vigra - vigra/sampling.hxx Source File

[ VIGRA Homepage | Function Index | Class Index | Namespaces | File List | Main Page ]

sampling.hxx |

1 /************************************************************************/
2 /* */
3 /* Copyright 2008-2009 by Ullrich Koethe and Rahul Nair */
4 /* */
5 /* This file is part of the VIGRA computer vision library. */
6 /* The VIGRA Website is */
7 /* http://hci.iwr.uni-heidelberg.de/vigra/ */
8 /* Please direct questions, bug reports, and contributions to */
9 /* ullrich.koethe@iwr.uni-heidelberg.de or */
10 /* vigra@informatik.uni-hamburg.de */
11 /* */
12 /* Permission is hereby granted, free of charge, to any person */
13 /* obtaining a copy of this software and associated documentation */
14 /* files (the "Software"), to deal in the Software without */
15 /* restriction, including without limitation the rights to use, */
16 /* copy, modify, merge, publish, distribute, sublicense, and/or */
17 /* sell copies of the Software, and to permit persons to whom the */
18 /* Software is furnished to do so, subject to the following */
19 /* conditions: */
20 /* */
21 /* The above copyright notice and this permission notice shall be */
22 /* included in all copies or substantial portions of the */
23 /* Software. */
24 /* */
25 /* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND */
26 /* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES */
27 /* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND */
28 /* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT */
29 /* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, */
30 /* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING */
31 /* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR */
32 /* OTHER DEALINGS IN THE SOFTWARE. */
33 /* */
34 /************************************************************************/
35
36 #ifndef VIGRA_SAMPLING_HXX
37 #define VIGRA_SAMPLING_HXX
38
39 #include "array_vector.hxx"
40 #include "random.hxx"
41 #include <map>
42 #include <memory>
43 #include <cmath>
44
45 namespace vigra
46 {
47
48 /** \addtogroup MachineLearning Machine Learning
49 **/
50 //@{
51
52
53 /**\brief Options object for the Sampler class.
54
55 <b>usage:</b>
56
57 \code
58 SamplerOptions opt = SamplerOptions()
59 .withReplacement()
60 .sampleProportion(0.5);
61 \endcode
62
63 Note that the return value of all methods is <tt>*this</tt> which makes
64 concatenating of options as above possible.
65 */
66 class SamplerOptions
67 {
68 public:
69
70 double sample_proportion;
71 unsigned int sample_size;
72 bool sample_with_replacement;
73 bool stratified_sampling;
74
75 SamplerOptions()
76 : sample_proportion(1.0),
77 sample_size(0),
78 sample_with_replacement(true),
79 stratified_sampling(false)
80 {}
81
82 /**\brief Sample from training population with replacement.
83 *
84 * <br> Default: true
85 */
86 SamplerOptions& withReplacement(bool in = true)
87 {
88 sample_with_replacement = in;
89 return *this;
90 }
91
92 /**\brief Sample from training population without replacement.
93 *
94 * <br> Default (if you don't call this function): false
95 */
96 SamplerOptions& withoutReplacement(bool in = true)
97 {
98 sample_with_replacement = !in;
99 return *this;
100 }
101
102 /**\brief Draw the given number of samples.
103 * If stratifiedSampling is true, the \a size is equally distributed
104 * across all strata (e.g. <tt>size / strataCount</tt> samples are taken
105 * from each stratum, subject to rounding).
106 *
107 * <br> Default: 0 (i.e. determine the count by means of sampleProportion())
108 */
109 SamplerOptions& sampleSize(unsigned int size)
110 {
111 sample_size = size;
112 return *this;
113 }
114
115
116 /**\brief Determine the number of samples to draw as a proportion of the total
117 * number. That is, we draw <tt>count = totalCount * proportion</tt> samples.
118 * This option is overridden when an absolute count is specified by sampleSize().
119 *
120 * If stratifiedSampling is true, the count is equally distributed
121 * across all strata (e.g. <tt>totalCount * proportion / strataCount</tt> samples are taken
122 * from each stratum).
123 *
124 * <br> Default: 1.0
125 */
126 SamplerOptions& sampleProportion(double proportion)
127 {
128 vigra_precondition(proportion >= 0.0,
129 "SamplerOptions::sampleProportion(): argument must not be negative.");
130 sample_proportion = proportion;
131 return *this;
132 }
133
134 /**\brief Draw equally many samples from each "stratum".
135 * A stratum is a group of like entities, e.g. pixels belonging
136 * to the same object class. This is useful to create balanced samples
137 * when the class probabilities are very unbalanced (e.g.
138 * when there are many background and few foreground pixels).
139 * Stratified sampling thus avoids that a trained classifier is biased
140 * towards the majority class.
141 *
142 * <br> Default (if you don't call this function): false
143 */
144 SamplerOptions& stratified(bool in = true)
145 {
146 stratified_sampling = in;
147 return *this;
148 }
149 };
150
151 /************************************************************/
152 /* */
153 /* Sampler */
154 /* */
155 /************************************************************/
156
157 /** \brief Create random samples from a sequence of indices.
158
159 Selecting data items at random is a basic task of machine learning,
160 for example in boostrapping, RandomForest training, and cross validation.
161 This class implements various ways to select random samples via their indices.
162 Indices are assumed to be consecutive in
163 the range <tt>0 &lt;= index &lt; total_sample_count</tt>.
164
165 The class always contains a current sample which can be accessed by
166 the index operator or by the function sampledIndices(). The indices
167 that are not in the current sample (out-of-bag indices) can be accessed
168 via the function oobIndices().
169
170 The sampling method (with/without replacement, stratified or not) and the
171 number of samples to draw are determined by the option object
172 SamplerOptions.
173
174 <b>Usage:</b>
175
176 <b>\#include</b> <vigra/sampling.hxx><br>
177 Namespace: vigra
178
179 Create a Sampler with default options, i.e. sample as many indices as there
180 are data elements, with replacement. On average, the sample will contain
181 <tt>0.63*totalCount</tt> distinct indices.
182
183 \code
184 int totalCount = 10000; // total number of data elements
185 int numberOfSamples = 20; // repeat experiment 20 times
186 Sampler<> sampler(totalCount);
187 for(int k=0; k<numberOfSamples; ++k)
188 {
189 // process current sample
190 for(int i=0; i<sampler.sampleSize(); ++i)
191 {
192 int currentIndex = sampler[i];
193 processData(data[currentIndex]);
194 }
195 // create next sample
196 sampler.sample();
197 }
198 \endcode
199
200 Create a Sampler for stratified sampling, without replacement.
201
202 \code
203 // prepare the strata (i.e. specify which stratum each element belongs to)
204 int stratumSize1 = 2000, stratumSize2 = 8000,
205 totalCount = stratumSize1 + stratumSize2;
206 ArrayVerctor<int> strata(totalCount);
207 for(int i=0; i<stratumSize1; ++i)
208 strata[i] = 1;
209 for(int i=stratumSize1; i<stratumSize2; ++i)
210 strata[i] = 2;
211
212 int sampleSize = 200; // i.e. sample 100 elements from each of the two strata
213 int numberOfSamples = 20; // repeat experiment 20 times
214 Sampler<> stratifiedSampler(strata.begin(), strata.end(),
215 SamplerOptions().withoutReplacement().stratified().sampleSize(sampleSize));
216 // create first sample
217 sampler.sample();
218
219 for(int k=0; k<numberOfSamples; ++k)
220 {
221 // process current sample
222 for(int i=0; i<sampler.sampleSize(); ++i)
223 {
224 int currentIndex = sampler[i];
225 processData(data[currentIndex]);
226 }
227 // create next sample
228 sampler.sample();
229 }
230 \endcode
231 */
232 template<class Random = MersenneTwister >
233 class Sampler
234 {
235 public:
236 /** Internal type of the indices.
237 Currently, 64-bit indices are not supported because this
238 requires extension of the random number generator classes.
239 */
240 typedef Int32 IndexType;
241
242 typedef ArrayVector<IndexType> IndexArrayType;
243
244 /** Type of the array view object that is returned by
245 sampledIndices() and oobIndices().
246 */
247 typedef ArrayVectorView <IndexType> IndexArrayViewType;
248
249 private:
250 typedef std::map<IndexType, IndexArrayType> StrataIndicesType;
251 typedef std::map<IndexType, int> StrataSizesType;
252 typedef ArrayVector<bool> IsUsedArrayType;
253 typedef ArrayVectorView<bool> IsUsedArrayViewType;
254
255 static const int oobInvalid = -1;
256
257 int total_count_, sample_size_;
258 mutable int current_oob_count_;
259 StrataIndicesType strata_indices_;
260 StrataSizesType strata_sample_size_;
261 IndexArrayType current_sample_;
262 mutable IndexArrayType current_oob_sample_;
263 IsUsedArrayType is_used_;
264 Random default_random_;
265 Random const & random_;
266 SamplerOptions options_;
267
268 void initStrataCount()
269 {
270 // compute how many samples to take from each stratum
271 // (may be unequal if sample_size_ is not a multiple of strataCount())
272 int strata_sample_size = (int)std::ceil(double(sample_size_) / strataCount());
273 int strata_total_count = strata_sample_size * strataCount();
274
275 for(StrataIndicesType::iterator i = strata_indices_.begin();
276 i != strata_indices_.end(); ++i)
277 {
278 if(strata_total_count > sample_size_)
279 {
280 strata_sample_size_[i->first] = strata_sample_size - 1;
281 --strata_total_count;
282 }
283 else
284 {
285 strata_sample_size_[i->first] = strata_sample_size;
286 }
287 }
288 }
289
290 public:
291
292 /** Create a sampler for \a totalCount data objects.
293
294 In each invocation of <tt>sample()</tt> below, it will sample
295 indices according to the options passed. If no options are given,
296 <tt>totalCount</tt> indices will be drawn with replacement.
297 */
298 Sampler(UInt32 totalCount, SamplerOptions const & opt = SamplerOptions(),
299 Random const * rnd = 0)
300 : total_count_(totalCount),
301 sample_size_(opt.sample_size == 0
302 ? (int)(std::ceil(total_count_ * opt.sample_proportion))
303 : opt.sample_size),
304 current_oob_count_(oobInvalid),
305 current_sample_(sample_size_),
306 current_oob_sample_(total_count_),
307 is_used_(total_count_),
308 default_random_(RandomSeed),
309 random_(rnd ? *rnd : default_random_),
310 options_(opt)
311 {
312 vigra_precondition(opt.sample_with_replacement || sample_size_ <= total_count_,
313 "Sampler(): Cannot draw without replacement when data size is smaller than sample count.");
314
315 vigra_precondition(!opt.stratified_sampling,
316 "Sampler(): Stratified sampling requested, but no strata given.");
317
318 // initialize a single stratum containing all data
319 strata_indices_[0].resize(total_count_);
320 for(int i=0; i<total_count_; ++i)
321 strata_indices_[0][i] = i;
322
323 initStrataCount();
324 //this is screwing up the random forest tests.
325 //sample();
326 }
327
328 /** Create a sampler for stratified sampling.
329
330 <tt>strataBegin</tt> and <tt>strataEnd</tt> must refer to a sequence
331 which specifies for each sample the stratum it belongs to. The
332 total number of data objects will be set to <tt>strataEnd - strataBegin</tt>.
333 Equally many samples (subject to rounding) will be drawn from each stratum,
334 unless the option object explicitly requests unstratified sampling,
335 in which case the strata are ignored.
336 */
337 template <class Iterator>
338 Sampler(Iterator strataBegin, Iterator strataEnd, SamplerOptions const & opt = SamplerOptions(),
339 Random const * rnd = 0)
340 : total_count_(strataEnd - strataBegin),
341 sample_size_(opt.sample_size == 0
342 ? (int)(std::ceil(total_count_ * opt.sample_proportion))
343 : opt.sample_size),
344 current_oob_count_(oobInvalid),
345 current_sample_(sample_size_),
346 current_oob_sample_(total_count_),
347 is_used_(total_count_),
348 default_random_(RandomSeed),
349 random_(rnd ? *rnd : default_random_),
350 options_(opt)
351 {
352 vigra_precondition(opt.sample_with_replacement || sample_size_ <= total_count_,
353 "Sampler(): Cannot draw without replacement when data size is smaller than sample count.");
354
355 // copy the strata indices
356 if(opt.stratified_sampling)
357 {
358 for(int i = 0; strataBegin != strataEnd; ++i, ++strataBegin)
359 {
360 strata_indices_[*strataBegin].push_back(i);
361 }
362 }
363 else
364 {
365 strata_indices_[0].resize(total_count_);
366 for(int i=0; i<total_count_; ++i)
367 strata_indices_[0][i] = i;
368 }
369
370 vigra_precondition(sample_size_ >= (int)strata_indices_.size(),
371 "Sampler(): Requested sample count must be at least as large as the number of strata.");
372
373 initStrataCount();
374 //this is screwing up the random forest tests.
375 //sample();
376 }
377
378 /** Return the k-th index in the current sample.
379 */
380 IndexType operator[](int k) const
381 {
382 return current_sample_[k];
383 }
384
385 /** Create a new sample.
386 */
387 void sample();
388
389 /** The total number of data elements.
390 */
391 int totalCount() const
392 {
393 return total_count_;
394 }
395
396 /** The number of data elements that have been sampled.
397 */
398 int sampleSize() const
399 {
400 return sample_size_;
401 }
402
403 /** Same as sampleSize().
404 */
405 int size() const
406 {
407 return sample_size_;
408 }
409
410 /** The number of strata to be used.
411 Will be 1 if no strata are given. Will be ignored when
412 stratifiedSampling() is false.
413 */
414 int strataCount() const
415 {
416 return strata_indices_.size();
417 }
418
419 /** Whether to use stratified sampling.
420 (If this is false, strata will be ignored even if present.)
421 */
422 bool stratifiedSampling() const
423 {
424 return options_.stratified_sampling;
425 }
426
427 /** Whether sampling should be performed with replacement.
428 */
429 bool withReplacement() const
430 {
431 return options_.sample_with_replacement;
432 }
433
434 /** Return an array view containing the indices in the current sample.
435 */
436 IndexArrayViewType sampledIndices() const
437 {
438 return current_sample_;
439 }
440
441 /** Return an array view containing the out-of-bag indices.
442 (i.e. the indices that are not in the current sample)
443 */
444 IndexArrayViewType oobIndices() const
445 {
446 if(current_oob_count_ == oobInvalid)
447 {
448 current_oob_count_ = 0;
449 for(int i = 0; i<total_count_; ++i)
450 {
451 if(!is_used_[i])
452 {
453 current_oob_sample_[current_oob_count_] = i;
454 ++current_oob_count_;
455 }
456 }
457 }
458 return current_oob_sample_.subarray(0, current_oob_count_);
459 }
460 IsUsedArrayType const & is_used() const
461 {
462 return is_used_;
463 }
464 };
465
466
467 template<class Random>
468 void Sampler<Random>::sample()
469 {
470 current_oob_count_ = oobInvalid;
471 is_used_.init(false);
472
473 if(options_.sample_with_replacement)
474 {
475 //Go thru all strata
476 int j = 0;
477 StrataIndicesType::iterator iter;
478 for(iter = strata_indices_.begin(); iter != strata_indices_.end(); ++iter)
479 {
480 // do sampling with replacement in each strata and copy data.
481 int stratum_size = iter->second.size();
482 for(int i = 0; i < (int)strata_sample_size_[iter->first]; ++i, ++j)
483 {
484 current_sample_[j] = iter->second[random_.uniformInt(stratum_size)];
485 is_used_[current_sample_[j]] = true;
486 }
487 }
488 }
489 else
490 {
491 //Go thru all strata
492 int j = 0;
493 StrataIndicesType::iterator iter;
494 for(iter = strata_indices_.begin(); iter != strata_indices_.end(); ++iter)
495 {
496 // do sampling without replacement in each strata and copy data.
497 int stratum_size = iter->second.size();
498 for(int i = 0; i < (int)strata_sample_size_[iter->first]; ++i, ++j)
499 {
500 std::swap(iter->second[i], iter->second[i+ random_.uniformInt(stratum_size - i)]);
501 current_sample_[j] = iter->second[i];
502 is_used_[current_sample_[j]] = true;
503 }
504 }
505 }
506 }
507
508 template<class Random =RandomTT800 >
509 class PoissonSampler
510 {
511 public:
512 Random randfloat;
513 typedef Int32 IndexType;
514 typedef vigra::ArrayVector <IndexType> IndexArrayType;
515 IndexArrayType used_indices_;
516 double lambda;
517 int minIndex;
518 int maxIndex;
519
520 PoissonSampler(double lambda,IndexType minIndex,IndexType maxIndex)
521 : lambda(lambda),
522 minIndex(minIndex),
523 maxIndex(maxIndex)
524 {}
525
526 void sample( )
527 {
528 used_indices_.clear();
529 IndexType i;
530 for(i=minIndex;i<maxIndex;++i)
531 {
532 //from http://en.wikipedia.org/wiki/Poisson_distribution
533 int k=0;
534 double p=1;
535 double L=exp(-lambda);
536 do
537 {
538 ++k;
539 p*=randfloat.uniform53();
540
541 }while(p>L);
542 --k;
543 //Insert i this many time
544 while(k>0)
545 {
546 used_indices_.push_back(i);
547 --k;
548 }
549 }
550 }
551
552 IndexType const & operator[](int in) const
553 {
554 return used_indices_[in];
555 }
556
557 int numOfSamples() const
558 {
559 return used_indices_.size();
560 }
561 };
562
563 //@}
564
565 } // namespace vigra
566
567 #endif /*VIGRA_SAMPLING_HXX*/

© Ullrich Köthe (ullrich.koethe@iwr.uni-heidelberg.de) Heidelberg Collaboratory for Image Processing, University of Heidelberg, Germany | html generated using doxygen and Python vigra 1.10.0 (Mon Nov 18 2013)