Merge pull request #1 from ziejd2/octave_php_separate

Octave php separate

16 files changed, 116 insertions, 0 deletions

diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/CVS/Entries b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/CVS/Entries
new file mode 100644
index 00000000..47f0e262
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/CVS/Entries
@@ -0,0 +1,8 @@
+/README/1.1.1.1/Wed May 29 15:59:52 2002//
+/adjustable_CPD.m/1.1.1.1/Wed May 29 15:59:52 2002//
+/display.m/1.1.1.1/Wed May 29 15:59:52 2002//
+/generic_CPD.m/1.1.1.1/Wed May 29 15:59:52 2002//
+/learn_params.m/1.1.1.1/Thu Jun 10 01:53:20 2004//
+/log_prior.m/1.1.1.1/Wed May 29 15:59:52 2002//
+/set_clamped.m/1.1.1.1/Wed May 29 15:59:52 2002//
+D
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/CVS/Entries.Log b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/CVS/Entries.Log
new file mode 100644
index 00000000..24f16336
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/CVS/Entries.Log
@@ -0,0 +1 @@
+A D/Old////
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/CVS/Repository b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/CVS/Repository
new file mode 100644
index 00000000..19ab61e0
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/CVS/Repository
@@ -0,0 +1 @@
+FullBNT/BNT/CPDs/@generic_CPD
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/CVS/Root b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/CVS/Root
new file mode 100644
index 00000000..f3bd14a6
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/CVS/Root
@@ -0,0 +1 @@
+:ext:nsaunier@bnt.cvs.sourceforge.net:/cvsroot/bnt
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/Old/BIC_score_CPD.m b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/Old/BIC_score_CPD.m
new file mode 100644
index 00000000..a73d073b
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/Old/BIC_score_CPD.m
@@ -0,0 +1,26 @@
+function score = BIC_score_CPD(CPD, fam, data, ns, cnodes)
+% BIC_score_CPD Compute the BIC score of a generic CPD
+% score = BIC_score_CPD(CPD, fam, data, ns, cnodes)
+%
+% We assume this node has a maximize_params method
+
+ncases = size(data, 2);
+CPD = reset_ess(CPD);
+% make a fully observed joint distribution over the family
+fmarginal.domain = fam;
+fmarginal.T = 1;
+fmarginal.mu = [];
+fmarginal.Sigma = [];
+if ~iscell(data)
+  cases = num2cell(data);
+else
+  cases = data;
+end
+for m=1:ncases
+  CPD = update_ess(CPD, fmarginal, cases(:,m), ns, cnodes);
+end
+CPD = maximize_params(CPD);
+self = fam(end);
+ps = fam(1:end-1);
+L = log_prob_node(CPD, cases(self,:), cases(ps,:));
+score = L - 0.5*CPD.nparams*log(ncases);
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/Old/CPD_to_dpots.m b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/Old/CPD_to_dpots.m
new file mode 100644
index 00000000..47daac88
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/Old/CPD_to_dpots.m
@@ -0,0 +1,16 @@
+function pots = CPD_to_dpots(CPD, domain, ns, cnodes, evidence)
+% CPD_TO_DPOTS Convert the CPD to several discrete potentials, for different instantiations (generic)
+% pots = CPD_to_dpots(CPD, domain, ns, cnodes, evidence)
+%
+% domain(:,i) is the domain of the i'th instantiation of CPD.
+% node_sizes(i) is the size of node i.
+% cnodes = all the cts nodes
+% evidence{i} is the evidence on the i'th node.
+%
+% This just calls CPD_to_dpot for each domain.
+    
+nCPDs = size(domain,2);
+pots = cell(1,nCPDs);
+for i=1:nCPDs
+  pots{i} = CPD_to_dpot(CPD, domain(:,i), ns, cnodes, evidence);
+end
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/Old/CVS/Entries b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/Old/CVS/Entries
new file mode 100644
index 00000000..505b09aa
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/Old/CVS/Entries
@@ -0,0 +1,3 @@
+/BIC_score_CPD.m/1.1.1.1/Wed May 29 15:59:52 2002//
+/CPD_to_dpots.m/1.1.1.1/Wed May 29 15:59:52 2002//
+D
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/Old/CVS/Repository b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/Old/CVS/Repository
new file mode 100644
index 00000000..96b94fc8
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/Old/CVS/Repository
@@ -0,0 +1 @@
+FullBNT/BNT/CPDs/@generic_CPD/Old
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/Old/CVS/Root b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/Old/CVS/Root
new file mode 100644
index 00000000..f3bd14a6
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/Old/CVS/Root
@@ -0,0 +1 @@
+:ext:nsaunier@bnt.cvs.sourceforge.net:/cvsroot/bnt
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/README b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/README
new file mode 100644
index 00000000..7a9b164b
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/README
@@ -0,0 +1,2 @@
+A generic CPD implements general purpose functions like 'display',
+that subtypes can inherit.
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/adjustable_CPD.m b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/adjustable_CPD.m
new file mode 100644
index 00000000..78feea55
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/adjustable_CPD.m
@@ -0,0 +1,5 @@
+function p = adjustable_CPD(CPD)
+% ADJUSTABLE_CPD Does this CPD have any adjustable params? (generic)
+% p = adjustable_CPD(CPD)
+   
+p = ~CPD.clamped;
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/display.m b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/display.m
new file mode 100644
index 00000000..001ab2c9
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/display.m
@@ -0,0 +1,3 @@
+function display(CPD)
+
+disp(struct(CPD));
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/generic_CPD.m b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/generic_CPD.m
new file mode 100644
index 00000000..66a85e6a
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/generic_CPD.m
@@ -0,0 +1,8 @@
+function CPD = generic_CPD(clamped)
+% GENERIC_CPD Virtual constructor for generic CPD
+% CPD = discrete_CPD(clamped)
+
+if nargin < 1, clamped = 0; end
+
+CPD.clamped = clamped;
+CPD = class(CPD, 'generic_CPD');
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/learn_params.m b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/learn_params.m
new file mode 100644
index 00000000..c36eb004
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/learn_params.m
@@ -0,0 +1,32 @@
+function CPD = learn_params(CPD, fam, data, ns, cnodes)
+% LEARN_PARAMS Compute the maximum likelihood estimate of the params of a generic CPD given complete data
+% CPD = learn_params(CPD, fam, data, ns, cnodes)
+%
+% data(i,m) is the value of node i in case m (can be cell array).
+% We assume this node has a maximize_params method.
+
+%error('no longer supported') % KPM 1 Feb 03
+
+if 1
+ncases = size(data, 2);
+CPD = reset_ess(CPD);
+% make a fully observed joint distribution over the family
+fmarginal.domain = fam;
+fmarginal.T = 1;
+fmarginal.mu = [];
+fmarginal.Sigma = [];
+if ~iscell(data)
+  cases = num2cell(data);
+else
+  cases = data;
+end
+hidden_bitv = zeros(1, max(fam));
+for m=1:ncases
+  % specify (as a bit vector) which elements in the family domain are hidden
+  hidden_bitv = zeros(1, max(fmarginal.domain));
+  ev = cases(:,m);
+  hidden_bitv(find(isempty(evidence)))=1;
+  CPD = update_ess(CPD, fmarginal, ev, ns, cnodes, hidden_bitv);
+end
+CPD = maximize_params(CPD);
+end
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/log_prior.m b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/log_prior.m
new file mode 100644
index 00000000..a73dcde0
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/log_prior.m
@@ -0,0 +1,5 @@
+function L = log_prior(CPD)
+% LOG_PRIOR Return log P(theta) for a generic CPD  - we return 0
+% L = log_prior(CPD)
+
+L = 0;
diff --git a/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/set_clamped.m b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/set_clamped.m
new file mode 100644
index 00000000..5ad68037
--- /dev/null
+++ b/sourcecodes/bnt-master/BNT/CPDs/@generic_CPD/set_clamped.m
@@ -0,0 +1,3 @@
+function CPD = set_clamped(CPD, bit)
+
+CPD.clamped = bit;