source: trunk/yat/classifier/KernelLookup.h @ 1268

Last change on this file since 1268 was 1206, checked in by Peter, 13 years ago

fixes #345

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1#ifndef _theplu_yat_classifier_kernel_lookup_
2#define _theplu_yat_classifier_kernel_lookup_
3
4// $Id$
5
6/*
7  Copyright (C) 2005 Jari Häkkinen, Peter Johansson
8  Copyright (C) 2006 Jari Häkkinen, Markus Ringnér, Peter Johansson
9  Copyright (C) 2007, 2008 Peter Johansson
10
11  This file is part of the yat library, http://trac.thep.lu.se/yat
12
13  The yat library is free software; you can redistribute it and/or
14  modify it under the terms of the GNU General Public License as
15  published by the Free Software Foundation; either version 2 of the
16  License, or (at your option) any later version.
17
18  The yat library is distributed in the hope that it will be useful,
19  but WITHOUT ANY WARRANTY; without even the implied warranty of
20  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
21  General Public License for more details.
22
23  You should have received a copy of the GNU General Public License
24  along with this program; if not, write to the Free Software
25  Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA
26  02111-1307, USA.
27*/
28
29#include "Kernel.h"
30#include "yat/utility/Container2DIterator.h"
31#include "yat/utility/Index.h"
32#include "yat/utility/iterator_traits.h"
33#include "yat/utility/SmartPtr.h"
34#include "yat/utility/StrideIterator.h"
35
36namespace theplu {
37namespace yat {
38namespace classifier {
39
40  class KernelFunction;
41  class MatrixLookup;
42  class MatrixLookupWeighted;
43
44  ///
45  /// @brief Lookup into Kernel
46  ///
47  /// This is the KernelLookup class to be used together with kernel
48  /// methods such as Support Vector Machines (SVM). The class does
49  /// not contain any data or values, but rather is a lookup into a
50  /// Kernel object. Each row and each column corresponds to a row and
51  /// a column in the Kernel, respectively. This design allows for fast
52  /// creation of sub-kernels, which is a common operation in most
53  /// traning/validation procedures.
54  ///
55  /// A KernelLookup can be created directly from a Kernel or from
56  /// another KernelLookup. In the latter case, the resulting
57  /// KernelLookup is looking directly into the underlying Kernel to
58  /// avoid multiple lookups.
59  ///
60  /// There is a possibility to set the KernelLookup as owner of the
61  /// underlying kernel. This implies that underlying kernel is deleted
62  /// in destructor of MatrixLookup, but only if there is no other
63  /// owner of the underlying kernel. A reference counter is used to
64  /// keep track of number of owners. Ownership is copied in copy
65  /// constructors and assignments.
66  ///
67  class KernelLookup
68  {
69
70  public:
71    /// 'Read Only' iterator
72    typedef utility::StrideIterator<
73    utility::Container2DIterator<const KernelLookup, const double, void, 
74                                 const double> >
75    const_iterator;
76
77    /**
78       'Read only' iterator intended to iterate over a column
79     */
80    typedef const_iterator const_column_iterator;
81
82    /**
83       'Read only' iterator intended to iterate over a row
84     */
85    typedef const_iterator const_row_iterator;
86
87    ///
88    /// @brief Constructor a Lookup into a Kernel
89    ///
90    /// Constructs a KernelLookup corresponding to the Kernel @a
91    /// kernel. By default @a owner is set to false, which means
92    /// KernelLookup does not own the underlying Kernel.
93    ///
94    /// @note If underlying Kernel goes out of scope or is deleted, the
95    /// KernelLookup becomes invalid and the result of further use is
96    /// undefined.
97    ///
98    /// @note Do not construct two KernelLookups from the same @a
99    /// kernel with @a owner set to true because that will cause
100    /// multiple deletion of @a kernel.
101    ///
102    KernelLookup(const Kernel& kernel, const bool owner=false);
103
104    ///
105    /// @brief Constructing a Lookup into a subKernel
106    ///
107    /// Creating a Lookup into parts of the Kernel. In the created
108    /// Lookup the element in the \f$ i \f$ th row in the \f$ j \f$ th
109    /// column is identical to the element in row row[i] and columns
110    /// column[j] in the underlying @a kernel. If @a owner is set to
111    /// true yhe underlying @a kernel is destroyed in the destructor.
112    ///
113    /// @note If @a kernel goes out of scope or is deleted, the
114    /// returned pointer becomes invalid and the result of further use is
115    /// undefined.
116    ///
117    /// @note For training usage row index shall always be equal to
118    /// column index.
119    ///
120    KernelLookup(const Kernel& kernel, const utility::Index& row, 
121                 const utility::Index& column, const bool owner=false);
122
123    ///
124    /// @brief Copy constructor.
125    ///
126    /// A Lookup is created looking into the
127    /// same underlying Kernel as @a kl is looking into.
128    ///
129    /// If \a kl is owner of underlying data, constructed
130    /// KernelLookup will also be set as owner of underlying data.
131    ///
132    KernelLookup(const KernelLookup& kl);
133
134
135    ///
136    /// @brief Contructing a sub-KernelLookup.
137    ///
138    /// Contructor building a sub-KernelLookup from a KernelLookup
139    /// defined by row index vector and column index vector. In the
140    /// created Lookup the element in the \f$ i \f$ th row in the
141    /// \f$ j \f$ th column is identical to the element in row row[i] and
142    /// columns column[j] in the copied @a kl. The resulting
143    /// KernelLookup is independent of the old KernelLookup, but is
144    /// undefined in case underlying Kernel is destroyed.
145    ///
146    /// If \a kl is owner of underlying data, constructed
147    /// KernelLookup will also be set as owner of underlying data.
148    ///
149    /// @note For training usage row index shall always be equal to
150    /// column index.
151    ///
152    KernelLookup(const KernelLookup& kl, const utility::Index& row, 
153                 const utility::Index& column);
154
155    ///
156    /// Constructor taking the column (default) or row index as
157    /// input. If @a row is false the created KernelLookup will have
158    /// equally many rows as @a kernel.
159    ///
160    /// If \a kl is owner of underlying data, constructed
161    /// KernelLookup will also be set as owner of underlying data.
162    ///
163    /// @note If underlying kernel goes out of scope or is deleted, the
164    /// KernelLookup becomes invalid and the result of further use is
165    /// undefined.
166    ///
167    KernelLookup(const KernelLookup& kl, const utility::Index&, 
168                 const bool row=false);
169
170    ///
171    /// @brief Destructor
172    ///
173    /// Deletes underlying Kernel if KernelLookup owns it and there is
174    /// no other owner.
175    ///
176    virtual ~KernelLookup(void);
177
178    /**
179       Iterator iterates along a row. When end of row is reached it
180       jumps to beginning of next row.
181
182       \return const_iterator pointing to upper-left element.
183     */
184    const_iterator begin(void) const;
185
186    /**
187       Iterator iterates along a column.
188
189       \return iterator pointing to first element of column \a i.
190     */
191    const_column_iterator begin_column(size_t) const;
192
193    /**
194       Iterator iterates along a column.
195
196       \return const_iterator pointing to first element of column \a i.
197     */
198    const_row_iterator begin_row(size_t) const;
199
200    /**
201       \return number of columns
202    */
203    size_t columns(void) const;
204
205    ///
206    /// Each column in returned DataLookup corresponds to the column
207    /// in KernelLookup.
208    ///
209    /// \return data that KernelLookup is built upon.
210    ///
211    /// \throw if KernelLookup is weighted
212    ///
213    MatrixLookup data(void) const;
214
215    ///
216    /// Each column in returned DataLookup corresponds to the column
217    /// in KernelLookup.
218    ///
219    /// \return data that KernelLookup is built upon.
220    ///
221    /// \throw if KernelLookup is unweighted
222    ///
223    MatrixLookupWeighted data_weighted(void) const;
224
225    /**
226       Function to calculate a new Kernel element using the underlying
227       KernelFunction. The value is calculated between @a vec and the
228       data vector of the \a i th sample, in other words, the
229       sample corresponding to the \a i th row.
230    */
231    double element(const DataLookup1D& vec, size_t i) const;
232
233    /**
234       Function to calculate a new Kernel element using the underlying
235       KernelFunction. The value is calulated between @a vec and the
236       data vector of the \f$ i \f$ th sample, in other words, the
237       sample corresponding to the \f$ i \f$ th row or \f$ i \f$ th
238       column. In case KernelLookup is a sub-Kernel and not symmetric,
239       the kernel value is calculated between @a vec and the data
240       vector corresponding to \f$ i \f$ th row.
241    */
242    double element(const DataLookupWeighted1D& vec, size_t i) const;
243
244    /**
245       \return const_iterator pointing to end of matrix
246     */
247    const_iterator end(void) const;
248
249    /**
250       \return const_iterator pointing to end of column \a i
251     */
252    const_column_iterator end_column(size_t) const;
253
254    /**
255       \return const_iterator pointing to end of row \a i
256     */
257    const_row_iterator end_row(size_t) const;
258
259    /**
260       \return number of rows
261    */
262    size_t rows(void) const;
263
264    /**
265       Each element in returned KernelLookup is calculated using only
266       selected features (defined by @a index). Each element
267       corresponds to the same pair of samples as in the original
268       KernelLookup.
269    */
270    KernelLookup selected(const utility::Index& index) const;
271   
272    /**
273       This function is useful when predicting on an independent data
274       set using a kernel-based classifier. In returned KernelLookup
275       column \f$ i \f$ corresponds to column \f$ i \f$ in @a
276       data. Row \f$ i \f$ in returned KernelLookup corresponds to
277       same sample as row \f$ i \f$ in @a this. In other words, this
278       function returns a KernelLookup containing the kernel elements
279       between the passed @a data and the internal underlying data @a
280       this was built from.
281    */
282    KernelLookup test_kernel(const MatrixLookup& data) const;
283
284    /**
285       This function is useful when predicting on an independent data
286       set using a kernel-based classifier. In returned KernelLookup
287       column \f$ i \f$ corresponds to column \f$ i \f$ in @a
288       data. Row \f$ i \f$ in returned KernelLookup corresponds to
289       same sample as row \f$ i \f$ in @a this. In other words, this
290       function returns a KernelLookup containing the kernel elements
291       between the passed @a data and the internal underlying data @a
292       this was built from.
293    */
294    KernelLookup test_kernel(const MatrixLookupWeighted& data) const;
295
296    /**
297       \return true if underlying Kernel is weighted
298    */
299    bool weighted(void) const;
300
301    /**
302       \return element at position (\a row, \a column) in the Kernel
303       matrix
304    */
305    double operator()(size_t row, size_t column) const;
306
307  private:
308    const KernelLookup& operator=(const KernelLookup&);
309    bool validate(const utility::Index&) const;
310
311    utility::Index column_index_;
312    utility::SmartPtr<const Kernel> kernel_;
313    utility::Index row_index_;
314   
315  }; // class KernelLookup
316
317}}} // of namespace classifier, yat, and theplu
318
319#endif
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