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

13 files changed, 144 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/CPD_to_CPT.m b/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/CPD_to_CPT.m
new file mode 100644
index 00000000..f3509acf
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/CPD_to_CPT.m
@@ -0,0 +1,5 @@
+function CPT = CPD_to_CPT(CPD)
+% CPD_TO_CPT Convert the tabular_decision_node to a CPT
+% CPT = CPD_to_CPT(CPD)
+
+CPT = CPD.CPT;
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/CVS/Entries b/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/CVS/Entries
new file mode 100644
index 00000000..70a7b527
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/CVS/Entries
@@ -0,0 +1,6 @@
+/CPD_to_CPT.m/1.1.1.1/Wed May 29 15:59:54 2002//
+/display.m/1.1.1.1/Wed May 29 15:59:54 2002//
+/get_field.m/1.1.1.1/Wed May 29 15:59:54 2002//
+/set_fields.m/1.1.1.1/Wed May 29 15:59:54 2002//
+/tabular_decision_node.m/1.1.1.1/Wed May 29 15:59:54 2002//
+D
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/CVS/Entries.Log b/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/CVS/Entries.Log
new file mode 100644
index 00000000..24f16336
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/CVS/Entries.Log
@@ -0,0 +1 @@
+A D/Old////
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/CVS/Repository b/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/CVS/Repository
new file mode 100644
index 00000000..df9f8a23
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/CVS/Repository
@@ -0,0 +1 @@
+FullBNT/BNT/CPDs/@tabular_decision_node
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/CVS/Root b/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/CVS/Root
new file mode 100644
index 00000000..f3bd14a6
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/CVS/Root
@@ -0,0 +1 @@
+:ext:nsaunier@bnt.cvs.sourceforge.net:/cvsroot/bnt
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/Old/CVS/Entries b/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/Old/CVS/Entries
new file mode 100644
index 00000000..f11d0269
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/Old/CVS/Entries
@@ -0,0 +1,2 @@
+/tabular_decision_node.m/1.1.1.1/Wed May 29 15:59:54 2002//
+D
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/Old/CVS/Repository b/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/Old/CVS/Repository
new file mode 100644
index 00000000..c14a3f7d
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/Old/CVS/Repository
@@ -0,0 +1 @@
+FullBNT/BNT/CPDs/@tabular_decision_node/Old
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/Old/CVS/Root b/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/Old/CVS/Root
new file mode 100644
index 00000000..f3bd14a6
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/Old/CVS/Root
@@ -0,0 +1 @@
+:ext:nsaunier@bnt.cvs.sourceforge.net:/cvsroot/bnt
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/Old/tabular_decision_node.m b/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/Old/tabular_decision_node.m
new file mode 100644
index 00000000..7c4c26d5
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/Old/tabular_decision_node.m
@@ -0,0 +1,39 @@
+function CPD = tabular_decision_node(sz, CPT)
+% TABULAR_DECISION_NODE Represent the randomized policy over a discrete decision/action node as a table
+% CPD = tabular_decision_node(sz, CPT)
+%
+% sz(1:end-1) is the sizes of the parents, sz(end) is the size of this node
+% By default, CPT is set to the uniform random policy
+
+if nargin==0
+  % This occurs if we are trying to load an object from a file.
+  CPD = init_fields;
+  CPD = class(CPD, 'tabular_decision_node');
+  return;
+elseif isa(sz, 'tabular_decision_node')
+  % This might occur if we are copying an object.
+  CPD = sz;
+  return;
+end
+CPD = init_fields;
+
+if nargin < 2
+  CPT = mk_stochastic(myones(sz)); 
+else
+  CPT = myreshape(CPT, sz);
+end
+
+CPD.CPT = CPT;
+CPD.size = sz;
+
+CPD = class(CPD, 'tabular_decision_node');
+
+%%%%%%%%%%%
+
+function CPD = init_fields()
+% This ensures we define the fields in the same order 
+% no matter whether we load an object from a file,
+% or create it from scratch. (Matlab requires this.)
+
+CPD.CPT = [];
+CPD.size = [];
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/display.m b/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/display.m
new file mode 100644
index 00000000..a029e5d6
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/display.m
@@ -0,0 +1,4 @@
+function display(CPD)
+
+disp('tabular decision node object');
+disp(struct(CPD)); 
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/get_field.m b/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/get_field.m
new file mode 100644
index 00000000..24c2cedc
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/get_field.m
@@ -0,0 +1,19 @@
+function vals = get_field(CPD, name)
+% GET_PARAMS Get the parameters (fields) for a tabular_decision_node object
+% vals = get_params(CPD, name)
+%
+% The following fields can be accessed
+%
+% policy - the table containing the policy
+%
+% e.g., policy = get_params(CPD, 'policy')
+
+args = varargin;
+nargs = length(args);
+for i=1:2:nargs
+  switch args{i},
+   case 'policy',  vals =  CPD.CPT;
+   otherwise,
+    error(['invalid argument name ' args{i}]);
+  end
+end               
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/set_fields.m b/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/set_fields.m
new file mode 100644
index 00000000..4fe62292
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/set_fields.m
@@ -0,0 +1,19 @@
+function CPD = set_params(CPD, varargin)
+% SET_PARAMS Set the parameters (fields) for a tabular_decision_node object
+% CPD = set_params(CPD, name/value pairs)
+%
+% The following optional arguments can be specified in the form of name/value pairs:
+%
+% policy - the table containing the policy
+%
+% e.g., CPD = set_params(CPD, 'policy', T)
+
+args = varargin;
+nargs = length(args);
+for i=1:2:nargs
+  switch args{i},
+   case 'policy',   CPD.CPT = args{i+1};
+   otherwise,
+    error(['invalid argument name ' args{i}]);
+  end
+end               
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/tabular_decision_node.m b/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/tabular_decision_node.m
new file mode 100644
index 00000000..75ca5780
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@tabular_decision_node/tabular_decision_node.m
@@ -0,0 +1,45 @@
+function CPD = tabular_decision_node(bnet, self, CPT)
+% TABULAR_DECISION_NODE Represent a stochastic policy over a discrete decision/action node as a table
+% CPD = tabular_decision_node(bnet, self, CPT)
+%
+% node is the number of a node in this equivalence class.
+% CPT is an optional argument (see tabular_CPD for details); by default, it is the uniform policy.
+
+if nargin==0
+  % This occurs if we are trying to load an object from a file.
+  CPD = init_fields;
+  CPD = class(CPD, 'tabular_decision_node', discrete_CPD(1, []));
+  return;
+elseif isa(bnet, 'tabular_decision_node')
+  % This might occur if we are copying an object.
+  CPD = bnet;
+  return;
+end
+CPD = init_fields;
+
+ns = bnet.node_sizes;
+fam = family(bnet.dag, self);
+ps = parents(bnet.dag, self);
+sz = ns(fam);
+
+if nargin < 3
+  CPT = mk_stochastic(myones(sz)); 
+else
+  CPT = myreshape(CPT, sz);
+end
+
+CPD.CPT = CPT;
+CPD.sizes = sz; 
+
+clamped = 1; % don't update using EM
+CPD = class(CPD, 'tabular_decision_node', discrete_CPD(clamped, ns([ps self])));
+
+%%%%%%%%%%%
+
+function CPD = init_fields()
+% This ensures we define the fields in the same order 
+% no matter whether we load an object from a file,
+% or create it from scratch. (Matlab requires this.)
+
+CPD.CPT = [];
+CPD.sizes = [];