-/*
- Copyright 2009 Charles Vaske <cvaske@soe.ucsc.edu>
- University of California Santa Cruz
-
- 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 3 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, see <http://www.gnu.org/licenses/>.
-*/
+/* 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 class Evidence, which stores multiple observations of joint states of variables
+
#ifndef __defined_libdai_evidence_h
#define __defined_libdai_evidence_h
-#include <istream>
+#include <istream>
#include <dai/daialg.h>
+
namespace dai {
-/// Store joint observations on a graphical model.
-class SampleData {
-private:
- std::string _name;
- std::map<Var, size_t> _obs;
-public:
- /// Construct an empty object
- SampleData() : _name(), _obs() {}
- /// Set the name of the sample
- void name(const std::string& name) { _name = name; }
- /// Get the name of the sample
- const std::string& name() const { return _name; }
- /// Read from the observation map
- const std::map<Var, size_t>& observations() const { return _obs; }
- /// Add an observation
- void addObservation(Var node, size_t setting);
- /// Add evidence by clamping variables to observed values.
- void applyEvidence(InfAlg& alg) const;
-};
-/// Store observations from a graphical model.
+/// 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 {
-private:
- std::map< std::string, SampleData > _samples;
-public:
- /// Start with empty obects, then fill with calls to addEvidenceTabFile()
- Evidence() : _samples() {}
-
- /** Read in tab-data from a stream. Each line contains one sample, and
- * the first line is a header line with names. The first column contains
- * names for each of the samples.
- */
- void addEvidenceTabFile(std::istream& is,
- std::map< std::string, Var >& varMap);
-
- /** Read in tab-data from a stream. Each line contains one sample,
- * and the first line is a header line with variable IDs. The first
- * column contains names for each of the samples.
- */
- void addEvidenceTabFile(std::istream& is, FactorGraph& fg);
-
- /// Total number of samples in this evidence file
- size_t nrSamples() const { return _samples.size(); }
-
- /// @name iterator interface
- //@{
- typedef std::map< std::string, SampleData >::iterator iterator;
- typedef std::map< std::string, SampleData >::const_iterator const_iterator;
- iterator begin() { return _samples.begin(); }
- const_iterator begin() const { return _samples.begin(); }
- iterator end() { return _samples.end(); }
- const_iterator end() const { return _samples.end(); }
- //@}
+ public:
+ /// Stores joint state of a set of variables
+ typedef std::map<Var, size_t> Observation;
+
+ private:
+ /// Each sample is an observed joint state of some variables
+ std::vector<Observation> _samples;
+
+ public:
+ /// Default constructor
+ Evidence() : _samples() {}
+ /// Construct from \a samples
+ Evidence( std::vector<Observation> &samples ) : _samples(samples) {}
+
+ /// 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 samples
+ typedef std::vector<Observation>::iterator iterator;
+ /// Constant iterator over the samples
+ typedef std::vector<Observation>::const_iterator const_iterator;
+
+ /// Returns iterator that points to the first sample
+ iterator begin() { return _samples.begin(); }
+ /// Returns constant iterator that points to the first sample
+ const_iterator begin() const { return _samples.begin(); }
+ /// Returns iterator that points beyond the last sample
+ iterator end() { return _samples.end(); }
+ /// 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 );
};
-
-}
+
+
+} // end of namespace dai
+
#endif
projects / libdai.git / blobdiff