leftright = varargin{i+1}; + case 'directed', directed = varargin{i+1}; + end +end +% minka +if ~directed + adj = triu(adj | adj'); +end + +fid = fopen(filename, 'w'); +if directed + fprintf(fid, 'digraph G {\n'); + arctxt = '->'; + if isempty(arc_label) + labeltxt = ''; + else + labeltxt = '[label="%s"]'; + end +else + fprintf(fid, 'graph G {\n'); + arctxt = '--'; + if isempty(arc_label) + labeltxt = '[dir=none]'; + else + labeltext = '[label="%s",dir=none]'; + end +end +edgeformat = strcat(['%d ',arctxt,' %d ',labeltxt,';\n']); +fprintf(fid, 'center = 1;\n'); +fprintf(fid, 'size=\"%d,%d\";\n', width, height); +if leftright + fprintf(fid, 'rankdir=LR;\n'); +end +Nnds = length(adj); +for node = 1:Nnds % process nodes + if isempty(node_label) + fprintf(fid, '%d;\n', node); + else + fprintf(fid, '%d [ label = "%s" ];\n', node, node_label{node}); + end +end +for node1 = 1:Nnds % process edges + arcs = find(adj(node1,:)); % children(adj, node); + for node2 = arcs + if ~isempty(arc_label) + fprintf(fid, edgeformat,node1,node2,arc_label{node1,node2}); + else + fprintf(fid, edgeformat, node1, node2); + end + end +end +fprintf(fid, '}'); +fclose(fid); diff --git a/sourcecodes/bnt-master/GraphViz/make_layout.m b/sourcecodes/bnt-master/GraphViz/make_layout.m new file mode 100644 index 00000000..69740b76 --- /dev/null +++ b/sourcecodes/bnt-master/GraphViz/make_layout.m @@ -0,0 +1,172 @@ +function [x, y] = make_layout(adj) + +%function [x, y] = layout_dag(adj) +% MAKE_LAYOUT Creates a layout from an adjacency matrix +% +% [X, Y] = MAKE_LAYOUT(ADJ) +% +% Inputs : +% ADJ = adjacency matrix (source, sink) +% +% Outputs : +% X, Y : Positions of nodes +% +% Usage Example : [X, Y] = make_layout(adj); +% +% +% Note : Uses some very simple heuristics, so any other +% algorithm would create a nicer layout +% +% See also + +% Uses : + +% Change History : +% Date Time Prog Note +% 13-Apr-2000 8:25 PM ATC Created under MATLAB 5.3.1.29215a (R11.1) + +% ATC = Ali Taylan Cemgil, +% SNN - University of Nijmegen, Department of Medical Physics and Biophysics +% e-mail : cemgil@mbfys.kun.nl + +N = size(adj,1); +tps = toposort(adj); + +if ~isempty(tps), % is directed ? + level = zeros(1,N); + for i=tps, + idx = find(adj(:,i)); + if ~isempty(idx), + l = max(level(idx)); + level(i)=l+1; + end; + end; +else + level = poset(adj,1)'-1; +end; + +y = (level+1)./(max(level)+2); +y = 1-y; +x = zeros(size(y)); +for i=0:max(level), + idx = find(level==i); + offset = (rem(i,2)-0.5)/10; + x(idx) = (1:length(idx))./(length(idx)+1)+offset; +end; + +%%%%%%% + +function [depth] = poset(adj, root) +% POSET Identify a partial ordering among the nodes of a graph +% +% [DEPTH] = POSET(ADJ,ROOT) +% +% Inputs : +% ADJ : Adjacency Matrix +% ROOT : Node to start with +% +% Outputs : +% DEPTH : Depth of the Node +% +% Usage Example : [depth] = poset(adj,12); +% +% +% Note : All Nodes must be connected +% See also + +% Uses : + +% Change History : +% Date Time Prog Note +% 17-Jun-1998 12:01 PM ATC Created under MATLAB 5.1.0.421 + +% ATC = Ali Taylan Cemgil, +% SNN - University of Nijmegen, Department of Medical Physics and Biophysics +% e-mail : cemgil@mbfys.kun.nl + +adj = adj+adj'; + +N = size(adj,1); +depth = zeros(N,1); +depth(root) = 1; +queue = root; + +while 1, + if isempty(queue), + if all(depth), break; + else + root = find(depth==0); + root = root(1); + depth(root) = 1; + queue = root; + end; + end; + r = queue(1); queue(1) = []; + idx = find(adj(r,:)); + idx2 = find(~depth(idx)); + idx = idx(idx2); + queue = [queue idx]; + depth(idx) = depth(r)+1; +end; + +%%%%%%%%% + +function [seq] = toposort(adj) +% TOPOSORT A Topological ordering of nodes in a directed graph +% +% [SEQ] = TOPOSORT(ADJ) +% +% Inputs : +% ADJ : Adjacency Matrix. +% ADJ(i,j)==1 ==> there exists a directed edge +% from i to j +% +% Outputs : +% SEQ : A topological ordered sequence of nodes. +% empty matrix if graph contains cycles. +% +% Usage Example : +% N=5; +% [l,u] = lu(rand(N)); +% adj = ~diag(ones(1,N)) & u>0.5; +% seq = toposort(adj); +% +% +% Note : +% See also + +% Uses : + +% Change History : +% Date Time Prog Note +% 18-May-1998 4:44 PM ATC Created under MATLAB 5.1.0.421 + +% ATC = Ali Taylan Cemgil, +% SNN - University of Nijmegen, Department of Medical Physics and Biophysics +% e-mail : cemgil@mbfys.kun.nl + +N = size(adj); +indeg = sum(adj,1); +outdeg = sum(adj,2); +seq = []; + +for i=1:N, + % Find nodes with indegree 0 + idx = find(indeg==0); + % If can't find than graph contains a cycle + if isempty(idx), + seq = []; + break; + end; + % Remove the node with the max number of connections + [dummy idx2] = max(outdeg(idx)); + indx = idx(idx2); + seq = [seq, indx]; + indeg(indx)=-1; + idx = find(adj(indx,:)); + indeg(idx) = indeg(idx)-1; +end; + + + + diff --git a/sourcecodes/bnt-master/GraphViz/my_call.m b/sourcecodes/bnt-master/GraphViz/my_call.m new file mode 100644 index 00000000..7059d1fc --- /dev/null +++ b/sourcecodes/bnt-master/GraphViz/my_call.m @@ -0,0 +1,3 @@ +function my_call(value) +fprintf('%d \n', value); % might check here whether this is a label at all + % since we get here by clicking on ANY text in figure diff --git a/sourcecodes/bnt-master/GraphViz/process_options.m b/sourcecodes/bnt-master/GraphViz/process_options.m new file mode 100644 index 00000000..5e17eb89 --- /dev/null +++ b/sourcecodes/bnt-master/GraphViz/process_options.m @@ -0,0 +1,132 @@ +% PROCESS_OPTIONS - Processes options passed to a Matlab function. +% This function provides a simple means of +% parsing attribute-value options. Each option is +% named by a unique string and is given a default +% value. +% +% Usage: [var1, var2, ..., varn[, unused]] = ... +% process_options(args, ... +% str1, def1, str2, def2, ..., strn, defn) +% +% Arguments: +% args - a cell array of input arguments, such +% as that provided by VARARGIN. Its contents +% should alternate between strings and +% values. +% str1, ..., strn - Strings that are associated with a +% particular variable +% def1, ..., defn - Default values returned if no option +% is supplied +% +% Returns: +% var1, ..., varn - values to be assigned to variables +% unused - an optional cell array of those +% string-value pairs that were unused; +% if this is not supplied, then a +% warning will be issued for each +% option in args that lacked a match. +% +% Examples: +% +% Suppose we wish to define a Matlab function 'func' that has +% required parameters x and y, and optional arguments 'u' and 'v'. +% With the definition +% +% function y = func(x, y, varargin) +% +% [u, v] = process_options(varargin, 'u', 0, 'v', 1); +% +% calling func(0, 1, 'v', 2) will assign 0 to x, 1 to y, 0 to u, and 2 +% to v. The parameter names are insensitive to case; calling +% func(0, 1, 'V', 2) has the same effect. The function call +% +% func(0, 1, 'u', 5, 'z', 2); +% +% will result in u having the value 5 and v having value 1, but +% will issue a warning that the 'z' option has not been used. On +% the other hand, if func is defined as +% +% function y = func(x, y, varargin) +% +% [u, v, unused_args] = process_options(varargin, 'u', 0, 'v', 1); +% +% then the call func(0, 1, 'u', 5, 'z', 2) will yield no warning, +% and unused_args will have the value {'z', 2}. This behaviour is +% useful for functions with options that invoke other functions +% with options; all options can be passed to the outer function and +% its unprocessed arguments can be passed to the inner function. + +% Copyright (C) 2002 Mark A. Paskin +% +% This program is free software; you can redistribute it and/or modify +% it under the terms of the GNU General Public License as published by +% the Free Software Foundation; either version 2 of the License, or +% (at your option) any later version. +% +% This program is distributed in the hope that it will be useful, but +% WITHOUT ANY WARRANTY; without even the implied warranty of +% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +% General Public License for more details. +% +% You should have received a copy of the GNU General Public License +% along with this program; if not, write to the Free Software +% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 +% USA. +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + +function [varargout] = process_options(args, varargin) + +% Check the number of input arguments +n = length(varargin); +if (mod(n, 2)) + error('Each option must be a string/value pair.'); +end + +% Check the number of supplied output arguments +if (nargout < (n / 2)) + error('Insufficient number of output arguments given'); +elseif (nargout == (n / 2)) + warn = 1; + nout = n / 2; +else + warn = 0; + nout = n / 2 + 1; +end + +% Set outputs to be defaults +varargout = cell(1, nout); +for i=2:2:n + varargout{i/2} = varargin{i}; +end + +% Now process all arguments +nunused = 0; +for i=1:2:length(args) + found = 0; + for j=1:2:n + if strcmpi(args{i}, varargin{j}) + varargout{(j + 1)/2} = args{i + 1}; + found = 1; + break; + end + end + if (~found) + if (warn) + warning(sprintf('Option ''%s'' not used.', args{i})); + args{i} + else + nunused = nunused + 1; + unused{2 * nunused - 1} = args{i}; + unused{2 * nunused} = args{i + 1}; + end + end +end + +% Assign the unused arguments +if (~warn) + if (nunused) + varargout{nout} = unused; + else + varargout{nout} = cell(0); + end +end |