New git HEAD version

[libdai.git] / include / dai / evidence.h

diff --git a/include/dai/evidence.h b/include/dai/evidence.h
index 1738732..27789ed 100644 (file)
--- a/include/dai/evidence.h
+++ b/include/dai/evidence.h
@@ -1,27 +1,13 @@
-/*  Copyright (C) 2009  Charles Vaske  [cvaske at soe dot ucsc dot edu]
-    University of California Santa Cruz
-
-    This file is part of libDAI.
-
-    libDAI 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.
-
-    libDAI 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 libDAI; if not, write to the Free Software
-    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301  USA
-*/
+/*  This file is part of libDAI - http://www.libdai.org/
+ *
+ *  Copyright (c) 2006-2011, The libDAI authors. All rights reserved.
+ *
+ *  Use of this source code is governed by a BSD-style license that can be found in the LICENSE file.
+ */
 
 
 /// \file
-/// \brief Defines classes Evidence and Observation
-/// \todo Describe tabular data file format
+/// \brief Defines class Evidence, which stores multiple observations of joint states of variables
 
 
 #ifndef __defined_libdai_evidence_h
@@ -35,74 +21,59 @@
 namespace dai {
 
 
-/// Stores observed values of a subset of variables
-class Observation {
-    private:
-        /// Used to store the state of some variables
-        std::map<Var, size_t> _obs;
-
-    public:
-        /// Default constructor
-        Observation() : _obs() {}
-
-        /// Get all observations
-        const std::map<Var, size_t>& observations() const { return _obs; }
-        
-        /// Add an observation
-        void addObservation( Var node, size_t setting );
-        
-        /// Clamp variables in the graphical model to their observed values
-        void applyEvidence( InfAlg& alg ) const;
-};
-
-
-/// Stores multiple joint observations of sets of variables.
-/** The Evidence class stores multiple samples, where each sample is the joint
- *  observation of the states of some variables.
+/// Stores a data set consisting of multiple samples, where each sample is the observed joint state of some variables.
+/** \note Each sample can describe the joint state of a different set of variables,
+ *  in order to be able to deal with missing data.
+ *
+ *  \author Charles Vaske
  */
 class Evidence {
+    public:
+        /// Stores joint state of a set of variables
+        typedef std::map<Var, size_t> Observation;
+
     private:
-        /// Each sample is the joint observation of the states of some variables
+        /// Each sample is an observed joint state of some variables
         std::vector<Observation> _samples;
 
     public:
         /// Default constructor
         Evidence() : _samples() {}
-      
-        /// Constructor with existing samples
-         Evidence(std::vector<Observation>& samples) : _samples(samples) {}
 
-/// Read in tabular data from a stream. 
-        /** Each line contains one sample, and the first line is a header line with names.
-         */
-        void addEvidenceTabFile( std::istream& is, std::map<std::string, Var> &varMap );
+        /// Construct from \a samples
+        Evidence( std::vector<Observation> &samples ) : _samples(samples) {}
 
-    
-        /// Read in tabular data from a stream. 
-        /** Each line contains one sample, and the first line is a header line with 
-         *  variable labels which should correspond with a subset of the variables in fg.
+        /// Read in tabular data from a stream and add the read samples to \c *this.
+        /** \param is Input stream in .tab file format, describing joint observations of variables in \a fg
+         *  \param fg Factor graph describing the corresponding variables
+         *  \see \ref fileformats-evidence
+         *  \throw INVALID_EVIDENCE_FILE if the input stream is not valid
          */
         void addEvidenceTabFile( std::istream& is, FactorGraph& fg );
-      
+
         /// Returns number of stored samples
         size_t nrSamples() const { return _samples.size(); }
 
-        /// @name Iterator interface
-        //@{
-        /// Iterator over the elements
+    /// \name Iterator interface
+    //@{
+        /// Iterator over the samples
         typedef std::vector<Observation>::iterator iterator;
-        /// Constant iterator over the elements
+        /// Constant iterator over the samples
         typedef std::vector<Observation>::const_iterator const_iterator;
 
-        /// Returns iterator that points to the first element
+        /// Returns iterator that points to the first sample
         iterator begin() { return _samples.begin(); }
-        /// Returns constant iterator that points to the first element
+        /// Returns constant iterator that points to the first sample
         const_iterator begin() const { return _samples.begin(); }
-        /// Returns iterator that points beyond the last element
+        /// Returns iterator that points beyond the last sample
         iterator end() { return _samples.end(); }
-        /// Returns constant iterator that points beyond the last element
+        /// Returns constant iterator that points beyond the last sample
         const_iterator end() const { return _samples.end(); }
-        //@}
+    //@}
+
+    private:
+        /// Read in tabular data from a stream and add the read samples to \c *this.
+        void addEvidenceTabFile( std::istream& is, std::map<std::string, Var> &varMap );
 };