annotate dataset.py @ 60:9165d86855ab

bugfix
author Frederic Bastien <bastienf@iro.umontreal.ca>
date Thu, 01 May 2008 16:26:34 -0400
parents 1aabd2e2bb5f
children a8b70a9117ad
rev   line source
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2 from lookup_list import LookupList
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3 Example = LookupList
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4 from misc import unique_elements_list_intersection
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5 from string import join
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6 from sys import maxint
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7 import numpy
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9 class AbstractFunction (Exception): """Derived class must override this function"""
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10 class NotImplementedYet (NotImplementedError): """Work in progress, this should eventually be implemented"""
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12 class DataSet(object):
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13 """A virtual base class for datasets.
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14
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15 A DataSet can be seen as a generalization of a matrix, meant to be used in conjunction
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16 with learning algorithms (for training and testing them): rows/records are called examples, and
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17 columns/attributes are called fields. The field value for a particular example can be an arbitrary
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18 python object, which depends on the particular dataset.
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19
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20 We call a DataSet a 'stream' when its length is unbounded (otherwise its __len__ method
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21 should return sys.maxint).
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23 A DataSet is a generator of iterators; these iterators can run through the
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24 examples or the fields in a variety of ways. A DataSet need not necessarily have a finite
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25 or known length, so this class can be used to interface to a 'stream' which
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26 feeds on-line learning (however, as noted below, some operations are not
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27 feasible or not recommanded on streams).
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28
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29 To iterate over examples, there are several possibilities:
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30 * for example in dataset([field1, field2,field3, ...]):
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31 * for val1,val2,val3 in dataset([field1, field2,field3]):
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32 * for minibatch in dataset.minibatches([field1, field2, ...],minibatch_size=N):
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33 * for mini1,mini2,mini3 in dataset.minibatches([field1, field2, field3], minibatch_size=N):
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34 * for example in dataset:
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35 print example['x']
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36 * for x,y,z in dataset:
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37 Each of these is documented below. All of these iterators are expected
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38 to provide, in addition to the usual 'next()' method, a 'next_index()' method
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39 which returns a non-negative integer pointing to the position of the next
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40 example that will be returned by 'next()' (or of the first example in the
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41 next minibatch returned). This is important because these iterators
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42 can wrap around the dataset in order to do multiple passes through it,
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43 in possibly unregular ways if the minibatch size is not a divisor of the
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44 dataset length.
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46 To iterate over fields, one can do
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47 * for field in dataset.fields():
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48 for field_value in field: # iterate over the values associated to that field for all the dataset examples
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49 * for field in dataset(field1,field2,...).fields() to select a subset of fields
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50 * for field in dataset.fields(field1,field2,...) to select a subset of fields
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51 and each of these fields is iterable over the examples:
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52 * for field_examples in dataset.fields():
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53 for example_value in field_examples:
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54 ...
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55 but when the dataset is a stream (unbounded length), it is not recommanded to do
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56 such things because the underlying dataset may refuse to access the different fields in
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57 an unsynchronized ways. Hence the fields() method is illegal for streams, by default.
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58 The result of fields() is a DataSetFields object, which iterates over fields,
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59 and whose elements are iterable over examples. A DataSetFields object can
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60 be turned back into a DataSet with its examples() method:
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61 dataset2 = dataset1.fields().examples()
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62 and dataset2 should behave exactly like dataset1 (in fact by default dataset2==dataset1).
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64 Note: Fields are not mutually exclusive, i.e. two fields can overlap in their actual content.
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66 Note: The content of a field can be of any type. Field values can also be 'missing'
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67 (e.g. to handle semi-supervised learning), and in the case of numeric (numpy array)
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68 fields (i.e. an ArrayFieldsDataSet), NaN plays the role of a missing value.
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69 What about non-numeric values? None.
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71 Dataset elements can be indexed and sub-datasets (with a subset
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72 of examples) can be extracted. These operations are not supported
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73 by default in the case of streams.
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75 * dataset[:n] returns a dataset with the n first examples.
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77 * dataset[i1:i2:s] returns a dataset with the examples i1,i1+s,...i2-s.
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78
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79 * dataset[i] returns an Example.
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81 * dataset[[i1,i2,...in]] returns a dataset with examples i1,i2,...in.
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82
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83 * dataset[fieldname] an iterable over the values of the field fieldname across
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84 the dataset (the iterable is obtained by default by calling valuesVStack
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85 over the values for individual examples).
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87 * dataset.<property> returns the value of a property associated with
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88 the name <property>. The following properties should be supported:
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89 - 'description': a textual description or name for the dataset
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90 - 'fieldtypes': a list of types (one per field)
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91
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92 Datasets can be concatenated either vertically (increasing the length) or
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93 horizontally (augmenting the set of fields), if they are compatible, using
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94 the following operations (with the same basic semantics as numpy.hstack
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95 and numpy.vstack):
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96
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97 * dataset1 | dataset2 | dataset3 == dataset.hstack([dataset1,dataset2,dataset3])
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98
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99 creates a new dataset whose list of fields is the concatenation of the list of
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100 fields of the argument datasets. This only works if they all have the same length.
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101
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102 * dataset1 & dataset2 & dataset3 == dataset.vstack([dataset1,dataset2,dataset3])
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103
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104 creates a new dataset that concatenates the examples from the argument datasets
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105 (and whose length is the sum of the length of the argument datasets). This only
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106 works if they all have the same fields.
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107
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108 According to the same logic, and viewing a DataSetFields object associated to
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109 a DataSet as a kind of transpose of it, fields1 & fields2 concatenates fields of
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110 a DataSetFields fields1 and fields2, and fields1 | fields2 concatenates their
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111 examples.
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112
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113 A dataset can hold arbitrary key-value pairs that may be used to access meta-data
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114 or other properties of the dataset or associated with the dataset or the result
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115 of a computation stored in a dataset. These can be accessed through the [key] syntax
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116 when key is a string (or more specifically, neither an integer, a slice, nor a list).
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117
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118 A DataSet sub-class should always redefine the following methods:
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119 * __len__ if it is not a stream
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120 * fieldNames
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121 * minibatches_nowrap (called by DataSet.minibatches())
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122 * valuesHStack
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123 * valuesVStack
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124 For efficiency of implementation, a sub-class might also want to redefine
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125 * hasFields
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126 * __getitem__ may not be feasible with some streams
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127 * __iter__
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128 """
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129
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130 def __init__(self,description=None,fieldtypes=None):
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131 if description is None:
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132 # by default return "<DataSetType>(<SuperClass1>,<SuperClass2>,...)"
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133 description = type(self).__name__ + " ( " + join([x.__name__ for x in type(self).__bases__]) + " )"
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134 self.description=description
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135 self.fieldtypes=fieldtypes
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136
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137 class MinibatchToSingleExampleIterator(object):
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138 """
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139 Converts the result of minibatch iterator with minibatch_size==1 into
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140 single-example values in the result. Therefore the result of
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141 iterating on the dataset itself gives a sequence of single examples
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142 (whereas the result of iterating over minibatches gives in each
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143 Example field an iterable object over the individual examples in
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144 the minibatch).
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145 """
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146 def __init__(self, minibatch_iterator):
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147 self.minibatch_iterator = minibatch_iterator
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148 self.minibatch = None
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149 def __iter__(self): #makes for loop work
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150 return self
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151 def next(self):
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152 size1_minibatch = self.minibatch_iterator.next()
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153 if not self.minibatch:
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154 self.minibatch = Example(size1_minibatch.keys(),[value[0] for value in size1_minibatch.values()])
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155 else:
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156 self.minibatch._values = [value[0] for value in size1_minibatch.values()]
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157 return self.minibatch
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158
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159 def next_index(self):
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160 return self.minibatch_iterator.next_index()
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161
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162 def __iter__(self):
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163 """Supports the syntax "for i in dataset: ..."
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164
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165 Using this syntax, "i" will be an Example instance (or equivalent) with
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166 all the fields of DataSet self. Every field of "i" will give access to
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167 a field of a single example. Fields should be accessible via
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168 i["fielname"] or i[3] (in the order defined by the elements of the
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169 Example returned by this iterator), but the derived class is free
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170 to accept any type of identifier, and add extra functionality to the iterator.
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171
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172 The default implementation calls the minibatches iterator and extracts the first example of each field.
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173 """
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174 return DataSet.MinibatchToSingleExampleIterator(self.minibatches(None, minibatch_size = 1))
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175
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176
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177 class MinibatchWrapAroundIterator(object):
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178 """
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179 An iterator for minibatches that handles the case where we need to wrap around the
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180 dataset because n_batches*minibatch_size > len(dataset). It is constructed from
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181 a dataset that provides a minibatch iterator that does not need to handle that problem.
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182 This class is a utility for dataset subclass writers, so that they do not have to handle
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183 this issue multiple times, nor check that fieldnames are valid, nor handle the
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184 empty fieldnames (meaning 'use all the fields').
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185 """
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186 def __init__(self,dataset,fieldnames,minibatch_size,n_batches,offset):
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187 self.dataset=dataset
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188 self.fieldnames=fieldnames
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189 self.minibatch_size=minibatch_size
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190 self.n_batches=n_batches
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191 self.n_batches_done=0
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192 self.next_row=offset
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193 self.L=len(dataset)
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194 assert offset+minibatch_size<=self.L
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195 ds_nbatches = (self.L-offset)/minibatch_size
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196 if n_batches is not None:
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197 ds_nbatches = max(n_batches,ds_nbatches)
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198 if fieldnames:
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199 assert dataset.hasFields(*fieldnames)
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200 else:
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201 fieldnames=dataset.fieldNames()
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202 self.iterator = dataset.minibatches_nowrap(fieldnames,minibatch_size,ds_nbatches,offset)
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203
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204 def __iter__(self):
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205 return self
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206
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207 def next_index(self):
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208 return self.next_row
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209
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210 def next(self):
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211 if self.n_batches and self.n_batches_done==self.n_batches:
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212 raise StopIteration
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213 upper = self.next_row+self.minibatch_size
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214 if upper <=self.L:
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215 minibatch = self.iterator.next()
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216 else:
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217 if not self.n_batches:
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218 raise StopIteration
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219 # we must concatenate (vstack) the bottom and top parts of our minibatch
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220 # first get the beginning of our minibatch (top of dataset)
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221 first_part = self.dataset.minibatches_nowrap(fieldnames,self.L-self.next_row,1,self.next_row).next()
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222 second_part = self.dataset.minibatches_nowrap(fieldnames,upper-self.L,1,0).next()
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223 minibatch = Example(self.fieldnames,
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224 [self.dataset.valuesVStack(name,[first_part[name],second_part[name]])
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225 for name in self.fieldnames])
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226 self.next_row=upper
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227 self.n_batches_done+=1
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228 if upper >= self.L and self.n_batches:
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229 self.next_row -= self.L
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230 return minibatch
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231
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232
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233 minibatches_fieldnames = None
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234 minibatches_minibatch_size = 1
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235 minibatches_n_batches = None
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236 def minibatches(self,
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237 fieldnames = minibatches_fieldnames,
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238 minibatch_size = minibatches_minibatch_size,
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239 n_batches = minibatches_n_batches,
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240 offset = 0):
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241 """
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242 Return an iterator that supports three forms of syntax:
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243
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244 for i in dataset.minibatches(None,**kwargs): ...
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245
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246 for i in dataset.minibatches([f1, f2, f3],**kwargs): ...
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247
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248 for i1, i2, i3 in dataset.minibatches([f1, f2, f3],**kwargs): ...
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249
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250 Using the first two syntaxes, "i" will be an indexable object, such as a list,
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251 tuple, or Example instance. In both cases, i[k] is a list-like container
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252 of a batch of current examples. In the second case, i[0] is
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253 list-like container of the f1 field of a batch current examples, i[1] is
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254 a list-like container of the f2 field, etc.
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255
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256 Using the first syntax, all the fields will be returned in "i".
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257 Using the third syntax, i1, i2, i3 will be list-like containers of the
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258 f1, f2, and f3 fields of a batch of examples on each loop iteration.
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259
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260 The minibatches iterator is expected to return upon each call to next()
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261 a DataSetFields object, which is a LookupList (indexed by the field names) whose
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262 elements are iterable over the minibatch examples, and which keeps a pointer to
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263 a sub-dataset that can be used to iterate over the individual examples
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264 in the minibatch. Hence a minibatch can be converted back to a regular
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265 dataset or its fields can be looked at individually (and possibly iterated over).
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266
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267 PARAMETERS
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268 - fieldnames (list of any type, default None):
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269 The loop variables i1, i2, i3 (in the example above) should contain the
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270 f1, f2, and f3 fields of the current batch of examples. If None, the
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271 derived class can choose a default, e.g. all fields.
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272
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273 - minibatch_size (integer, default 1)
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274 On every iteration, the variables i1, i2, i3 will have
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275 exactly minibatch_size elements. e.g. len(i1) == minibatch_size
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276
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277 - n_batches (integer, default None)
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278 The iterator will loop exactly this many times, and then stop. If None,
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279 the derived class can choose a default. If (-1), then the returned
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280 iterator should support looping indefinitely.
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281
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282 - offset (integer, default 0)
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283 The iterator will start at example 'offset' in the dataset, rather than the default.
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284
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285 Note: A list-like container is something like a tuple, list, numpy.ndarray or
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286 any other object that supports integer indexing and slicing.
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287
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288 """
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289 return DataSet.MinibatchWrapAroundIterator(self,fieldnames,minibatch_size,n_batches,offset)
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290
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291 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
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292 """
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293 This is the minibatches iterator generator that sub-classes must define.
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294 It does not need to worry about wrapping around multiple times across the dataset,
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295 as this is handled by MinibatchWrapAroundIterator when DataSet.minibatches() is called.
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296 The next() method of the returned iterator does not even need to worry about
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297 the termination condition (as StopIteration will be raised by DataSet.minibatches
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298 before an improper call to minibatches_nowrap's next() is made).
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299 That next() method can assert that its next row will always be within [0,len(dataset)).
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300 The iterator returned by minibatches_nowrap does not need to implement
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301 a next_index() method either, as this will be provided by MinibatchWrapAroundIterator.
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302 """
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303 raise AbstractFunction()
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304
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305 def __len__(self):
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306 """
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307 len(dataset) returns the number of examples in the dataset.
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308 By default, a DataSet is a 'stream', i.e. it has an unbounded length (sys.maxint).
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309 Sub-classes which implement finite-length datasets should redefine this method.
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310 Some methods only make sense for finite-length datasets.
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311 """
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312 return sys.maxint
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313
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314 def is_unbounded(self):
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315 """
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316 Tests whether a dataset is unbounded (e.g. a stream).
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317 """
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318 return len(self)==sys.maxint
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319
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320 def hasFields(self,*fieldnames):
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321 """
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322 Return true if the given field name (or field names, if multiple arguments are
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323 given) is recognized by the DataSet (i.e. can be used as a field name in one
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324 of the iterators).
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325
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326 The default implementation may be inefficient (O(# fields in dataset)), as it calls the fieldNames()
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327 method. Many datasets may store their field names in a dictionary, which would allow more efficiency.
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328 """
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329 return len(unique_elements_list_intersection(fieldnames,self.fieldNames()))>0
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330
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331 def fieldNames(self):
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332 """
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333 Return the list of field names that are supported by the iterators,
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334 and for which hasFields(fieldname) would return True.
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335 """
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336 raise AbstractFunction()
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337
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338 def __call__(self,*fieldnames):
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339 """
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340 Return a dataset that sees only the fields whose name are specified.
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341 """
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342 assert self.hasFields(*fieldnames)
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343 return self.fields(*fieldnames).examples()
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344
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345 def fields(self,*fieldnames):
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346 """
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347 Return a DataSetFields object associated with this dataset.
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348 """
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349 return DataSetFields(self,*fieldnames)
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350
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351 def __getitem__(self,i):
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352 """
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353 dataset[i] returns the (i+1)-th example of the dataset.
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354 dataset[i:j] returns the subdataset with examples i,i+1,...,j-1.
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355 dataset[i:j:s] returns the subdataset with examples i,i+2,i+4...,j-2.
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356 dataset[[i1,i2,..,in]] returns the subdataset with examples i1,i2,...,in.
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357 dataset['key'] returns a property associated with the given 'key' string.
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358 If 'key' is a fieldname, then the VStacked field values (iterable over
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359 field values) for that field is returned. Other keys may be supported
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360 by different dataset subclasses. The following key names are encouraged:
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361 - 'description': a textual description or name for the dataset
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362 - '<fieldname>.type': a type name or value for a given <fieldname>
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363
39
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364 Note that some stream datasets may be unable to implement random access, i.e.
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365 arbitrary slicing/indexing
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366 because they can only iterate through examples one or a minibatch at a time
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367 and do not actually store or keep past (or future) examples.
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368
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369 The default implementation of getitem uses the minibatches iterator
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370 to obtain one example, one slice, or a list of examples. It may not
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371 always be the most efficient way to obtain the result, especially if
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372 the data are actually stored in a memory array.
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373 """
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374 # check for an index
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375 if type(i) is int:
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376 return DataSet.MinibatchToSingleExampleIterator(
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377 self.minibatches(minibatch_size=1,n_batches=1,offset=i)).next()
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378 rows=None
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379 # or a slice
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380 if type(i) is slice:
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381 if not i.start: i.start=0
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382 if not i.step: i.step=1
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383 if i.step is 1:
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384 return self.minibatches(minibatch_size=i.stop-i.start,n_batches=1,offset=i.start).next().examples()
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385 rows = range(i.start,i.stop,i.step)
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386 # or a list of indices
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387 elif type(i) is list:
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388 rows = i
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389 if rows is not None:
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390 examples = [self[row] for row in rows]
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391 fields_values = zip(*examples)
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392 return MinibatchDataSet(
41
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diff changeset
393 Example(self.fieldNames(),[ self.valuesVStack(fieldname,field_values)
283e95c15b47 Added ArrayDataSet
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diff changeset
394 for fieldname,field_values
283e95c15b47 Added ArrayDataSet
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parents: 40
diff changeset
395 in zip(self.fieldNames(),fields_values)]))
283e95c15b47 Added ArrayDataSet
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parents: 40
diff changeset
396 # else check for a fieldname
283e95c15b47 Added ArrayDataSet
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parents: 40
diff changeset
397 if self.hasFields(i):
283e95c15b47 Added ArrayDataSet
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diff changeset
398 return self.minibatches(fieldnames=[i],minibatch_size=len(self),n_batches=1,offset=0).next()[0]
283e95c15b47 Added ArrayDataSet
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parents: 40
diff changeset
399 # else we are trying to access a property of the dataset
283e95c15b47 Added ArrayDataSet
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parents: 40
diff changeset
400 assert i in self.__dict__ # else it means we are trying to access a non-existing property
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parents: 40
diff changeset
401 return self.__dict__[i]
22
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
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parents: 20
diff changeset
402
36
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diff changeset
403 def valuesHStack(self,fieldnames,fieldvalues):
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diff changeset
404 """
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
405 Return a value that corresponds to concatenating (horizontally) several field values.
438440ba0627 Rewriting dataset.py completely
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diff changeset
406 This can be useful to merge some fields. The implementation of this operation is likely
438440ba0627 Rewriting dataset.py completely
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diff changeset
407 to involve a copy of the original values. When the values are numpy arrays, the
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
408 result should be numpy.hstack(values). If it makes sense, this operation should
438440ba0627 Rewriting dataset.py completely
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diff changeset
409 work as well when each value corresponds to multiple examples in a minibatch
438440ba0627 Rewriting dataset.py completely
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diff changeset
410 e.g. if each value is a Ni-vector and a minibatch of length L is a LxNi matrix,
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parents: 29
diff changeset
411 then the result should be a Lx(N1+N2+..) matrix equal to numpy.hstack(values).
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412 The default is to use numpy.hstack for numpy.ndarray values, and a list
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413 pointing to the original values for other data types.
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diff changeset
414 """
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parents: 29
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415 all_numpy=True
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diff changeset
416 for value in fieldvalues:
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diff changeset
417 if not type(value) is numpy.ndarray:
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diff changeset
418 all_numpy=False
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diff changeset
419 if all_numpy:
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420 return numpy.hstack(fieldvalues)
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421 # the default implementation of horizontal stacking is to put values in a list
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422 return fieldvalues
26
672fe4b23032 Fixed dataset errors so that _test_dataset.py works again.
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diff changeset
423
672fe4b23032 Fixed dataset errors so that _test_dataset.py works again.
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parents: 23
diff changeset
424
36
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425 def valuesVStack(self,fieldname,values):
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diff changeset
426 """
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427 Return a value that corresponds to concatenating (vertically) several values of the
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
428 same field. This can be important to build a minibatch out of individual examples. This
438440ba0627 Rewriting dataset.py completely
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429 is likely to involve a copy of the original values. When the values are numpy arrays, the
438440ba0627 Rewriting dataset.py completely
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diff changeset
430 result should be numpy.vstack(values).
438440ba0627 Rewriting dataset.py completely
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431 The default is to use numpy.vstack for numpy.ndarray values, and a list
438440ba0627 Rewriting dataset.py completely
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432 pointing to the original values for other data types.
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diff changeset
433 """
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434 all_numpy=True
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diff changeset
435 for value in values:
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diff changeset
436 if not type(value) is numpy.ndarray:
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437 all_numpy=False
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438 if all_numpy:
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439 return numpy.vstack(values)
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440 # the default implementation of vertical stacking is to put values in a list
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441 return values
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
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diff changeset
442
36
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443 def __or__(self,other):
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444 """
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445 dataset1 | dataset2 returns a dataset whose list of fields is the concatenation of the list of
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parents: 29
diff changeset
446 fields of the argument datasets. This only works if they all have the same length.
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parents: 29
diff changeset
447 """
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448 return HStackedDataSet(self,other)
3
378b68d5c4ad Added first (untested) version of ArrayDataSet
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parents: 2
diff changeset
449
40
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
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parents: 39
diff changeset
450 def __and__(self,other):
36
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diff changeset
451 """
40
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
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parents: 39
diff changeset
452 dataset1 & dataset2 is a dataset that concatenates the examples from the argument datasets
36
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diff changeset
453 (and whose length is the sum of the length of the argument datasets). This only
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
454 works if they all have the same fields.
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diff changeset
455 """
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456 return VStackedDataSet(self,other)
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
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parents: 22
diff changeset
457
36
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458 def hstack(datasets):
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diff changeset
459 """
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parents: 29
diff changeset
460 hstack(dataset1,dataset2,...) returns dataset1 | datataset2 | ...
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
461 which is a dataset whose fields list is the concatenation of the fields
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parents: 29
diff changeset
462 of the individual datasets.
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diff changeset
463 """
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parents: 29
diff changeset
464 assert len(datasets)>0
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diff changeset
465 if len(datasets)==1:
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466 return datasets[0]
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467 return HStackedDataSet(datasets)
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
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parents: 16 12
diff changeset
468
36
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469 def vstack(datasets):
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diff changeset
470 """
40
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
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parents: 39
diff changeset
471 vstack(dataset1,dataset2,...) returns dataset1 & datataset2 & ...
36
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diff changeset
472 which is a dataset which iterates first over the examples of dataset1, then
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parents: 29
diff changeset
473 over those of dataset2, etc.
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diff changeset
474 """
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parents: 29
diff changeset
475 assert len(datasets)>0
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parents: 29
diff changeset
476 if len(datasets)==1:
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diff changeset
477 return datasets[0]
438440ba0627 Rewriting dataset.py completely
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diff changeset
478 return VStackedDataSet(datasets)
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
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parents: 16 12
diff changeset
479
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
480 class FieldsSubsetDataSet(DataSet):
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
481 """
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
482 A sub-class of DataSet that selects a subset of the fields.
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
483 """
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
484 def __init__(self,src,fieldnames):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
485 self.src=src
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
486 self.fieldnames=fieldnames
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
487 assert src.hasFields(*fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
488 self.valuesHStack = src.valuesHStack
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
489 self.valuesVStack = src.valuesVStack
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
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parents: 16 12
diff changeset
490
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
491 def __len__(self): return len(self.src)
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
492
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
493 def fieldNames(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
494 return self.fieldnames
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
495
9b68774fcc6b Testing basic functionality and removing obvious bugs
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diff changeset
496 def __iter__(self):
44
5a85fda9b19b Fixed some more iterator bugs
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parents: 43
diff changeset
497 class FieldsSubsetIterator(object):
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
498 def __init__(self,ds):
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
499 self.ds=ds
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
500 self.src_iter=ds.src.__iter__()
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
501 self.example=None
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
502 def __iter__(self): return self
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
503 def next(self):
44
5a85fda9b19b Fixed some more iterator bugs
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parents: 43
diff changeset
504 complete_example = self.src_iter.next()
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
505 if self.example:
5a85fda9b19b Fixed some more iterator bugs
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parents: 43
diff changeset
506 self.example._values=[complete_example[field]
5a85fda9b19b Fixed some more iterator bugs
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parents: 43
diff changeset
507 for field in self.ds.fieldnames]
5a85fda9b19b Fixed some more iterator bugs
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parents: 43
diff changeset
508 else:
5a85fda9b19b Fixed some more iterator bugs
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parents: 43
diff changeset
509 self.example=Example(self.ds.fieldnames,
5a85fda9b19b Fixed some more iterator bugs
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parents: 43
diff changeset
510 [complete_example[field] for field in self.ds.fieldnames])
5a85fda9b19b Fixed some more iterator bugs
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parents: 43
diff changeset
511 return self.example
5a85fda9b19b Fixed some more iterator bugs
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parents: 43
diff changeset
512 return FieldsSubsetIterator(self)
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
513
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
514 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
515 assert self.hasFields(*fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
516 return self.src.minibatches_nowrap(fieldnames,minibatch_size,n_batches,offset)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
517 def __getitem__(self,i):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
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518 return FieldsSubsetDataSet(self.src[i],self.fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
519
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
520
36
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diff changeset
521 class DataSetFields(LookupList):
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parents: 29
diff changeset
522 """
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parents: 29
diff changeset
523 Although a DataSet iterates over examples (like rows of a matrix), an associated
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
524 DataSetFields iterates over fields (like columns of a matrix), and can be understood
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
525 as a transpose of the associated dataset.
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
526
36
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parents: 29
diff changeset
527 To iterate over fields, one can do
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
528 * for fields in dataset.fields()
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
529 * for fields in dataset(field1,field2,...).fields() to select a subset of fields
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parents: 29
diff changeset
530 * for fields in dataset.fields(field1,field2,...) to select a subset of fields
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parents: 29
diff changeset
531 and each of these fields is iterable over the examples:
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diff changeset
532 * for field_examples in dataset.fields():
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diff changeset
533 for example_value in field_examples:
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diff changeset
534 ...
438440ba0627 Rewriting dataset.py completely
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diff changeset
535 but when the dataset is a stream (unbounded length), it is not recommanded to do
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
536 such things because the underlying dataset may refuse to access the different fields in
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diff changeset
537 an unsynchronized ways. Hence the fields() method is illegal for streams, by default.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
538 The result of fields() is a DataSetFields object, which iterates over fields,
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
539 and whose elements are iterable over examples. A DataSetFields object can
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
540 be turned back into a DataSet with its examples() method:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
541 dataset2 = dataset1.fields().examples()
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
542 and dataset2 should behave exactly like dataset1 (in fact by default dataset2==dataset1).
40
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
543
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
544 DataSetFields can be concatenated vertically or horizontally. To be consistent with
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
545 the syntax used for DataSets, the | concatenates the fields and the & concatenates
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
546 the examples.
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
547 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
548 def __init__(self,dataset,*fieldnames):
40
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
549 if not fieldnames:
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
550 fieldnames=dataset.fieldNames()
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
551 elif fieldnames is not dataset.fieldNames():
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
552 dataset = FieldsSubsetDataSet(dataset,fieldnames)
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
553 assert dataset.hasFields(*fieldnames)
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
554 self.dataset=dataset
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
555 minibatch_iterator = dataset.minibatches(fieldnames,
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
556 minibatch_size=len(dataset),
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
557 n_batches=1)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
558 minibatch=minibatch_iterator.next()
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
559 LookupList.__init__(self,fieldnames,minibatch)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
560
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
561 def examples(self):
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bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
562 return self.dataset
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bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
563
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
564 def __or__(self,other):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
565 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
566 fields1 | fields2 is a DataSetFields that whose list of examples is the concatenation
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
567 of the list of examples of DataSetFields fields1 and fields2.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
568 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
569 return (self.examples() + other.examples()).fields()
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
570
40
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
571 def __and__(self,other):
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
572 """
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
573 fields1 + fields2 is a DataSetFields that whose list of fields is the concatenation
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
574 of the fields of DataSetFields fields1 and fields2.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
575 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
576 return (self.examples() | other.examples()).fields()
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
577
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
578
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
579 class MinibatchDataSet(DataSet):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
580 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
581 Turn a LookupList of same-length fields into an example-iterable dataset.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
582 Each element of the lookup-list should be an iterable and sliceable, all of the same length.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
583 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
584 def __init__(self,fields_lookuplist,values_vstack=DataSet().valuesVStack,
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
585 values_hstack=DataSet().valuesHStack):
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
586 """
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
587 The user can (and generally should) also provide values_vstack(fieldname,fieldvalues)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
588 and a values_hstack(fieldnames,fieldvalues) functions behaving with the same
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
589 semantics as the DataSet methods of the same name (but without the self argument).
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
590 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
591 self.fields=fields_lookuplist
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
592 assert len(fields_lookuplist)>0
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
593 self.length=len(fields_lookuplist[0])
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
594 for field in fields_lookuplist[1:]:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
595 assert self.length==len(field)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
596 self.values_vstack=values_vstack
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
597 self.values_hstack=values_hstack
3
378b68d5c4ad Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents: 2
diff changeset
598
378b68d5c4ad Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents: 2
diff changeset
599 def __len__(self):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
600 return self.length
28
541a273bc89f Removed __array__ method from dataset, whose
bengioy@grenat.iro.umontreal.ca
parents: 26
diff changeset
601
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
602 def __getitem__(self,i):
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
603 if type(i) in (int,slice,list):
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
604 return DataSetFields(MinibatchDataSet(
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
605 Example(self.fields.keys(),[field[i] for field in self.fields])),self.fields)
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
606 if self.hasFields(i):
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
607 return self.fields[i]
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
608 assert i in self.__dict__ # else it means we are trying to access a non-existing property
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
609 return self.__dict__[i]
11
be128b9127c8 Debugged (to the extent of my tests) the new version of dataset
bengioy@esprit.iro.umontreal.ca
parents: 9
diff changeset
610
29
46c5c90019c2 Changed apply_function so that it propagates methods of the source.
bengioy@grenat.iro.umontreal.ca
parents: 28
diff changeset
611 def fieldNames(self):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
612 return self.fields.keys()
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
613
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
614 def hasFields(self,*fieldnames):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
615 for fieldname in fieldnames:
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
616 if fieldname not in self.fields.keys():
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
617 return False
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
618 return True
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
619
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
620 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
621 class Iterator(object):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
622 def __init__(self,ds):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
623 self.ds=ds
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
624 self.next_example=offset
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
625 assert minibatch_size > 0
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
626 if offset+minibatch_size > ds.length:
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
627 raise NotImplementedError()
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
628 def __iter__(self):
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
629 return self
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
630 def next(self):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
631 upper = next_example+minibatch_size
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
632 assert upper<=self.ds.length
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
633 minibatch = Example(self.ds.fields.keys(),
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
634 [field[next_example:upper]
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
635 for field in self.ds.fields])
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
636 self.next_example+=minibatch_size
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
637 return DataSetFields(MinibatchDataSet(minibatch),fieldnames)
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
638
40
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
639 return Iterator(self)
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
640
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
641 def valuesVStack(self,fieldname,fieldvalues):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
642 return self.values_vstack(fieldname,fieldvalues)
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
643
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
644 def valuesHStack(self,fieldnames,fieldvalues):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
645 return self.values_hstack(fieldnames,fieldvalues)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
646
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
647 class HStackedDataSet(DataSet):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
648 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
649 A DataSet that wraps several datasets and shows a view that includes all their fields,
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
650 i.e. whose list of fields is the concatenation of their lists of fields.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
651
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
652 If a field name is found in more than one of the datasets, then either an error is
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
653 raised or the fields are renamed (either by prefixing the __name__ attribute
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
654 of the dataset + ".", if it exists, or by suffixing the dataset index in the argument list).
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
655
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
656 TODO: automatically detect a chain of stacked datasets due to A | B | C | D ...
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
657 """
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
658 def __init__(self,datasets,accept_nonunique_names=False,description=None,field_types=None):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
659 DataSet.__init__(self,description,field_types)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
660 self.datasets=datasets
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
661 self.accept_nonunique_names=accept_nonunique_names
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
662 self.fieldname2dataset={}
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
663
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
664 def rename_field(fieldname,dataset,i):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
665 if hasattr(dataset,"__name__"):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
666 return dataset.__name__ + "." + fieldname
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
667 return fieldname+"."+str(i)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
668
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
669 # make sure all datasets have the same length and unique field names
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
670 self.length=None
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
671 names_to_change=[]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
672 for i in xrange(len(datasets)):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
673 dataset = datasets[i]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
674 length=len(dataset)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
675 if self.length:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
676 assert self.length==length
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
677 else:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
678 self.length=length
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
679 for fieldname in dataset.fieldNames():
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
680 if fieldname in self.fieldname2dataset: # name conflict!
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
681 if accept_nonunique_names:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
682 fieldname=rename_field(fieldname,dataset,i)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
683 names2change.append((fieldname,i))
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
684 else:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
685 raise ValueError("Incompatible datasets: non-unique field name = "+fieldname)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
686 self.fieldname2dataset[fieldname]=i
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
687 for fieldname,i in names_to_change:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
688 del self.fieldname2dataset[fieldname]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
689 self.fieldname2dataset[rename_field(fieldname,self.datasets[i],i)]=i
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
690
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
691 def hasFields(self,*fieldnames):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
692 for fieldname in fieldnames:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
693 if not fieldname in self.fieldname2dataset:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
694 return False
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
695 return True
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
696
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
697 def fieldNames(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
698 return self.fieldname2dataset.keys()
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
699
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
700 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
701
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
702 class HStackedIterator(object):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
703 def __init__(self,hsds,iterators):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
704 self.hsds=hsds
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
705 self.iterators=iterators
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
706 def __iter__(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
707 return self
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
708 def next(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
709 # concatenate all the fields of the minibatches
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
710 minibatch = reduce(LookupList.__add__,[iterator.next() for iterator in self.iterators])
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
711 # and return a DataSetFields whose dataset is the transpose (=examples()) of this minibatch
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
712 return DataSetFields(MinibatchDataSet(minibatch,self.hsds.valuesVStack,
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
713 self.hsds.valuesHStack),
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
714 fieldnames if fieldnames else hsds.fieldNames())
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
715
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
716 assert self.hasfields(fieldnames)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
717 # find out which underlying datasets are necessary to service the required fields
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
718 # and construct corresponding minibatch iterators
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
719 if fieldnames:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
720 datasets=set([])
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
721 fields_in_dataset=dict([(dataset,[]) for dataset in datasets])
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
722 for fieldname in fieldnames:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
723 dataset=self.datasets[self.fieldnames2dataset[fieldname]]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
724 datasets.add(dataset)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
725 fields_in_dataset[dataset].append(fieldname)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
726 datasets=list(datasets)
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
727 iterators=[dataset.minibatches(fields_in_dataset[dataset],minibatch_size,n_batches,offset)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
728 for dataset in datasets]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
729 else:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
730 datasets=self.datasets
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
731 iterators=[dataset.minibatches(None,minibatch_size,n_batches,offset) for dataset in datasets]
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
732 return HStackedIterator(self,iterators)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
733
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
734
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
735 def valuesVStack(self,fieldname,fieldvalues):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
736 return self.datasets[self.fieldname2dataset[fieldname]].valuesVStack(fieldname,fieldvalues)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
737
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
738 def valuesHStack(self,fieldnames,fieldvalues):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
739 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
740 We will use the sub-dataset associated with the first fieldname in the fieldnames list
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
741 to do the work, hoping that it can cope with the other values (i.e. won't care
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
742 about the incompatible fieldnames). Hence this heuristic will always work if
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
743 all the fieldnames are of the same sub-dataset.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
744 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
745 return self.datasets[self.fieldname2dataset[fieldnames[0]]].valuesHStack(fieldnames,fieldvalues)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
746
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
747 class VStackedDataSet(DataSet):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
748 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
749 A DataSet that wraps several datasets and shows a view that includes all their examples,
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
750 in the order provided. This clearly assumes that they all have the same field names
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
751 and all (except possibly the last one) are of finite length.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
752
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
753 TODO: automatically detect a chain of stacked datasets due to A + B + C + D ...
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
754 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
755 def __init__(self,datasets):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
756 self.datasets=datasets
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
757 self.length=0
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
758 self.index2dataset={}
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
759 assert len(datasets)>0
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
760 fieldnames = datasets[-1].fieldNames()
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
761 self.datasets_start_row=[]
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
762 # We use this map from row index to dataset index for constant-time random access of examples,
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
763 # to avoid having to search for the appropriate dataset each time and slice is asked for.
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
764 for dataset,k in enumerate(datasets[0:-1]):
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
765 assert dataset.is_unbounded() # All VStacked datasets (except possibly the last) must be bounded (have a length).
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
766 L=len(dataset)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
767 for i in xrange(L):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
768 self.index2dataset[self.length+i]=k
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
769 self.datasets_start_row.append(self.length)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
770 self.length+=L
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
771 assert dataset.fieldNames()==fieldnames
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
772 self.datasets_start_row.append(self.length)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
773 self.length+=len(datasets[-1])
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
774 # If length is very large, we should use a more memory-efficient mechanism
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
775 # that does not store all indices
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
776 if self.length>1000000:
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
777 # 1 million entries would require about 60 meg for the index2dataset map
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
778 # TODO
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
779 print "A more efficient mechanism for index2dataset should be implemented"
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
780
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
781 def __len__(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
782 return self.length
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
783
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
784 def fieldNames(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
785 return self.datasets[0].fieldNames()
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
786
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
787 def hasFields(self,*fieldnames):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
788 return self.datasets[0].hasFields(*fieldnames)
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
789
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
790 def locate_row(self,row):
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
791 """Return (dataset_index, row_within_dataset) for global row number"""
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
792 dataset_index = self.index2dataset[row]
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
793 row_within_dataset = self.datasets_start_row[dataset_index]
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
794 return dataset_index, row_within_dataset
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
795
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
796 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
797
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
798 class VStackedIterator(object):
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
799 def __init__(self,vsds):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
800 self.vsds=vsds
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
801 self.next_row=offset
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
802 self.next_dataset_index,self.next_dataset_row=self.vsds.locate_row(offset)
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
803 self.current_iterator,self.n_left_at_the_end_of_ds,self.n_left_in_mb= \
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
804 self.next_iterator(vsds.datasets[0],offset,n_batches)
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
805
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
806 def next_iterator(self,dataset,starting_offset,batches_left):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
807 L=len(dataset)
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
808 ds_nbatches = (L-starting_offset)/minibatch_size
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
809 if batches_left is not None:
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
810 ds_nbatches = max(batches_left,ds_nbatches)
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
811 if minibatch_size>L:
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
812 ds_minibatch_size=L
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
813 n_left_in_mb=minibatch_size-L
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
814 ds_nbatches=1
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
815 else:
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
816 n_left_in_mb=0
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
817 return dataset.minibatches(fieldnames,minibatch_size,ds_nbatches,starting_offset), \
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
818 L-(starting_offset+ds_nbatches*minibatch_size), n_left_in_mb
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
819
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
820 def move_to_next_dataset(self):
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
821 if self.n_left_at_the_end_of_ds>0:
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
822 self.current_iterator,self.n_left_at_the_end_of_ds,self.n_left_in_mb= \
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
823 self.next_iterator(vsds.datasets[self.next_dataset_index],
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
824 self.n_left_at_the_end_of_ds,1)
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
825 else:
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
826 self.next_dataset_index +=1
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
827 if self.next_dataset_index==len(self.vsds.datasets):
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
828 self.next_dataset_index = 0
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
829 self.current_iterator,self.n_left_at_the_end_of_ds,self.n_left_in_mb= \
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
830 self.next_iterator(vsds.datasets[self.next_dataset_index],starting_offset,n_batches)
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
831
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
832 def __iter__(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
833 return self
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
834
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
835 def next(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
836 dataset=self.vsds.datasets[self.next_dataset_index]
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
837 mb = self.next_iterator.next()
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
838 if self.n_left_in_mb:
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
839 extra_mb = []
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
840 while self.n_left_in_mb>0:
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
841 self.move_to_next_dataset()
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
842 extra_mb.append(self.next_iterator.next())
40
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
843 examples = Example(names,
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
844 [dataset.valuesVStack(name,
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
845 [mb[name]]+[b[name] for b in extra_mb])
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
846 for name in fieldnames])
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
847 mb = DataSetFields(MinibatchDataSet(examples),fieldnames)
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
848
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
849 self.next_row+=minibatch_size
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
850 self.next_dataset_row+=minibatch_size
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
851 if self.next_row+minibatch_size>len(dataset):
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
852 self.move_to_next_dataset()
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
853 return examples
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
854 return VStackedIterator(self)
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
855
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
856 class ArrayFieldsDataSet(DataSet):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
857 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
858 Virtual super-class of datasets whose field values are numpy array,
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
859 thus defining valuesHStack and valuesVStack for sub-classes.
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
860 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
861 def __init__(self,description=None,field_types=None):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
862 DataSet.__init__(self,description,field_types)
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
863 def valuesHStack(self,fieldnames,fieldvalues):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
864 """Concatenate field values horizontally, e.g. two vectors
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
865 become a longer vector, two matrices become a wider matrix, etc."""
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
866 return numpy.hstack(fieldvalues)
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
867 def valuesVStack(self,fieldname,values):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
868 """Concatenate field values vertically, e.g. two vectors
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
869 become a two-row matrix, two matrices become a longer matrix, etc."""
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
870 return numpy.vstack(values)
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
871
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
872 class ArrayDataSet(ArrayFieldsDataSet):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
873 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
874 An ArrayDataSet stores the fields as groups of columns in a numpy tensor,
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
875 whose first axis iterates over examples, second axis determines fields.
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
876 If the underlying array is N-dimensional (has N axes), then the field
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
877 values are (N-2)-dimensional objects (i.e. ordinary numbers if N=2).
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
878 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
879
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
880 def __init__(self, data_array, fields_columns):
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
881 """
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
882 Construct an ArrayDataSet from the underlying numpy array (data) and
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
883 a map (fields_columns) from fieldnames to field columns. The columns of a field are specified
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
884 using the standard arguments for indexing/slicing: integer for a column index,
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
885 slice for an interval of columns (with possible stride), or iterable of column indices.
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
886 """
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
887 self.data=data_array
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
888 self.fields_columns=fields_columns
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
889
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
890 # check consistency and complete slices definitions
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
891 for fieldname, fieldcolumns in self.fields_columns.items():
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
892 if type(fieldcolumns) is int:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
893 assert fieldcolumns>=0 and fieldcolumns<data_array.shape[1]
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
894 elif type(fieldcolumns) is slice:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
895 start,step=None,None
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
896 if not fieldcolumns.start:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
897 start=0
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
898 if not fieldcolumns.step:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
899 step=1
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
900 if start or step:
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
901 self.fields_columns[fieldname]=slice(start,fieldcolumns.stop,step)
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
902 elif hasattr(fieldcolumns,"__iter__"): # something like a list
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
903 for i in fieldcolumns:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
904 assert i>=0 and i<data_array.shape[1]
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
905
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
906 def fieldNames(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
907 return self.fields_columns.keys()
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
908
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
909 def __len__(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
910 return len(self.data)
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
911
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
912 def __getitem__(self,i):
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
913 """More efficient implementation than the default __getitem__"""
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
914 fieldnames=self.fields_columns.keys()
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
915 if type(i) is int:
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
916 return Example(fieldnames,
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
917 [self.data[i,self.fields_columns[f]] for f in fieldnames])
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
918 if type(i) in (slice,list):
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
919 return MinibatchDataSet(Example(fieldnames,
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
920 [self.data[i,self.fields_columns[f]] for f in fieldnames]))
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
921 # else check for a fieldname
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
922 if self.hasFields(i):
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
923 return Example([i],[self.data[self.fields_columns[i],:]])
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
924 # else we are trying to access a property of the dataset
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
925 assert i in self.__dict__ # else it means we are trying to access a non-existing property
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
926 return self.__dict__[i]
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
927
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
928
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
929 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
930 class ArrayDataSetIterator(object):
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
931 def __init__(self,dataset,fieldnames,minibatch_size,n_batches,offset):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
932 if fieldnames is None: fieldnames = dataset.fieldNames()
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
933 # store the resulting minibatch in a lookup-list of values
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
934 self.minibatch = LookupList(fieldnames,[0]*len(fieldnames))
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
935 self.dataset=dataset
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
936 self.minibatch_size=minibatch_size
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
937 assert offset>=0 and offset<len(dataset.data)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
938 assert offset+minibatch_size<=len(dataset.data)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
939 self.current=offset
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
940 def __iter__(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
941 return self
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
942 def next(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
943 sub_data = self.dataset.data[self.current:self.current+self.minibatch_size]
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
944 self.minibatch._values = [sub_data[:,self.dataset.fields_columns[f]] for f in self.minibatch._names]
43
e92244f30116 Corrected iterator logic errors
bengioy@grenat.iro.umontreal.ca
parents: 42
diff changeset
945 self.current+=self.minibatch_size
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
946 return self.minibatch
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
947
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
948 return ArrayDataSetIterator(self,fieldnames,minibatch_size,n_batches,offset)
57
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
949
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
950
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
951 class CachedDataSet(DataSet):
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
952 """
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
953 Wrap a dataset whose values are computationally expensive to obtain
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
954 (e.g. because they involve some computation, or disk access),
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
955 so that repeated accesses to the same example are done cheaply,
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
956 by caching every example value that has been accessed at least once.
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
957
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
958 Optionally, for finite-length dataset, all the values can be computed
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
959 (and cached) upon construction of the CachedDataSet, rather at the
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
960 first access.
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
961 """
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
962
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
963 class ApplyFunctionDataSet(DataSet):
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
964 """
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
965 A dataset that contains as fields the results of applying a given function
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
966 example-wise or minibatch-wise to all the fields of an input dataset.
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
967 The output of the function should be an iterable (e.g. a list or a LookupList)
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
968 over the resulting values. In minibatch mode, the function is expected
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
969 to work on minibatches (takes a minibatch in input and returns a minibatch
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
970 in output).
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
971
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
972 The function is applied each time an example or a minibatch is accessed.
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
973 To avoid re-doing computation, wrap this dataset inside a CachedDataSet.
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
974 """
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
975
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
976
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
977 def supervised_learning_dataset(src_dataset,input_fields,target_fields,weight_field=None):
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
978 """
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
979 Wraps an arbitrary DataSet into one for supervised learning tasks by forcing the
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
980 user to define a set of fields as the 'input' field and a set of fields
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
981 as the 'target' field. Optionally, a single weight_field can also be defined.
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
982 """
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
983 args = ((input_fields,'input'),(output_fields,'target'))
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
984 if weight_field: args+=(([weight_field],'weight'))
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
985 return src_dataset.merge_fields(*args)
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
986
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
987
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
988
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
989