annotate dataset.py @ 48:b6730f9a336d

Fixing MinibatchDataSet getitem
author bengioy@grenat.iro.umontreal.ca
date Tue, 29 Apr 2008 13:40:13 -0400
parents c5b07e87b0cb
children e3ac93e27e16 66619ce44497
rev   line source
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ff4e551490f1 Added LookupList type in lookup_list.py and used it to keep order
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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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a5c70dc42972 Test functions for dataset.py
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7 import numpy
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759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
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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, ...],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 fields in dataset(field1,field2,...).fields() to select a subset of fields
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50 * for fields 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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63
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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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65
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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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74
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75 * dataset[:n] returns a dataset with the n first examples.
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76
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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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80
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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['key'] returns a property associated with the given 'key' string.
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84 If 'key' is a fieldname, then the VStacked field values (iterable over
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85 field values) for that field is returned. Other keys may be supported
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86 by different dataset subclasses. The following key names are should be supported:
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87 - 'description': a textual description or name for the dataset
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88 - '<fieldname>.type': a type name or value for a given <fieldname>
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89
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90 Datasets can be concatenated either vertically (increasing the length) or
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91 horizontally (augmenting the set of fields), if they are compatible, using
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92 the following operations (with the same basic semantics as numpy.hstack
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93 and numpy.vstack):
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94
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95 * dataset1 | dataset2 | dataset3 == dataset.hstack([dataset1,dataset2,dataset3])
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96
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97 creates a new dataset whose list of fields is the concatenation of the list of
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98 fields of the argument datasets. This only works if they all have the same length.
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99
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100 * dataset1 & dataset2 & dataset3 == dataset.vstack([dataset1,dataset2,dataset3])
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101
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102 creates a new dataset that concatenates the examples from the argument datasets
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103 (and whose length is the sum of the length of the argument datasets). This only
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104 works if they all have the same fields.
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105
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106 According to the same logic, and viewing a DataSetFields object associated to
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107 a DataSet as a kind of transpose of it, fields1 & fields2 concatenates fields of
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108 a DataSetFields fields1 and fields2, and fields1 | fields2 concatenates their
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109 examples.
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110
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111 A dataset can hold arbitrary key-value pairs that may be used to access meta-data
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112 or other properties of the dataset or associated with the dataset or the result
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113 of a computation stored in a dataset. These can be accessed through the [key] syntax
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114 when key is a string (or more specifically, neither an integer, a slice, nor a list).
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115
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116 A DataSet sub-class should always redefine the following methods:
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117 * __len__ if it is not a stream
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118 * fieldNames
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119 * minibatches_nowrap (called by DataSet.minibatches())
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120 * valuesHStack
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121 * valuesVStack
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122 For efficiency of implementation, a sub-class might also want to redefine
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123 * hasFields
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124 * __getitem__ may not be feasible with some streams
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125 * __iter__
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126 """
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127
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128 def __init__(self,description=None,field_types=None):
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129 if description is None:
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130 # by default return "<DataSetType>(<SuperClass1>,<SuperClass2>,...)"
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131 description = type(self).__name__ + " ( " + join([x.__name__ for x in type(self).__bases__]) + " )"
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132 self.description=description
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133 self.field_types=field_types
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134
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135 class MinibatchToSingleExampleIterator(object):
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136 """
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137 Converts the result of minibatch iterator with minibatch_size==1 into
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138 single-example values in the result. Therefore the result of
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139 iterating on the dataset itself gives a sequence of single examples
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140 (whereas the result of iterating over minibatches gives in each
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141 Example field an iterable object over the individual examples in
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142 the minibatch).
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143 """
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144 def __init__(self, minibatch_iterator):
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145 self.minibatch_iterator = minibatch_iterator
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146 self.minibatch = None
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147 def __iter__(self): #makes for loop work
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148 return self
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149 def next(self):
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150 size1_minibatch = self.minibatch_iterator.next()
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151 if not self.minibatch:
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152 self.minibatch = Example(size1_minibatch.keys(),[value[0] for value in size1_minibatch.values()])
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153 else:
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154 self.minibatch._values = [value[0] for value in size1_minibatch.values()]
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155 return self.minibatch
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156
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157 def next_index(self):
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158 return self.minibatch_iterator.next_index()
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159
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160 def __iter__(self):
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161 """Supports the syntax "for i in dataset: ..."
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162
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163 Using this syntax, "i" will be an Example instance (or equivalent) with
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164 all the fields of DataSet self. Every field of "i" will give access to
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165 a field of a single example. Fields should be accessible via
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166 i["fielname"] or i[3] (in the order defined by the elements of the
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167 Example returned by this iterator), but the derived class is free
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168 to accept any type of identifier, and add extra functionality to the iterator.
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169
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170 The default implementation calls the minibatches iterator and extracts the first example of each field.
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171 """
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172 return DataSet.MinibatchToSingleExampleIterator(self.minibatches(None, minibatch_size = 1))
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173
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174
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175 class MinibatchWrapAroundIterator(object):
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176 """
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177 An iterator for minibatches that handles the case where we need to wrap around the
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178 dataset because n_batches*minibatch_size > len(dataset). It is constructed from
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179 a dataset that provides a minibatch iterator that does not need to handle that problem.
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180 This class is a utility for dataset subclass writers, so that they do not have to handle
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181 this issue multiple times, nor check that fieldnames are valid, nor handle the
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182 empty fieldnames (meaning 'use all the fields').
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183 """
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184 def __init__(self,dataset,fieldnames,minibatch_size,n_batches,offset):
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185 self.dataset=dataset
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186 self.fieldnames=fieldnames
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187 self.minibatch_size=minibatch_size
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188 self.n_batches=n_batches
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189 self.n_batches_done=0
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190 self.next_row=offset
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191 self.L=len(dataset)
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192 assert offset+minibatch_size<=self.L
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193 ds_nbatches = (self.L-offset)/minibatch_size
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194 if n_batches is not None:
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195 ds_nbatches = max(n_batches,ds_nbatches)
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196 if fieldnames:
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197 assert dataset.hasFields(*fieldnames)
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198 else:
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199 fieldnames=dataset.fieldNames()
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200 self.iterator = dataset.minibatches_nowrap(fieldnames,minibatch_size,ds_nbatches,offset)
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201
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202 def __iter__(self):
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203 return self
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204
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205 def next_index(self):
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206 return self.next_row
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207
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208 def next(self):
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209 if self.n_batches and self.n_batches_done==self.n_batches:
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210 raise StopIteration
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211 upper = self.next_row+self.minibatch_size
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212 if upper <=self.L:
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213 minibatch = self.iterator.next()
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214 else:
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215 if not self.n_batches:
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216 raise StopIteration
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217 # we must concatenate (vstack) the bottom and top parts of our minibatch
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218 # first get the beginning of our minibatch (top of dataset)
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219 first_part = self.dataset.minibatches_nowrap(fieldnames,self.L-self.next_row,1,self.next_row).next()
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220 second_part = self.dataset.minibatches_nowrap(fieldnames,upper-self.L,1,0).next()
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221 minibatch = Example(self.fieldnames,
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222 [self.dataset.valuesVStack(name,[first_part[name],second_part[name]])
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223 for name in self.fieldnames])
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224 self.next_row=upper
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225 self.n_batches_done+=1
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226 if upper >= self.L and self.n_batches:
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227 self.next_row -= self.L
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228 return minibatch
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229
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230
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231 minibatches_fieldnames = None
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232 minibatches_minibatch_size = 1
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233 minibatches_n_batches = None
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234 def minibatches(self,
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235 fieldnames = minibatches_fieldnames,
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236 minibatch_size = minibatches_minibatch_size,
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237 n_batches = minibatches_n_batches,
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238 offset = 0):
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239 """
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240 Return an iterator that supports three forms of syntax:
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241
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242 for i in dataset.minibatches(None,**kwargs): ...
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243
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244 for i in dataset.minibatches([f1, f2, f3],**kwargs): ...
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245
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246 for i1, i2, i3 in dataset.minibatches([f1, f2, f3],**kwargs): ...
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247
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248 Using the first two syntaxes, "i" will be an indexable object, such as a list,
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249 tuple, or Example instance. In both cases, i[k] is a list-like container
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250 of a batch of current examples. In the second case, i[0] is
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251 list-like container of the f1 field of a batch current examples, i[1] is
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252 a list-like container of the f2 field, etc.
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253
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254 Using the first syntax, all the fields will be returned in "i".
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255 Using the third syntax, i1, i2, i3 will be list-like containers of the
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256 f1, f2, and f3 fields of a batch of examples on each loop iteration.
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257
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258 The minibatches iterator is expected to return upon each call to next()
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259 a DataSetFields object, which is a LookupList (indexed by the field names) whose
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260 elements are iterable over the minibatch examples, and which keeps a pointer to
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261 a sub-dataset that can be used to iterate over the individual examples
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262 in the minibatch. Hence a minibatch can be converted back to a regular
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263 dataset or its fields can be looked at individually (and possibly iterated over).
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264
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265 PARAMETERS
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266 - fieldnames (list of any type, default None):
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267 The loop variables i1, i2, i3 (in the example above) should contain the
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268 f1, f2, and f3 fields of the current batch of examples. If None, the
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269 derived class can choose a default, e.g. all fields.
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270
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271 - minibatch_size (integer, default 1)
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272 On every iteration, the variables i1, i2, i3 will have
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273 exactly minibatch_size elements. e.g. len(i1) == minibatch_size
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274
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275 - n_batches (integer, default None)
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276 The iterator will loop exactly this many times, and then stop. If None,
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277 the derived class can choose a default. If (-1), then the returned
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278 iterator should support looping indefinitely.
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279
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280 - offset (integer, default 0)
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281 The iterator will start at example 'offset' in the dataset, rather than the default.
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282
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283 Note: A list-like container is something like a tuple, list, numpy.ndarray or
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284 any other object that supports integer indexing and slicing.
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285
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286 """
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287 return DataSet.MinibatchWrapAroundIterator(self,fieldnames,minibatch_size,n_batches,offset)
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288
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289 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
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290 """
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291 This is the minibatches iterator generator that sub-classes must define.
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292 It does not need to worry about wrapping around multiple times across the dataset,
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293 as this is handled by MinibatchWrapAroundIterator when DataSet.minibatches() is called.
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294 The next() method of the returned iterator does not even need to worry about
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295 the termination condition (as StopIteration will be raised by DataSet.minibatches
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296 before an improper call to minibatches_nowrap's next() is made).
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297 That next() method can assert that its next row will always be within [0,len(dataset)).
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298 The iterator returned by minibatches_nowrap does not need to implement
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299 a next_index() method either, as this will be provided by MinibatchWrapAroundIterator.
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300 """
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301 raise AbstractFunction()
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302
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303 def __len__(self):
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304 """
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305 len(dataset) returns the number of examples in the dataset.
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306 By default, a DataSet is a 'stream', i.e. it has an unbounded length (sys.maxint).
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307 Sub-classes which implement finite-length datasets should redefine this method.
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308 Some methods only make sense for finite-length datasets.
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309 """
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310 return sys.maxint
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311
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312 def is_unbounded(self):
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313 """
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314 Tests whether a dataset is unbounded (e.g. a stream).
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315 """
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316 return len(self)==sys.maxint
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317
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318 def hasFields(self,*fieldnames):
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319 """
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320 Return true if the given field name (or field names, if multiple arguments are
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321 given) is recognized by the DataSet (i.e. can be used as a field name in one
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322 of the iterators).
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323
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324 The default implementation may be inefficient (O(# fields in dataset)), as it calls the fieldNames()
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325 method. Many datasets may store their field names in a dictionary, which would allow more efficiency.
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326 """
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327 return len(unique_elements_list_intersection(fieldnames,self.fieldNames()))>0
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328
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329 def fieldNames(self):
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330 """
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331 Return the list of field names that are supported by the iterators,
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332 and for which hasFields(fieldname) would return True.
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333 """
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334 raise AbstractFunction()
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335
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336 def __call__(self,*fieldnames):
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337 """
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338 Return a dataset that sees only the fields whose name are specified.
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339 """
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340 assert self.hasFields(*fieldnames)
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341 return self.fields(*fieldnames).examples()
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342
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343 def fields(self,*fieldnames):
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344 """
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345 Return a DataSetFields object associated with this dataset.
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346 """
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347 return DataSetFields(self,*fieldnames)
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348
2
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349 def __getitem__(self,i):
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350 """
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351 dataset[i] returns the (i+1)-th example of the dataset.
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352 dataset[i:j] returns the subdataset with examples i,i+1,...,j-1.
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353 dataset[i:j:s] returns the subdataset with examples i,i+2,i+4...,j-2.
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354 dataset[[i1,i2,..,in]] returns the subdataset with examples i1,i2,...,in.
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355 dataset['key'] returns a property associated with the given 'key' string.
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356 If 'key' is a fieldname, then the VStacked field values (iterable over
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357 field values) for that field is returned. Other keys may be supported
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358 by different dataset subclasses. The following key names are encouraged:
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359 - 'description': a textual description or name for the dataset
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360 - '<fieldname>.type': a type name or value for a given <fieldname>
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361
39
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362 Note that some stream datasets may be unable to implement random access, i.e.
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363 arbitrary slicing/indexing
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364 because they can only iterate through examples one or a minibatch at a time
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365 and do not actually store or keep past (or future) examples.
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366
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367 The default implementation of getitem uses the minibatches iterator
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368 to obtain one example, one slice, or a list of examples. It may not
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369 always be the most efficient way to obtain the result, especially if
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370 the data are actually stored in a memory array.
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371 """
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372 # check for an index
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373 if type(i) is int:
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374 return DataSet.MinibatchToSingleExampleIterator(
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375 self.minibatches(minibatch_size=1,n_batches=1,offset=i)).next()
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376 rows=None
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377 # or a slice
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378 if type(i) is slice:
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379 if not i.start: i.start=0
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380 if not i.step: i.step=1
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381 if i.step is 1:
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382 return self.minibatches(minibatch_size=i.stop-i.start,n_batches=1,offset=i.start).next().examples()
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383 rows = range(i.start,i.stop,i.step)
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384 # or a list of indices
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385 elif type(i) is list:
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386 rows = i
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387 if rows is not None:
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388 examples = [self[row] for row in rows]
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389 fields_values = zip(*examples)
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390 return MinibatchDataSet(
41
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391 Example(self.fieldNames(),[ self.valuesVStack(fieldname,field_values)
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392 for fieldname,field_values
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393 in zip(self.fieldNames(),fields_values)]))
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394 # else check for a fieldname
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parents: 40
diff changeset
395 if self.hasFields(i):
283e95c15b47 Added ArrayDataSet
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diff changeset
396 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
397 # else we are trying to access a property of the dataset
283e95c15b47 Added ArrayDataSet
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parents: 40
diff changeset
398 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
399 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
400
36
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diff changeset
401 def valuesHStack(self,fieldnames,fieldvalues):
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402 """
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403 Return a value that corresponds to concatenating (horizontally) several field values.
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parents: 29
diff changeset
404 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
405 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
406 result should be numpy.hstack(values). If it makes sense, this operation should
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
407 work as well when each value corresponds to multiple examples in a minibatch
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diff changeset
408 e.g. if each value is a Ni-vector and a minibatch of length L is a LxNi matrix,
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diff changeset
409 then the result should be a Lx(N1+N2+..) matrix equal to numpy.hstack(values).
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410 The default is to use numpy.hstack for numpy.ndarray values, and a list
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411 pointing to the original values for other data types.
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diff changeset
412 """
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parents: 29
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413 all_numpy=True
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diff changeset
414 for value in fieldvalues:
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parents: 29
diff changeset
415 if not type(value) is numpy.ndarray:
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diff changeset
416 all_numpy=False
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diff changeset
417 if all_numpy:
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418 return numpy.hstack(fieldvalues)
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419 # the default implementation of horizontal stacking is to put values in a list
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420 return fieldvalues
26
672fe4b23032 Fixed dataset errors so that _test_dataset.py works again.
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diff changeset
421
672fe4b23032 Fixed dataset errors so that _test_dataset.py works again.
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parents: 23
diff changeset
422
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423 def valuesVStack(self,fieldname,values):
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diff changeset
424 """
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425 Return a value that corresponds to concatenating (vertically) several values of the
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parents: 29
diff changeset
426 same field. This can be important to build a minibatch out of individual examples. This
438440ba0627 Rewriting dataset.py completely
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427 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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428 result should be numpy.vstack(values).
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429 The default is to use numpy.vstack for numpy.ndarray values, and a list
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430 pointing to the original values for other data types.
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diff changeset
431 """
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432 all_numpy=True
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433 for value in values:
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434 if not type(value) is numpy.ndarray:
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435 all_numpy=False
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diff changeset
436 if all_numpy:
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437 return numpy.vstack(values)
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438 # the default implementation of vertical stacking is to put values in a list
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parents: 29
diff changeset
439 return values
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
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diff changeset
440
36
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diff changeset
441 def __or__(self,other):
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diff changeset
442 """
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443 dataset1 | dataset2 returns a dataset whose list of fields is the concatenation of the list of
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parents: 29
diff changeset
444 fields of the argument datasets. This only works if they all have the same length.
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parents: 29
diff changeset
445 """
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diff changeset
446 return HStackedDataSet(self,other)
3
378b68d5c4ad Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents: 2
diff changeset
447
40
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
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parents: 39
diff changeset
448 def __and__(self,other):
36
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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 dataset1 & dataset2 is a dataset that concatenates the examples from the argument datasets
36
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diff changeset
451 (and whose length is the sum of the length of the argument datasets). This only
438440ba0627 Rewriting dataset.py completely
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diff changeset
452 works if they all have the same fields.
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diff changeset
453 """
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diff changeset
454 return VStackedDataSet(self,other)
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
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parents: 22
diff changeset
455
36
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456 def hstack(datasets):
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diff changeset
457 """
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458 hstack(dataset1,dataset2,...) returns dataset1 | datataset2 | ...
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
459 which is a dataset whose fields list is the concatenation of the fields
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parents: 29
diff changeset
460 of the individual datasets.
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diff changeset
461 """
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diff changeset
462 assert len(datasets)>0
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diff changeset
463 if len(datasets)==1:
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diff changeset
464 return datasets[0]
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diff changeset
465 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
466
36
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467 def vstack(datasets):
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diff changeset
468 """
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
469 vstack(dataset1,dataset2,...) returns dataset1 & datataset2 & ...
36
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diff changeset
470 which is a dataset which iterates first over the examples of dataset1, then
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parents: 29
diff changeset
471 over those of dataset2, etc.
438440ba0627 Rewriting dataset.py completely
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diff changeset
472 """
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diff changeset
473 assert len(datasets)>0
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diff changeset
474 if len(datasets)==1:
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diff changeset
475 return datasets[0]
438440ba0627 Rewriting dataset.py completely
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diff changeset
476 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
477
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
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diff changeset
478 class FieldsSubsetDataSet(DataSet):
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
479 """
9b68774fcc6b Testing basic functionality and removing obvious bugs
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diff changeset
480 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
481 """
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
482 def __init__(self,src,fieldnames):
9b68774fcc6b Testing basic functionality and removing obvious bugs
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diff changeset
483 self.src=src
9b68774fcc6b Testing basic functionality and removing obvious bugs
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diff changeset
484 self.fieldnames=fieldnames
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
485 assert src.hasFields(*fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
486 self.valuesHStack = src.valuesHStack
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
487 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
488
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
489 def __len__(self): return len(self.src)
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
490
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
491 def fieldNames(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
492 return self.fieldnames
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
493
9b68774fcc6b Testing basic functionality and removing obvious bugs
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diff changeset
494 def __iter__(self):
44
5a85fda9b19b Fixed some more iterator bugs
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parents: 43
diff changeset
495 class FieldsSubsetIterator(object):
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
496 def __init__(self,ds):
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
497 self.ds=ds
9b68774fcc6b Testing basic functionality and removing obvious bugs
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diff changeset
498 self.src_iter=ds.src.__iter__()
44
5a85fda9b19b Fixed some more iterator bugs
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parents: 43
diff changeset
499 self.example=None
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
500 def __iter__(self): return self
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
501 def next(self):
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
502 complete_example = self.src_iter.next()
5a85fda9b19b Fixed some more iterator bugs
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parents: 43
diff changeset
503 if self.example:
5a85fda9b19b Fixed some more iterator bugs
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parents: 43
diff changeset
504 self.example._values=[complete_example[field]
5a85fda9b19b Fixed some more iterator bugs
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parents: 43
diff changeset
505 for field in self.ds.fieldnames]
5a85fda9b19b Fixed some more iterator bugs
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parents: 43
diff changeset
506 else:
5a85fda9b19b Fixed some more iterator bugs
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parents: 43
diff changeset
507 self.example=Example(self.ds.fieldnames,
5a85fda9b19b Fixed some more iterator bugs
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parents: 43
diff changeset
508 [complete_example[field] for field in self.ds.fieldnames])
5a85fda9b19b Fixed some more iterator bugs
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parents: 43
diff changeset
509 return self.example
5a85fda9b19b Fixed some more iterator bugs
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parents: 43
diff changeset
510 return FieldsSubsetIterator(self)
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
511
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
512 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
513 assert self.hasFields(*fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
514 return self.src.minibatches_nowrap(fieldnames,minibatch_size,n_batches,offset)
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
515 def __getitem__(self,i):
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
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516 return FieldsSubsetDataSet(self.src[i],self.fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
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diff changeset
517
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
518
36
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diff changeset
519 class DataSetFields(LookupList):
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parents: 29
diff changeset
520 """
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parents: 29
diff changeset
521 Although a DataSet iterates over examples (like rows of a matrix), an associated
438440ba0627 Rewriting dataset.py completely
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diff changeset
522 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
523 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
524
36
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parents: 29
diff changeset
525 To iterate over fields, one can do
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
526 * for fields in dataset.fields()
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
527 * for fields in dataset(field1,field2,...).fields() to select a subset of fields
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diff changeset
528 * for fields in dataset.fields(field1,field2,...) to select a subset of fields
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parents: 29
diff changeset
529 and each of these fields is iterable over the examples:
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diff changeset
530 * for field_examples in dataset.fields():
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diff changeset
531 for example_value in field_examples:
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diff changeset
532 ...
438440ba0627 Rewriting dataset.py completely
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diff changeset
533 but when the dataset is a stream (unbounded length), it is not recommanded to do
438440ba0627 Rewriting dataset.py completely
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diff changeset
534 such things because the underlying dataset may refuse to access the different fields in
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diff changeset
535 an unsynchronized ways. Hence the fields() method is illegal for streams, by default.
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
536 The result of fields() is a DataSetFields object, which iterates over fields,
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
537 and whose elements are iterable over examples. A DataSetFields object can
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
538 be turned back into a DataSet with its examples() method:
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parents: 29
diff changeset
539 dataset2 = dataset1.fields().examples()
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
540 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
541
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
542 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
543 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
544 the examples.
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
545 """
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parents: 29
diff changeset
546 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
547 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
548 fieldnames=dataset.fieldNames()
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
549 elif fieldnames is not dataset.fieldNames():
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
550 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
551 assert dataset.hasFields(*fieldnames)
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
552 self.dataset=dataset
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
553 minibatch_iterator = dataset.minibatches(fieldnames,
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
554 minibatch_size=len(dataset),
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
555 n_batches=1)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
556 minibatch=minibatch_iterator.next()
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
557 LookupList.__init__(self,fieldnames,minibatch)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
558
36
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parents: 29
diff changeset
559 def examples(self):
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parents: 29
diff changeset
560 return self.dataset
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parents: 29
diff changeset
561
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parents: 29
diff changeset
562 def __or__(self,other):
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parents: 29
diff changeset
563 """
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parents: 29
diff changeset
564 fields1 | fields2 is a DataSetFields that whose list of examples is the concatenation
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
565 of the list of examples of DataSetFields fields1 and fields2.
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parents: 29
diff changeset
566 """
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parents: 29
diff changeset
567 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
568
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
569 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
570 """
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
571 fields1 + fields2 is a DataSetFields that whose list of fields is the concatenation
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parents: 29
diff changeset
572 of the fields of DataSetFields fields1 and fields2.
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parents: 29
diff changeset
573 """
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parents: 29
diff changeset
574 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
575
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
576
36
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bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
577 class MinibatchDataSet(DataSet):
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parents: 29
diff changeset
578 """
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parents: 29
diff changeset
579 Turn a LookupList of same-length fields into an example-iterable dataset.
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parents: 29
diff changeset
580 Each element of the lookup-list should be an iterable and sliceable, all of the same length.
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bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
581 """
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parents: 29
diff changeset
582 def __init__(self,fields_lookuplist,values_vstack=DataSet().valuesVStack,
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parents: 29
diff changeset
583 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
584 """
36
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parents: 29
diff changeset
585 The user can (and generally should) also provide values_vstack(fieldname,fieldvalues)
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bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
586 and a values_hstack(fieldnames,fieldvalues) functions behaving with the same
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
587 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
588 """
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parents: 29
diff changeset
589 self.fields=fields_lookuplist
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
590 assert len(fields_lookuplist)>0
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
591 self.length=len(fields_lookuplist[0])
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parents: 29
diff changeset
592 for field in fields_lookuplist[1:]:
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parents: 29
diff changeset
593 assert self.length==len(field)
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
594 self.values_vstack=values_vstack
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parents: 29
diff changeset
595 self.values_hstack=values_hstack
3
378b68d5c4ad Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents: 2
diff changeset
596
378b68d5c4ad Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents: 2
diff changeset
597 def __len__(self):
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
598 return self.length
28
541a273bc89f Removed __array__ method from dataset, whose
bengioy@grenat.iro.umontreal.ca
parents: 26
diff changeset
599
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
600 def __getitem__(self,i):
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
601 if type(i) in (int,slice,list):
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
602 return DataSetFields(MinibatchDataSet(
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
603 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
604 if self.hasFields(i):
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
605 return self.fields[i]
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
606 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
607
29
46c5c90019c2 Changed apply_function so that it propagates methods of the source.
bengioy@grenat.iro.umontreal.ca
parents: 28
diff changeset
608 def fieldNames(self):
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
609 return self.fields.keys()
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
610
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
611 def hasFields(self,*fieldnames):
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
612 for fieldname in fieldnames:
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
613 if fieldname not in self.fields.keys():
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
614 return False
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
615 return True
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
616
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
617 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
36
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parents: 29
diff changeset
618 class Iterator(object):
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parents: 29
diff changeset
619 def __init__(self,ds):
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parents: 29
diff changeset
620 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
621 self.next_example=offset
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
622 assert minibatch_size > 0
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
623 if offset+minibatch_size > ds.length:
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
624 raise NotImplementedError()
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
625 def __iter__(self):
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
626 return self
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
627 def next(self):
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
628 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
629 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
630 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
631 [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
632 for field in self.ds.fields])
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
633 self.next_example+=minibatch_size
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
634 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
635
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
636 return Iterator(self)
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
637
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
638 def valuesVStack(self,fieldname,fieldvalues):
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parents: 29
diff changeset
639 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
640
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
641 def valuesHStack(self,fieldnames,fieldvalues):
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parents: 29
diff changeset
642 return self.values_hstack(fieldnames,fieldvalues)
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parents: 29
diff changeset
643
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
644 class HStackedDataSet(DataSet):
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parents: 29
diff changeset
645 """
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parents: 29
diff changeset
646 A DataSet that wraps several datasets and shows a view that includes all their fields,
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
647 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
648
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
649 If a field name is found in more than one of the datasets, then either an error is
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
650 raised or the fields are renamed (either by prefixing the __name__ attribute
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
651 of the dataset + ".", if it exists, or by suffixing the dataset index in the argument list).
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parents: 29
diff changeset
652
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
653 TODO: automatically detect a chain of stacked datasets due to A | B | C | D ...
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
654 """
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
655 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
656 DataSet.__init__(self,description,field_types)
36
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parents: 29
diff changeset
657 self.datasets=datasets
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parents: 29
diff changeset
658 self.accept_nonunique_names=accept_nonunique_names
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parents: 29
diff changeset
659 self.fieldname2dataset={}
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parents: 29
diff changeset
660
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
661 def rename_field(fieldname,dataset,i):
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parents: 29
diff changeset
662 if hasattr(dataset,"__name__"):
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parents: 29
diff changeset
663 return dataset.__name__ + "." + fieldname
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parents: 29
diff changeset
664 return fieldname+"."+str(i)
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parents: 29
diff changeset
665
438440ba0627 Rewriting dataset.py completely
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diff changeset
666 # make sure all datasets have the same length and unique field names
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diff changeset
667 self.length=None
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parents: 29
diff changeset
668 names_to_change=[]
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parents: 29
diff changeset
669 for i in xrange(len(datasets)):
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parents: 29
diff changeset
670 dataset = datasets[i]
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parents: 29
diff changeset
671 length=len(dataset)
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parents: 29
diff changeset
672 if self.length:
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
673 assert self.length==length
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parents: 29
diff changeset
674 else:
438440ba0627 Rewriting dataset.py completely
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diff changeset
675 self.length=length
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
676 for fieldname in dataset.fieldNames():
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
677 if fieldname in self.fieldname2dataset: # name conflict!
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
678 if accept_nonunique_names:
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
679 fieldname=rename_field(fieldname,dataset,i)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
680 names2change.append((fieldname,i))
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
681 else:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
682 raise ValueError("Incompatible datasets: non-unique field name = "+fieldname)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
683 self.fieldname2dataset[fieldname]=i
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
684 for fieldname,i in names_to_change:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
685 del self.fieldname2dataset[fieldname]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
686 self.fieldname2dataset[rename_field(fieldname,self.datasets[i],i)]=i
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
687
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
688 def hasFields(self,*fieldnames):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
689 for fieldname in fieldnames:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
690 if not fieldname in self.fieldname2dataset:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
691 return False
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
692 return True
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
693
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
694 def fieldNames(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
695 return self.fieldname2dataset.keys()
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
696
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
697 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
698
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
699 class HStackedIterator(object):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
700 def __init__(self,hsds,iterators):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
701 self.hsds=hsds
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
702 self.iterators=iterators
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
703 def __iter__(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
704 return self
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
705 def next(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
706 # concatenate all the fields of the minibatches
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
707 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
708 # 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
709 return DataSetFields(MinibatchDataSet(minibatch,self.hsds.valuesVStack,
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
710 self.hsds.valuesHStack),
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
711 fieldnames if fieldnames else hsds.fieldNames())
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
712
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
713 assert self.hasfields(fieldnames)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
714 # 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
715 # and construct corresponding minibatch iterators
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
716 if fieldnames:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
717 datasets=set([])
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
718 fields_in_dataset=dict([(dataset,[]) for dataset in datasets])
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
719 for fieldname in fieldnames:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
720 dataset=self.datasets[self.fieldnames2dataset[fieldname]]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
721 datasets.add(dataset)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
722 fields_in_dataset[dataset].append(fieldname)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
723 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
724 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
725 for dataset in datasets]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
726 else:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
727 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
728 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
729 return HStackedIterator(self,iterators)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
730
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
731
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
732 def valuesVStack(self,fieldname,fieldvalues):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
733 return self.datasets[self.fieldname2dataset[fieldname]].valuesVStack(fieldname,fieldvalues)
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 valuesHStack(self,fieldnames,fieldvalues):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
736 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
737 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
738 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
739 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
740 all the fieldnames are of the same sub-dataset.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
741 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
742 return self.datasets[self.fieldname2dataset[fieldnames[0]]].valuesHStack(fieldnames,fieldvalues)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
743
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
744 class VStackedDataSet(DataSet):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
745 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
746 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
747 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
748 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
749
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
750 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
751 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
752 def __init__(self,datasets):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
753 self.datasets=datasets
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
754 self.length=0
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
755 self.index2dataset={}
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
756 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
757 fieldnames = datasets[-1].fieldNames()
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
758 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
759 # 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
760 # 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
761 for dataset,k in enumerate(datasets[0:-1]):
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
762 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
763 L=len(dataset)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
764 for i in xrange(L):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
765 self.index2dataset[self.length+i]=k
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
766 self.datasets_start_row.append(self.length)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
767 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
768 assert dataset.fieldNames()==fieldnames
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+=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
771 # 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
772 # 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
773 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
774 # 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
775 # TODO
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
776 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
777
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
778 def __len__(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
779 return self.length
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 fieldNames(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.datasets[0].fieldNames()
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 hasFields(self,*fieldnames):
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].hasFields(*fieldnames)
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
786
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
787 def locate_row(self,row):
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
788 """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
789 dataset_index = self.index2dataset[row]
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
790 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
791 return dataset_index, row_within_dataset
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
792
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
793 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
794
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
795 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
796 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
797 self.vsds=vsds
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
798 self.next_row=offset
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
799 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
800 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
801 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
802
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
803 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
804 L=len(dataset)
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
805 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
806 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
807 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
808 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
809 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
810 n_left_in_mb=minibatch_size-L
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
811 ds_nbatches=1
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
812 else:
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
813 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
814 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
815 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
816
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
817 def move_to_next_dataset(self):
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
818 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
819 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
820 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
821 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
822 else:
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
823 self.next_dataset_index +=1
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
824 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
825 self.next_dataset_index = 0
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
826 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
827 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
828
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
829 def __iter__(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
830 return self
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 next(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
833 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
834 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
835 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
836 extra_mb = []
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
837 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
838 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
839 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
840 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
841 [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
842 [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
843 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
844 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
845
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
846 self.next_row+=minibatch_size
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
847 self.next_dataset_row+=minibatch_size
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
848 if self.next_row+minibatch_size>len(dataset):
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
849 self.move_to_next_dataset()
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
850 return examples
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
851 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
852
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
853 class ArrayFieldsDataSet(DataSet):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
854 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
855 Virtual super-class of datasets whose field values are numpy array,
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
856 thus defining valuesHStack and valuesVStack for sub-classes.
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 def __init__(self,description=None,field_types=None):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
859 DataSet.__init__(self,description,field_types)
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
860 def valuesHStack(self,fieldnames,fieldvalues):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
861 """Concatenate field values horizontally, e.g. two vectors
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
862 become a longer vector, two matrices become a wider matrix, etc."""
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
863 return numpy.hstack(fieldvalues)
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
864 def valuesVStack(self,fieldname,values):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
865 """Concatenate field values vertically, e.g. two vectors
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
866 become a two-row matrix, two matrices become a longer matrix, etc."""
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
867 return numpy.vstack(values)
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
868
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
869 class ArrayDataSet(ArrayFieldsDataSet):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
870 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
871 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
872 whose first axis iterates over examples, second axis determines fields.
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
873 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
874 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
875 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
876
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
877 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
878 Construct an ArrayDataSet from the underlying numpy array (data) and
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
879 a map (fields_columns) from fieldnames to field columns. The columns of a field are specified
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
880 using the standard arguments for indexing/slicing: integer for a column index,
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
881 slice for an interval of columns (with possible stride), or iterable of column indices.
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
882 """
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
883 def __init__(self, data_array, fields_columns):
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
884 self.data=data_array
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
885 self.fields_columns=fields_columns
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
886
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
887 # check consistency and complete slices definitions
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
888 for fieldname, fieldcolumns in self.fields_columns.items():
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
889 if type(fieldcolumns) is int:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
890 assert fieldcolumns>=0 and fieldcolumns<data_array.shape[1]
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
891 elif type(fieldcolumns) is slice:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
892 start,step=None,None
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
893 if not fieldcolumns.start:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
894 start=0
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
895 if not fieldcolumns.step:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
896 step=1
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
897 if start or step:
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
898 self.fields_columns[fieldname]=slice(start,fieldcolumns.stop,step)
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
899 elif hasattr(fieldcolumns,"__iter__"): # something like a list
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
900 for i in fieldcolumns:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
901 assert i>=0 and i<data_array.shape[1]
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
902
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
903 def fieldNames(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
904 return self.fields_columns.keys()
41
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 __len__(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
907 return len(self.data)
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 __getitem__(self,i):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
910 # """More efficient implementation than the default"""
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
911
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
912 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
913 class ArrayDataSetIterator(object):
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
914 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
915 if fieldnames is None: fieldnames = dataset.fieldNames()
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
916 # 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
917 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
918 self.dataset=dataset
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
919 self.minibatch_size=minibatch_size
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
920 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
921 assert offset+minibatch_size<=len(dataset.data)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
922 self.current=offset
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
923 def __iter__(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
924 return self
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
925 def next(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
926 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
927 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
928 self.current+=self.minibatch_size
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
929 return self.minibatch
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
930
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
931 return ArrayDataSetIterator(self,fieldnames,minibatch_size,n_batches,offset)
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
932
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
933 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
934 """
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
935 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
936 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
937 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
938 """
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
939 args = ((input_fields,'input'),(output_fields,'target'))
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
940 if weight_field: args+=(([weight_field],'weight'))
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
941 return src_dataset.merge_fields(*args)
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
942
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
943
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
944
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
945