BNW using Octave instead of Matlab.

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

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

1 files changed, 153 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/SLP/misc/export_dnet.m b/sourcecodes/bnt-master/SLP/misc/export_dnet.m
new file mode 100644
index 00000000..9b0cbd04
--- /dev/null
+++ b/sourcecodes/bnt-master/SLP/misc/export_dnet.m
@@ -0,0 +1,153 @@
+function S = export_dnet(bnet, file, proba)
+% filepath = export_dnet(bnet, 'filename', includeparameters)
+%  filename and includeparameters ([0] or 1) are optional
+%
+% Exports BNT bnets to Netica dnet
+%
+% Written by Francois.Olivier.C.H@gmail.com
+%
+% Informations could be found here http://www.norsys.com/downloads/
+%
+% Version 80806
+% Supports only discret bayesian network
+
+if nargin==1, file=['dnet' datestr(now,'-yymmdd-HHMMSS')]; end
+if nargin<3, proba=0; end
+
+% generating filename
+if length(file)>4,
+  if prod(double(file((end-4):end)~='.dnet')), file=[file '.dnet']; end
+  name = file(1:end-5);
+else
+  name = file;
+  file = [file '.dnet'];
+end
+
+% generating node names 1:N if non existant
+N=length(bnet.dag);
+if isempty(bnet.names),
+  for i=1:N,
+    keys{i}=['' num2str(i) ''];
+    vals{i}=i;
+  end
+  bnet.names = assocarray(keys, vals);
+end
+
+% header of the file
+fid = fopen(file, 'w');
+fprintf(fid, '// ~->[DNET-1]->~\n\n');
+fprintf(fid, '// exported from the Bayes Net Toolbox with export_dnet function \n');
+fprintf(fid, '// please report bugs to francois.olivier.c.h@gmail.com\n');
+if proba, fprintf(fid, '// Take care !  Parents'' order isn''t the same in probability table comments\n'); end
+fprintf(fid, ['\nbnet ' name ' {']);
+
+% main loop
+for node = 1:N
+  name = get_key(bnet.names,node);
+
+  fprintf(fid, ['\nnode ' name ' {']);
+
+  fprintf(fid, '\n\tkind = NATURE;');
+
+  fprintf(fid, '\n\tdiscrete = TRUE;');
+
+% states names are x1,x2:xsize(node)
+  fprintf(fid, '\n\tstates = (');
+  for l=1:bnet.node_sizes(node),
+    fprintf(fid, 'x%d',l);
+    if l~=bnet.node_sizes(node), fprintf(fid, ', '); end
+  end, fprintf(fid, ');');
+
+% declare parent in counter order to be coherent with prob section
+  fprintf(fid, '\n\tparents = (');
+  par = bnet.parents{node};
+  for l=length(par):-1:1
+    fprintf(fid, '%s',get_key(bnet.names,par(l)));
+    if l~=1, fprintf(fid, ', '); end
+  end, fprintf(fid, ');');
+
+% fill probs if proba==1
+    if proba,
+        fprintf(fid, '\n\tprobs =\n');
+        % inits
+        fprintf(fid, '\t//\t');
+        for l = 1:bnet.node_sizes(node),
+            fprintf(fid, 'x%d\t', l);
+        end
+            fprintf(fid, '\t//');
+        if ~isempty(par),
+            for l = unique(par), %right order this time because of the way both BNT and netica work
+                fprintf(fid, '\t%s', get_key(bnet.names,l));
+            end
+        end
+
+        % opens tab
+        fprintf(fid, '\n\t');
+        for l = unique(par),
+            fprintf(fid, '(');
+        end
+
+        % fullfils probs
+        CPT = CPT_from_bnet(bnet);
+        CPT = CPT{node};
+        CPT=CPT(:);            % good order whatever the node size ????
+        if isempty(par),
+            fprintf(fid, '\t');
+            for i=1:length(CPT)-1,
+                fprintf(fid, '%1.4f, ', CPT(i));
+            end
+            fprintf(fid, '%1.4f);',CPT(end));
+        else                   % if there are parents
+            endi=0;
+            parsiz = prod(bnet.node_sizes([par]));
+            parentstates = ones(1,length(par)); parentstates(end)=0;
+            for i=1:parsiz
+                % prints probas
+                fprintf(fid, '(\t');
+                for j = 1:bnet.node_sizes(node)
+                    prob = CPT(i+parsiz*(j-1));
+                    if j~=bnet.node_sizes(node), fprintf(fid, '%1.4f, ',prob);
+                    else fprintf(fid, '%1.4f',prob); end
+                end
+
+                % closes parenthesis if needed
+                endii=endi;
+                if i~=parsiz,
+                    while endi>0, fprintf(fid, ')');endi=endi-1; end
+                    fprintf(fid, '),\t//\t');
+                else % close tab
+                    for l = unique(par), fprintf(fid, ')'); end
+                    fprintf(fid, ');\t//\t');
+                end
+
+                % prints node states
+                res=i;
+                for l=1:length(par)-1
+                    if mod(i+1, prod(bnet.node_sizes(par(1:l))))==0, endi=endi+1; end  % counts parenthesis
+
+                    resaff = mod(res, bnet.node_sizes(l));
+                    if resaff==0, resaff=bnet.node_sizes(par(l)); end
+                    res = div(res-1, bnet.node_sizes(par(l)))+1;
+
+                    fprintf(fid, '%d\t',resaff);
+                end
+
+                resaff = div(i-1, prod(bnet.node_sizes(par(1:end-1))))+1;
+                fprintf(fid, '%d',resaff);
+
+                % opens parenthesis if needed
+                if i~=parsiz, fprintf(fid, '\n'); end
+                fprintf(fid, '\t');
+                if i~=parsiz, while endii>0, fprintf(fid, '(');endii=endii-1; end, end
+            end
+        end
+    end
+    fprintf(fid, '\n\t};');
+end
+
+% closes file
+fprintf(fid,'\n};\n');
+fclose(fid);
+
+% outputs string
+S = [pwd '/' file];