Added EM code by Charlie Vaske (and cleaned up the style a bit)
[libdai.git] / include / dai / evidence.h
1 /* Copyright (C) 2009 Charles Vaske [cvaske at soe dot ucsc dot edu]
2 University of California Santa Cruz
3
4 This file is part of libDAI.
5
6 libDAI is free software; you can redistribute it and/or modify
7 it under the terms of the GNU General Public License as published by
8 the Free Software Foundation; either version 2 of the License, or
9 (at your option) any later version.
10
11 libDAI is distributed in the hope that it will be useful,
12 but WITHOUT ANY WARRANTY; without even the implied warranty of
13 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14 GNU General Public License for more details.
15
16 You should have received a copy of the GNU General Public License
17 along with libDAI; if not, write to the Free Software
18 Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
19 */
20
21
22 /// \file
23 /// \brief Defines classes Evidence and SampleData
24 /// \todo Improve documentation
25
26
27 #ifndef __defined_libdai_evidence_h
28 #define __defined_libdai_evidence_h
29
30
31 #include <istream>
32 #include <dai/daialg.h>
33
34
35 namespace dai {
36
37
38 /// Stores a set of observations on a graphical model.
39 class SampleData {
40 private:
41 std::string _name;
42 std::map<Var, size_t> _obs;
43 public:
44 /// Construct an empty object
45 SampleData() : _name(), _obs() {}
46 /// Set the name of the sample
47 void name(const std::string& name) { _name = name; }
48 /// Get the name of the sample
49 const std::string& name() const { return _name; }
50 /// Read from the observation map
51 const std::map<Var, size_t>& observations() const { return _obs; }
52 /// Add an observation
53 void addObservation(Var node, size_t setting);
54 /// Add evidence by clamping variables to observed values.
55 void applyEvidence(InfAlg& alg) const;
56 };
57
58
59 /// Store observations from a graphical model.
60 class Evidence {
61 private:
62 std::map<std::string, SampleData> _samples;
63 public:
64 /// Start with empty obects, then fill with calls to addEvidenceTabFile()
65 Evidence() : _samples() {}
66
67 /** Read in tab-data from a stream. Each line contains one sample, and
68 * the first line is a header line with names. The first column contains
69 * names for each of the samples.
70 */
71 void addEvidenceTabFile(std::istream& is, std::map< std::string, Var >& varMap);
72
73 /** Read in tab-data from a stream. Each line contains one sample,
74 * and the first line is a header line with variable IDs. The first
75 * column contains names for each of the samples.
76 */
77 void addEvidenceTabFile(std::istream& is, FactorGraph& fg);
78
79 /// Total number of samples in this evidence file
80 size_t nrSamples() const { return _samples.size(); }
81
82 /// @name iterator interface
83 //@{
84 typedef std::map< std::string, SampleData >::iterator iterator;
85 typedef std::map< std::string, SampleData >::const_iterator const_iterator;
86 iterator begin() { return _samples.begin(); }
87 const_iterator begin() const { return _samples.begin(); }
88 iterator end() { return _samples.end(); }
89 const_iterator end() const { return _samples.end(); }
90 //@}
91 };
92
93
94 } // end of namespace dai
95
96
97 #endif