annotate dataset.py @ 318:e2eab74b6a28

NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
author Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
date Wed, 11 Jun 2008 16:59:03 -0400
parents 14081904d8f3
children 6441e568745e
rev   line source
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2 from lookup_list import LookupList as Example
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3 from misc import unique_elements_list_intersection
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4 from string import join
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5 from sys import maxint
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6 import numpy, copy
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8 from exceptions import *
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9
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10 class AttributesHolder(object):
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11 def __init__(self): pass
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12
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13 def attributeNames(self):
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14 raise AbstractFunction()
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15
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16 def setAttributes(self,attribute_names,attribute_values,make_copies=False):
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17 """
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18 Allow the attribute_values to not be a list (but a single value) if the attribute_names is of length 1.
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19 """
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20 if len(attribute_names)==1 and not (isinstance(attribute_values,list) or isinstance(attribute_values,tuple) ):
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21 attribute_values = [attribute_values]
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22 if make_copies:
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23 for name,value in zip(attribute_names,attribute_values):
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24 self.__setattr__(name,copy.deepcopy(value))
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25 else:
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26 for name,value in zip(attribute_names,attribute_values):
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27 self.__setattr__(name,value)
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29 def getAttributes(self,attribute_names=None, return_copy=False):
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30 """
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31 Return all (if attribute_names=None, in the order of attributeNames()) or a specified subset of attributes.
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32 """
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33 if attribute_names is None:
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34 attribute_names = self.attributeNames()
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35 if return_copy:
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36 return [copy.copy(self.__getattribute__(name)) for name in attribute_names]
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37 else:
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38 return [self.__getattribute__(name) for name in attribute_names]
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39
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40 class DataSet(AttributesHolder):
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41 """A virtual base class for datasets.
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42
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43 A DataSet can be seen as a generalization of a matrix, meant to be used in conjunction
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44 with learning algorithms (for training and testing them): rows/records are called examples, and
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45 columns/attributes are called fields. The field value for a particular example can be an arbitrary
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46 python object, which depends on the particular dataset.
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47
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48 We call a DataSet a 'stream' when its length is unbounded (in which case its __len__ method
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49 should return sys.maxint).
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50
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51 A DataSet is a generator of iterators; these iterators can run through the
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52 examples or the fields in a variety of ways. A DataSet need not necessarily have a finite
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53 or known length, so this class can be used to interface to a 'stream' which
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54 feeds on-line learning (however, as noted below, some operations are not
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55 feasible or not recommended on streams).
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56
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57 To iterate over examples, there are several possibilities:
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58 - for example in dataset:
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59 - for val1,val2,... in dataset:
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60 - for example in dataset(field1, field2,field3, ...):
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61 - for val1,val2,val3 in dataset(field1, field2,field3):
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62 - for minibatch in dataset.minibatches([field1, field2, ...],minibatch_size=N):
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63 - for mini1,mini2,mini3 in dataset.minibatches([field1, field2, field3], minibatch_size=N):
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64 Each of these is documented below. All of these iterators are expected
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65 to provide, in addition to the usual 'next()' method, a 'next_index()' method
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66 which returns a non-negative integer pointing to the position of the next
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67 example that will be returned by 'next()' (or of the first example in the
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68 next minibatch returned). This is important because these iterators
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69 can wrap around the dataset in order to do multiple passes through it,
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70 in possibly unregular ways if the minibatch size is not a divisor of the
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71 dataset length.
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73 To iterate over fields, one can do
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74 - for field in dataset.fields():
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75 for field_value in field: # iterate over the values associated to that field for all the dataset examples
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76 - for field in dataset(field1,field2,...).fields() to select a subset of fields
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77 - for field in dataset.fields(field1,field2,...) to select a subset of fields
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78 and each of these fields is iterable over the examples:
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79 - for field_examples in dataset.fields():
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80 for example_value in field_examples:
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81 ...
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82 but when the dataset is a stream (unbounded length), it is not recommended to do
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83 such things because the underlying dataset may refuse to access the different fields in
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84 an unsynchronized ways. Hence the fields() method is illegal for streams, by default.
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85 The result of fields() is a L{DataSetFields} object, which iterates over fields,
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86 and whose elements are iterable over examples. A DataSetFields object can
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87 be turned back into a DataSet with its examples() method::
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88 dataset2 = dataset1.fields().examples()
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89 and dataset2 should behave exactly like dataset1 (in fact by default dataset2==dataset1).
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90
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91 Note: Fields are not mutually exclusive, i.e. two fields can overlap in their actual content.
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92
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93 Note: The content of a field can be of any type. Field values can also be 'missing'
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94 (e.g. to handle semi-supervised learning), and in the case of numeric (numpy array)
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95 fields (i.e. an ArrayFieldsDataSet), NaN plays the role of a missing value.
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96 What about non-numeric values? None.
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97
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98 Dataset elements can be indexed and sub-datasets (with a subset
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99 of examples) can be extracted. These operations are not supported
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100 by default in the case of streams.
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101
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102 - dataset[:n] returns an Example with the n first examples.
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103
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104 - dataset[i1:i2:s] returns an Example with the examples i1,i1+s,...i2-s.
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105
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106 - dataset[i] returns an Example.
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107
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108 - dataset[[i1,i2,...in]] returns a. Example with examples i1,i2,...in.
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109
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110 A similar command gives you a DataSet instead of Examples :
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111
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112 - dataset.subset[:n] returns a DataSet with the n first examples.
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113
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114 - dataset.subset[i1:i2:s] returns a DataSet with the examples i1,i1+s,...i2-s.
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115
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116 - dataset.subset[i] returns a DataSet.
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117
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118 - dataset.subset[[i1,i2,...in]] returns a DataSet with examples i1,i2,...in.
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119
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120
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121 - dataset.<property> returns the value of a property associated with
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122 the name <property>. The following properties should be supported:
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123 - 'description': a textual description or name for the dataset
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124 - 'fieldtypes': a list of types (one per field)
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125 A DataSet may have other attributes that it makes visible to other objects. These are
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126 used to store information that is not example-wise but global to the dataset.
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127 The list of names of these attributes is given by the attribute_names() method.
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128
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129 Datasets can be concatenated either vertically (increasing the length) or
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130 horizontally (augmenting the set of fields), if they are compatible, using
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131 the following operations (with the same basic semantics as numpy.hstack
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132 and numpy.vstack):
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133
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134 - dataset1 | dataset2 | dataset3 == dataset.hstack([dataset1,dataset2,dataset3])
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135
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136 creates a new dataset whose list of fields is the concatenation of the list of
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137 fields of the argument datasets. This only works if they all have the same length.
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138
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139 - dataset1 & dataset2 & dataset3 == dataset.vstack([dataset1,dataset2,dataset3])
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140
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141 creates a new dataset that concatenates the examples from the argument datasets
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142 (and whose length is the sum of the length of the argument datasets). This only
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143 works if they all have the same fields.
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144
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145 According to the same logic, and viewing a DataSetFields object associated to
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146 a DataSet as a kind of transpose of it, fields1 & fields2 concatenates fields of
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147 a DataSetFields fields1 and fields2, and fields1 | fields2 concatenates their
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148 examples.
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149
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150 A dataset can hold arbitrary key-value pairs that may be used to access meta-data
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151 or other properties of the dataset or associated with the dataset or the result
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152 of a computation stored in a dataset. These can be accessed through the [key] syntax
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153 when key is a string (or more specifically, neither an integer, a slice, nor a list).
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154
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155 A DataSet sub-class should always redefine the following methods:
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156 - __len__ if it is not a stream
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157 - fieldNames
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158 - minibatches_nowrap (called by DataSet.minibatches())
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159 For efficiency of implementation, a sub-class might also want to redefine
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160 - valuesHStack
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161 - valuesVStack
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162 - hasFields
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163 - __getitem__ may not be feasible with some streams
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164 - __iter__
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165 A sub-class should also append attributes to self._attribute_names
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166 (the default value returned by attributeNames()).
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167 By convention, attributes not in attributeNames() should have a name
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168 starting with an underscore.
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169 @todo enforce/test that convention!
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170 """
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171
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172 numpy_vstack = lambda fieldname,values: numpy.vstack(values)
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173 numpy_hstack = lambda fieldnames,values: numpy.hstack(values)
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174
292
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175 def __init__(self, description=None, fieldnames=None, fieldtypes=None):
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176 """
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177 @type fieldnames: list of strings
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178 @type fieldtypes: list of python types, same length as fieldnames
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179 @type description: string
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180 @param description: description/name for this dataset
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181 """
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182 def default_desc():
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183 return type(self).__name__ \
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184 + " ( " + join([x.__name__ for x in type(self).__bases__]) + " )"
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185
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186 #self.fieldnames = fieldnames
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187
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188 self.fieldtypes = fieldtypes if fieldtypes is not None \
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189 else [None]*1 #len(fieldnames)
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190
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191 self.description = default_desc() if description is None \
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192 else description
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193 self._attribute_names = ["description"]
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194
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195 attributeNames = property(lambda self: copy.copy(self._attribute_names))
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196
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197 def __contains__(self, fieldname):
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198 return (fieldname in self.fieldNames()) \
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199 or (fieldname in self.attributeNames())
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200
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201 def __iter__(self):
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202 """Supports the syntax "for i in dataset: ..."
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203
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204 Using this syntax, "i" will be an Example instance (or equivalent) with
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205 all the fields of DataSet self. Every field of "i" will give access to
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206 a field of a single example. Fields should be accessible via
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207 i["fielname"] or i[3] (in the order defined by the elements of the
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208 Example returned by this iterator), but the derived class is free
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209 to accept any type of identifier, and add extra functionality to the iterator.
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210
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211 The default implementation calls the minibatches iterator and extracts the first example of each field.
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212 """
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213 return DataSet.MinibatchToSingleExampleIterator(self.minibatches(None, minibatch_size = 1))
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214
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215 def __len__(self):
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216 """
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217 len(dataset) returns the number of examples in the dataset.
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218 By default, a DataSet is a 'stream', i.e. it has an unbounded length (sys.maxint).
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219 Sub-classes which implement finite-length datasets should redefine this method.
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220 Some methods only make sense for finite-length datasets.
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221 """
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222 return None
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223
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224
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225 class MinibatchToSingleExampleIterator(object):
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226 """
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227 Converts the result of minibatch iterator with minibatch_size==1 into
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228 single-example values in the result. Therefore the result of
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229 iterating on the dataset itself gives a sequence of single examples
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230 (whereas the result of iterating over minibatches gives in each
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231 Example field an iterable object over the individual examples in
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232 the minibatch).
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233 """
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234 def __init__(self, minibatch_iterator):
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235 self.minibatch_iterator = minibatch_iterator
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236 self.minibatch = None
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237 def __iter__(self): #makes for loop work
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238 return self
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239 def next(self):
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240 size1_minibatch = self.minibatch_iterator.next()
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241 if not self.minibatch:
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242 self.minibatch = Example(size1_minibatch.keys(),[value[0] for value in size1_minibatch.values()])
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243 else:
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244 self.minibatch._values = [value[0] for value in size1_minibatch.values()]
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245 return self.minibatch
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246
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247 def next_index(self):
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248 return self.minibatch_iterator.next_index()
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249
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250 class MinibatchWrapAroundIterator(object):
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251 """
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252 An iterator for minibatches that handles the case where we need to wrap around the
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253 dataset because n_batches*minibatch_size > len(dataset). It is constructed from
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254 a dataset that provides a minibatch iterator that does not need to handle that problem.
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255 This class is a utility for dataset subclass writers, so that they do not have to handle
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256 this issue multiple times, nor check that fieldnames are valid, nor handle the
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257 empty fieldnames (meaning 'use all the fields').
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258 """
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259 def __init__(self,dataset,fieldnames,minibatch_size,n_batches,offset):
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260 self.dataset=dataset
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261 self.fieldnames=fieldnames
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262 self.minibatch_size=minibatch_size
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263 self.n_batches=n_batches
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264 self.n_batches_done=0
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265 self.next_row=offset
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266 self.L=len(dataset)
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267 self.offset=offset % self.L
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268 ds_nbatches = (self.L-self.next_row)/self.minibatch_size
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269 if n_batches is not None:
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270 ds_nbatches = min(n_batches,ds_nbatches)
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271 if fieldnames:
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272 assert dataset.hasFields(*fieldnames)
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273 else:
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274 self.fieldnames=dataset.fieldNames()
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275 self.iterator = self.dataset.minibatches_nowrap(self.fieldnames,self.minibatch_size, ds_nbatches,self.next_row)
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276
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277 def __iter__(self):
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278 return self
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279
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280 def next_index(self):
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281 return self.next_row
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282
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283 def next(self):
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284 if self.n_batches and self.n_batches_done==self.n_batches:
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285 raise StopIteration
101
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286 elif not self.n_batches and self.next_row ==self.L:
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287 raise StopIteration
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288 upper = self.next_row+self.minibatch_size
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289 if upper <=self.L:
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290 minibatch = self.iterator.next()
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291 else:
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292 if not self.n_batches:
101
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293 upper=min(upper, self.L)
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294 # if their is not a fixed number of batch, we continue to the end of the dataset.
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295 # this can create a minibatch that is smaller then the minibatch_size
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296 assert (self.L-self.next_row)<=self.minibatch_size
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297 minibatch = self.dataset.minibatches_nowrap(self.fieldnames,self.L-self.next_row,1,self.next_row).next()
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298 else:
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299 # we must concatenate (vstack) the bottom and top parts of our minibatch
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300 # first get the beginning of our minibatch (top of dataset)
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301 first_part = self.dataset.minibatches_nowrap(self.fieldnames,self.L-self.next_row,1,self.next_row).next()
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302 second_part = self.dataset.minibatches_nowrap(self.fieldnames,upper-self.L,1,0).next()
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diff changeset
303 minibatch = Example(self.fieldnames,
268
3f1cd8897fda reverting dataset
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304 [self.dataset.valuesVStack(name,[first_part[name],second_part[name]])
101
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parents: 99
diff changeset
305 for name in self.fieldnames])
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306 self.next_row=upper
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307 self.n_batches_done+=1
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diff changeset
308 if upper >= self.L and self.n_batches:
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diff changeset
309 self.next_row -= self.L
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310 ds_nbatches = (self.L-self.next_row)/self.minibatch_size
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311 if self.n_batches is not None:
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312 ds_nbatches = min(self.n_batches,ds_nbatches)
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313 self.iterator = self.dataset.minibatches_nowrap(self.fieldnames,self.minibatch_size,
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diff changeset
314 ds_nbatches,self.next_row)
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69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
315 return DataSetFields(MinibatchDataSet(minibatch,self.dataset.valuesVStack,
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diff changeset
316 self.dataset.valuesHStack),
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b4159cbdc06b Fixed errors raised by test_dataset
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parents: 73
diff changeset
317 minibatch.keys())
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318
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319
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320 minibatches_fieldnames = None
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321 minibatches_minibatch_size = 1
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322 minibatches_n_batches = None
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323 def minibatches(self,
37
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324 fieldnames = minibatches_fieldnames,
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325 minibatch_size = minibatches_minibatch_size,
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326 n_batches = minibatches_n_batches,
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diff changeset
327 offset = 0):
6
d5738b79089a Removed MinibatchIterator and instead made minibatch_size a field of all DataSets,
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328 """
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329 Return an iterator that supports three forms of syntax:
22
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330
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331 for i in dataset.minibatches(None,**kwargs): ...
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diff changeset
332
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333 for i in dataset.minibatches([f1, f2, f3],**kwargs): ...
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diff changeset
334
17
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335 for i1, i2, i3 in dataset.minibatches([f1, f2, f3],**kwargs): ...
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336
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337 Using the first two syntaxes, "i" will be an indexable object, such as a list,
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338 tuple, or Example instance. In both cases, i[k] is a list-like container
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339 of a batch of current examples. In the second case, i[0] is
17
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340 list-like container of the f1 field of a batch current examples, i[1] is
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341 a list-like container of the f2 field, etc.
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342
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343 Using the first syntax, all the fields will be returned in "i".
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344 Using the third syntax, i1, i2, i3 will be list-like containers of the
17
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345 f1, f2, and f3 fields of a batch of examples on each loop iteration.
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346
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347 The minibatches iterator is expected to return upon each call to next()
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
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diff changeset
348 a DataSetFields object, which is a Example (indexed by the field names) whose
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
349 elements are iterable and indexable over the minibatch examples, and which keeps a pointer to
36
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diff changeset
350 a sub-dataset that can be used to iterate over the individual examples
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diff changeset
351 in the minibatch. Hence a minibatch can be converted back to a regular
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352 dataset or its fields can be looked at individually (and possibly iterated over).
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353
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354 PARAMETERS
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355 - fieldnames (list of any type, default None):
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356 The loop variables i1, i2, i3 (in the example above) should contain the
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357 f1, f2, and f3 fields of the current batch of examples. If None, the
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358 derived class can choose a default, e.g. all fields.
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diff changeset
359
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360 - minibatch_size (integer, default 1)
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361 On every iteration, the variables i1, i2, i3 will have
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362 exactly minibatch_size elements. e.g. len(i1) == minibatch_size
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diff changeset
363
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364 - n_batches (integer, default None)
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365 The iterator will loop exactly this many times, and then stop. If None,
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366 the derived class can choose a default. If (-1), then the returned
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367 iterator should support looping indefinitely.
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diff changeset
368
37
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369 - offset (integer, default 0)
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370 The iterator will start at example 'offset' in the dataset, rather than the default.
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diff changeset
371
17
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diff changeset
372 Note: A list-like container is something like a tuple, list, numpy.ndarray or
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373 any other object that supports integer indexing and slicing.
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diff changeset
374
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375 """
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376 return DataSet.MinibatchWrapAroundIterator(self,fieldnames,minibatch_size,n_batches,offset)
37
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377
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378 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
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379 """
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diff changeset
380 This is the minibatches iterator generator that sub-classes must define.
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381 It does not need to worry about wrapping around multiple times across the dataset,
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diff changeset
382 as this is handled by MinibatchWrapAroundIterator when DataSet.minibatches() is called.
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383 The next() method of the returned iterator does not even need to worry about
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diff changeset
384 the termination condition (as StopIteration will be raised by DataSet.minibatches
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diff changeset
385 before an improper call to minibatches_nowrap's next() is made).
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diff changeset
386 That next() method can assert that its next row will always be within [0,len(dataset)).
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387 The iterator returned by minibatches_nowrap does not need to implement
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388 a next_index() method either, as this will be provided by MinibatchWrapAroundIterator.
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389 """
17
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390 raise AbstractFunction()
22
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diff changeset
391
48
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392 def is_unbounded(self):
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393 """
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394 Tests whether a dataset is unbounded (e.g. a stream).
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diff changeset
395 """
123
Frederic Bastien <bastienf@iro.umontreal.ca>
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diff changeset
396 return len(self)==maxint
36
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diff changeset
397
26
672fe4b23032 Fixed dataset errors so that _test_dataset.py works again.
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398 def hasFields(self,*fieldnames):
20
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parents: 19
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399 """
22
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400 Return true if the given field name (or field names, if multiple arguments are
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401 given) is recognized by the DataSet (i.e. can be used as a field name in one
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parents: 20
diff changeset
402 of the iterators).
29
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parents: 28
diff changeset
403
36
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404 The default implementation may be inefficient (O(# fields in dataset)), as it calls the fieldNames()
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parents: 29
diff changeset
405 method. Many datasets may store their field names in a dictionary, which would allow more efficiency.
11
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parents: 9
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406 """
36
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407 return len(unique_elements_list_intersection(fieldnames,self.fieldNames()))>0
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408
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409 def fieldNames(self):
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410 """
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411 Return the list of field names that are supported by the iterators,
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412 and for which hasFields(fieldname) would return True.
11
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parents: 9
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413 """
17
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parents: 16 12
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414 raise AbstractFunction()
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parents: 16 12
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415
36
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416 def __call__(self,*fieldnames):
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417 """
36
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418 Return a dataset that sees only the fields whose name are specified.
20
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419 """
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
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420 assert self.hasFields(*fieldnames)
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421 return self.fields(*fieldnames).examples()
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422
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423 def fields(self,*fieldnames):
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424 """
36
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425 Return a DataSetFields object associated with this dataset.
17
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426 """
74
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427 return DataSetFields(self,fieldnames)
11
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428
269
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429 def getitem_key(self, fieldname):
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430 """A not-so-well thought-out place to put code that used to be in
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431 getitem.
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432 """
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433 #removing as per discussion June 4. --JSB
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434
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435 i = fieldname
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436 # else check for a fieldname
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437 if self.hasFields(i):
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438 return self.minibatches(fieldnames=[i],minibatch_size=len(self),n_batches=1,offset=0).next()[0]
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439 # else we are trying to access a property of the dataset
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440 assert i in self.__dict__ # else it means we are trying to access a non-existing property
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441 return self.__dict__[i]
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442
2
3fddb1c8f955 Rewrote DataSet interface and created FiniteDataSet interface.
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443 def __getitem__(self,i):
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444 """
290
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445 @rtype: Example
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446 @returns: single or multiple examples
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447
290
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448 @type i: integer or slice or <iterable> of integers
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449 @param i:
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450 dataset[i] returns the (i+1)-th example of the dataset.
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451 dataset[i:j] returns a LookupList with examples i,i+1,...,j-1.
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452 dataset[i:j:s] returns a LookupList with examples i,i+2,i+4...,j-2.
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453 dataset[[i1,i2,..,in]] returns a LookupList with examples i1,i2,...,in.
290
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454
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455 @note:
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456 Some stream datasets may be unable to implement random access, i.e.
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457 arbitrary slicing/indexing because they can only iterate through
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458 examples one or a minibatch at a time and do not actually store or keep
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459 past (or future) examples.
40
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parents: 39
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460
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461 The default implementation of getitem uses the minibatches iterator
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462 to obtain one example, one slice, or a list of examples. It may not
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463 always be the most efficient way to obtain the result, especially if
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464 the data are actually stored in a memory array.
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465 """
290
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466
40
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467 if type(i) is int:
309
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468 assert i >= 0 # TBM: see if someone complains and want negative i
313
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469 if i >= len(self) :
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470 raise IndexError
290
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471 i_batch = self.minibatches_nowrap(self.fieldNames(),
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472 minibatch_size=1, n_batches=1, offset=i)
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473 return DataSet.MinibatchToSingleExampleIterator(i_batch).next()
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474
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475 #if i is a contiguous slice
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476 if type(i) is slice and (i.step in (None, 1)):
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477 offset = 0 if i.start is None else i.start
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478 upper_bound = len(self) if i.stop is None else i.stop
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479 upper_bound = min(len(self) , upper_bound)
309
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480 #return MinibatchDataSet(self.minibatches_nowrap(self.fieldNames(),
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481 # minibatch_size=upper_bound - offset,
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482 # n_batches=1,
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483 # offset=offset).next())
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484 # now returns a LookupList
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485 return self.minibatches_nowrap(self.fieldNames(),
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486 minibatch_size=upper_bound - offset,
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487 n_batches=1,
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488 offset=offset).next()
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489
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490 # if slice has a step param, convert it to list and handle it with the
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491 # list code
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492 if type(i) is slice:
290
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493 offset = 0 if i.start is None else i.start
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494 upper_bound = len(self) if i.stop is None else i.stop
314
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495 upper_bound = min(len(self) , upper_bound)
290
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496 i = list(range(offset, upper_bound, i.step))
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497
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498 # handle tuples, arrays, lists
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499 if hasattr(i, '__getitem__'):
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500 for idx in i:
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501 #dis-allow nested slices
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502 if not isinstance(idx, int):
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503 raise TypeError(idx)
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504 if idx >= len(self) :
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505 raise IndexError
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506 # call back into self.__getitem__
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507 examples = [self.minibatches_nowrap(self.fieldNames(),
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508 minibatch_size=1, n_batches=1, offset=ii).next()
290
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509 for ii in i]
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510 # re-index the fields in each example by field instead of by example
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511 field_values = [[] for blah in self.fieldNames()]
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512 for e in examples:
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513 for f,v in zip(field_values, e):
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514 f.append(v)
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515 #build them into a LookupList (a.ka. Example)
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516 zz = zip(self.fieldNames(),field_values)
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517 vst = [self.valuesVStack(fieldname,field_values) for fieldname,field_values in zz]
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518 example = Example(self.fieldNames(), vst)
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519 #return MinibatchDataSet(example, self.valuesVStack, self.valuesHStack)
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520 # now returns a LookupList
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521 return example
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522
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523 # what in the world is i?
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diff changeset
524 raise TypeError(i, type(i))
22
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
525
310
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
526
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
527 """
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Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
528 Enables the call dataset.subset[a:b:c] that will return a DataSet
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
529 around the examples returned by __getitem__(slice(a,b,c))
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
530
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
531 @SEE DataSet.__getsubset(self)
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
532 """
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
533 subset = property(lambda s : s.__getsubset(),doc="returns a subset as a DataSet")
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
534
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
535
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
536 def __getsubset(self) :
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
537 """
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
538 Enables the call data.subset[a:b:c], returns a DataSet.
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
539 Default implementation is a simple wrap around __getitem__() using MinibatchDataSet.
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
540
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
541 @RETURN DataSet
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
542 @SEE DataSet.subset = property(lambda s : s.__getsubset())
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
543 """
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
544 _self = self
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
545 class GetSliceReturnsDataSet(object) :
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
546 def __getitem__(self,slice) :
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
547 return MinibatchDataSet(_self.__getitem__(slice))
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
548 return GetSliceReturnsDataSet()
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
549
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
550
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
551
36
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parents: 29
diff changeset
552 def valuesHStack(self,fieldnames,fieldvalues):
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parents: 29
diff changeset
553 """
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parents: 29
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554 Return a value that corresponds to concatenating (horizontally) several field values.
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parents: 29
diff changeset
555 This can be useful to merge some fields. The implementation of this operation is likely
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
556 to involve a copy of the original values. When the values are numpy arrays, the
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parents: 29
diff changeset
557 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
558 work as well when each value corresponds to multiple examples in a minibatch
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
559 e.g. if each value is a Ni-vector and a minibatch of length L is a LxNi matrix,
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parents: 29
diff changeset
560 then the result should be a Lx(N1+N2+..) matrix equal to numpy.hstack(values).
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parents: 29
diff changeset
561 The default is to use numpy.hstack for numpy.ndarray values, and a list
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parents: 29
diff changeset
562 pointing to the original values for other data types.
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bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
563 """
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parents: 29
diff changeset
564 all_numpy=True
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parents: 29
diff changeset
565 for value in fieldvalues:
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parents: 29
diff changeset
566 if not type(value) is numpy.ndarray:
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diff changeset
567 all_numpy=False
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diff changeset
568 if all_numpy:
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
569 return numpy.hstack(fieldvalues)
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parents: 29
diff changeset
570 # the default implementation of horizontal stacking is to put values in a list
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parents: 29
diff changeset
571 return fieldvalues
26
672fe4b23032 Fixed dataset errors so that _test_dataset.py works again.
bengioy@grenat.iro.umontreal.ca
parents: 23
diff changeset
572
36
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parents: 29
diff changeset
573 def valuesVStack(self,fieldname,values):
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parents: 29
diff changeset
574 """
290
9b533cc7874a trying to get default implemenations to work
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diff changeset
575 @param fieldname: the name of the field from which the values were taken
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James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
576 @type fieldname: any type
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
577
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
578 @param values: bits near the beginning or end of the dataset
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
579 @type values: list of minibatches (returned by minibatch_nowrap)
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James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
580
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
581 @return: the concatenation (stacking) of the values
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
582 @rtype: something suitable as a minibatch field
36
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diff changeset
583 """
290
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
584 rval = []
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James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
585 for v in values:
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
586 rval.extend(v)
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
587 return rval
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
588
36
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diff changeset
589 def __or__(self,other):
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bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
590 """
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parents: 29
diff changeset
591 dataset1 | dataset2 returns a dataset whose list of fields is the concatenation of the list of
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bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
592 fields of the argument datasets. This only works if they all have the same length.
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bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
593 """
135
0d8e721cc63c Fixed bugs in dataset to make test_mlp.py work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 134
diff changeset
594 return HStackedDataSet([self,other])
3
378b68d5c4ad Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents: 2
diff changeset
595
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
596 def __and__(self,other):
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
597 """
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
598 dataset1 & dataset2 is a dataset that concatenates the examples from the argument datasets
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
599 (and whose length is the sum of the length of the argument datasets). This only
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
600 works if they all have the same fields.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
601 """
135
0d8e721cc63c Fixed bugs in dataset to make test_mlp.py work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 134
diff changeset
602 return VStackedDataSet([self,other])
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
603
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
604 def hstack(datasets):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
605 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
606 hstack(dataset1,dataset2,...) returns dataset1 | datataset2 | ...
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
607 which is a dataset whose fields list is the concatenation of the fields
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
608 of the individual datasets.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
609 """
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bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
610 assert len(datasets)>0
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bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
611 if len(datasets)==1:
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
612 return datasets[0]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
613 return HStackedDataSet(datasets)
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
614
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
615 def vstack(datasets):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
616 """
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
617 vstack(dataset1,dataset2,...) returns dataset1 & datataset2 & ...
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
618 which is a dataset which iterates first over the examples of dataset1, then
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bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
619 over those of dataset2, etc.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
620 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
621 assert len(datasets)>0
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parents: 29
diff changeset
622 if len(datasets)==1:
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bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
623 return datasets[0]
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bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
624 return VStackedDataSet(datasets)
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
625
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
626 class FieldsSubsetDataSet(DataSet):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
627 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
628 A sub-class of L{DataSet} that selects a subset of the fields.
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
629 """
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
630 def __init__(self,src,fieldnames):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
631 self.src=src
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
632 self.fieldnames=fieldnames
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
633 assert src.hasFields(*fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
634 self.valuesHStack = src.valuesHStack
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
635 self.valuesVStack = src.valuesVStack
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
636
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
637 def __len__(self): return len(self.src)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
638
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
639 def fieldNames(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
640 return self.fieldnames
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
641
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
642 def __iter__(self):
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
643 class FieldsSubsetIterator(object):
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
644 def __init__(self,ds):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
645 self.ds=ds
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
646 self.src_iter=ds.src.__iter__()
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
647 self.example=None
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
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diff changeset
648 def __iter__(self): return self
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
649 def next(self):
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
650 complete_example = self.src_iter.next()
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
651 if self.example:
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bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
652 self.example._values=[complete_example[field]
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
653 for field in self.ds.fieldnames]
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
654 else:
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
655 self.example=Example(self.ds.fieldnames,
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
656 [complete_example[field] for field in self.ds.fieldnames])
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
657 return self.example
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
658 return FieldsSubsetIterator(self)
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
659
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
660 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
661 assert self.hasFields(*fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
662 return self.src.minibatches_nowrap(fieldnames,minibatch_size,n_batches,offset)
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
663 def dontuse__getitem__(self,i):
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
664 return FieldsSubsetDataSet(self.src[i],self.fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
665
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
666
290
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diff changeset
667 class DataSetFields(Example):
36
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diff changeset
668 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
669 Although a L{DataSet} iterates over examples (like rows of a matrix), an associated
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
670 DataSetFields iterates over fields (like columns of a matrix), and can be understood
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
671 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
672
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
673 To iterate over fields, one can do
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
674 * for fields in dataset.fields()
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
675 * for fields in dataset(field1,field2,...).fields() to select a subset of fields
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
676 * for fields in dataset.fields(field1,field2,...) to select a subset of fields
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
677 and each of these fields is iterable over the examples:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
678 * for field_examples in dataset.fields():
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
679 for example_value in field_examples:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
680 ...
241
ddb88a8e9fd2 If I understand properly, the length of an unbounded stream is sys.maxint
delallea@opale.iro.umontreal.ca
parents: 231
diff changeset
681 but when the dataset is a stream (unbounded length), it is not recommended to do
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
682 such things because the underlying dataset may refuse to access the different fields in
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
683 an unsynchronized ways. Hence the fields() method is illegal for streams, by default.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
684 The result of fields() is a DataSetFields object, which iterates over fields,
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
685 and whose elements are iterable over examples. A DataSetFields object can
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
686 be turned back into a DataSet with its examples() method:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
687 dataset2 = dataset1.fields().examples()
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
688 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
689
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
690 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
691 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
692 the examples.
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
693 """
74
b4159cbdc06b Fixed errors raised by test_dataset
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 73
diff changeset
694 def __init__(self,dataset,fieldnames):
65
d48eba49a2f4 fixed the infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 64
diff changeset
695 original_dataset=dataset
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
696 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
697 fieldnames=dataset.fieldNames()
274
ed70580f2324 bugfix in FieldSubsetDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 273
diff changeset
698 elif not list(fieldnames)==list(dataset.fieldNames()):
ed70580f2324 bugfix in FieldSubsetDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 273
diff changeset
699 #we must cast to list, othersize('x','y')!=['x','y']
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
700 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
701 assert dataset.hasFields(*fieldnames)
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
702 self.dataset=dataset
66
dde1fb1b63ba fixed test and removed print
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 65
diff changeset
703
64
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
704 if isinstance(dataset,MinibatchDataSet):
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
705 Example.__init__(self,fieldnames,list(dataset._fields))
65
d48eba49a2f4 fixed the infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 64
diff changeset
706 elif isinstance(original_dataset,MinibatchDataSet):
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
707 Example.__init__(self,fieldnames,
65
d48eba49a2f4 fixed the infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 64
diff changeset
708 [original_dataset._fields[field]
d48eba49a2f4 fixed the infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 64
diff changeset
709 for field in fieldnames])
64
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
710 else:
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
711 minibatch_iterator = dataset.minibatches(fieldnames,
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
712 minibatch_size=len(dataset),
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
713 n_batches=1)
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
714 minibatch=minibatch_iterator.next()
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
715 Example.__init__(self,fieldnames,minibatch)
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
716
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
717 def examples(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
718 return self.dataset
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
719
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
720 def __or__(self,other):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
721 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
722 fields1 | fields2 is a DataSetFields that whose list of examples is the concatenation
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
723 of the list of examples of DataSetFields fields1 and fields2.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
724 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
725 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
726
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
727 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
728 """
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
729 fields1 + fields2 is a DataSetFields that whose list of fields is the concatenation
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
730 of the fields of DataSetFields fields1 and fields2.
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 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
733
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
734
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
735 class MinibatchDataSet(DataSet):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
736 """
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
737 Turn a L{Example} of same-length (iterable) fields into an example-iterable dataset.
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
738 Each element of the lookup-list should be an iterable and sliceable, all of the same length.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
739 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
740 def __init__(self,fields_lookuplist,values_vstack=DataSet().valuesVStack,
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
741 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
742 """
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
743 The user can (and generally should) also provide values_vstack(fieldname,fieldvalues)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
744 and a values_hstack(fieldnames,fieldvalues) functions behaving with the same
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
745 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
746 """
211
bd728c83faff in __get__, problem if the i.stop was None, i being the slice, added one line replacing None by the len(self)
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 203
diff changeset
747
61
a8b70a9117ad bugfix: in MinibatchDataSet renamed the class variable fields to _fields as parent class have a function called field.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 60
diff changeset
748 self._fields=fields_lookuplist
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
749 assert len(fields_lookuplist)>0
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
750 self.length=len(fields_lookuplist[0])
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
751 for field in fields_lookuplist[1:]:
223
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
752 if self.length != len(field) :
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
753 print 'self.length = ',self.length
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
754 print 'len(field) = ', len(field)
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
755 print 'self._fields.keys() = ', self._fields.keys()
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
756 print 'field=',field
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
757 print 'fields_lookuplist=', fields_lookuplist
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
758 assert self.length==len(field)
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
759 self.valuesVStack=values_vstack
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
760 self.valuesHStack=values_hstack
3
378b68d5c4ad Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents: 2
diff changeset
761
378b68d5c4ad Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents: 2
diff changeset
762 def __len__(self):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
763 return self.length
28
541a273bc89f Removed __array__ method from dataset, whose
bengioy@grenat.iro.umontreal.ca
parents: 26
diff changeset
764
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
765 def dontuse__getitem__(self,i):
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
766 if type(i) in (slice,list):
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
767 return DataSetFields(MinibatchDataSet(
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
768 Example(self._fields.keys(),[field[i] for field in self._fields])),self.fieldNames())
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
769 if type(i) is int:
85
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 83
diff changeset
770 return Example(self._fields.keys(),[field[i] for field in self._fields])
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
771 if self.hasFields(i):
61
a8b70a9117ad bugfix: in MinibatchDataSet renamed the class variable fields to _fields as parent class have a function called field.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 60
diff changeset
772 return self._fields[i]
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
773 assert i in self.__dict__ # else it means we are trying to access a non-existing property
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
774 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
775
29
46c5c90019c2 Changed apply_function so that it propagates methods of the source.
bengioy@grenat.iro.umontreal.ca
parents: 28
diff changeset
776 def fieldNames(self):
61
a8b70a9117ad bugfix: in MinibatchDataSet renamed the class variable fields to _fields as parent class have a function called field.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 60
diff changeset
777 return self._fields.keys()
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
778
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
779 def hasFields(self,*fieldnames):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
780 for fieldname in fieldnames:
61
a8b70a9117ad bugfix: in MinibatchDataSet renamed the class variable fields to _fields as parent class have a function called field.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 60
diff changeset
781 if fieldname not in self._fields.keys():
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
782 return False
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
783 return True
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
784
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
785 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
223
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
786 #@TODO bug somewhere here, fieldnames doesnt seem to be well handled
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
787 class Iterator(object):
223
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
788 def __init__(self,ds,fieldnames):
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
789 # tbm: added two next lines to handle fieldnames
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
790 if fieldnames is None: fieldnames = ds._fields.keys()
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
791 self.fieldnames = fieldnames
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
792
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
793 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
794 self.next_example=offset
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
795 assert minibatch_size >= 0
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
796 if offset+minibatch_size > ds.length:
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
797 raise NotImplementedError()
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
798 def __iter__(self):
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
799 return self
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
800 def next(self):
61
a8b70a9117ad bugfix: in MinibatchDataSet renamed the class variable fields to _fields as parent class have a function called field.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 60
diff changeset
801 upper = self.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
802 assert upper<=self.ds.length
223
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
803 #minibatch = Example(self.ds._fields.keys(),
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
804 # [field[self.next_example:upper]
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
805 # for field in self.ds._fields])
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
806 # tbm: modif to use fieldnames
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
807 values = []
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
808 for f in self.fieldnames :
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
809 #print 'we have field',f,'in fieldnames'
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
810 values.append( self.ds._fields[f][self.next_example:upper] )
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
811 minibatch = Example(self.fieldnames,values)
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
812 #print minibatch
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
813 self.next_example+=minibatch_size
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
814 return minibatch
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
815
223
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
816 # tbm: added fieldnames to handle subset of fieldnames
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
817 return Iterator(self,fieldnames)
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
818
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
819 class HStackedDataSet(DataSet):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
820 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
821 A L{DataSet} that wraps several datasets and shows a view that includes all their fields,
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
822 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
823
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
824 If a field name is found in more than one of the datasets, then either an error is
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
825 raised or the fields are renamed (either by prefixing the __name__ attribute
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
826 of the dataset + ".", if it exists, or by suffixing the dataset index in the argument list).
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
827
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
828 @todo: automatically detect a chain of stacked datasets due to A | B | C | D ...
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
829 """
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
830 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
831 DataSet.__init__(self,description,field_types)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
832 self.datasets=datasets
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
833 self.accept_nonunique_names=accept_nonunique_names
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
834 self.fieldname2dataset={}
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
835
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
836 def rename_field(fieldname,dataset,i):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
837 if hasattr(dataset,"__name__"):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
838 return dataset.__name__ + "." + fieldname
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
839 return fieldname+"."+str(i)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
840
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
841 # make sure all datasets have the same length and unique field names
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
842 self.length=None
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
843 names_to_change=[]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
844 for i in xrange(len(datasets)):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
845 dataset = datasets[i]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
846 length=len(dataset)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
847 if self.length:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
848 assert self.length==length
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
849 else:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
850 self.length=length
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
851 for fieldname in dataset.fieldNames():
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
852 if fieldname in self.fieldname2dataset: # name conflict!
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
853 if accept_nonunique_names:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
854 fieldname=rename_field(fieldname,dataset,i)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
855 names2change.append((fieldname,i))
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
856 else:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
857 raise ValueError("Incompatible datasets: non-unique field name = "+fieldname)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
858 self.fieldname2dataset[fieldname]=i
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
859 for fieldname,i in names_to_change:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
860 del self.fieldname2dataset[fieldname]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
861 self.fieldname2dataset[rename_field(fieldname,self.datasets[i],i)]=i
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
862
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
863 def hasFields(self,*fieldnames):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
864 for fieldname in fieldnames:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
865 if not fieldname in self.fieldname2dataset:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
866 return False
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
867 return True
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
868
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
869 def fieldNames(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
870 return self.fieldname2dataset.keys()
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
871
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
872 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
873
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
874 class HStackedIterator(object):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
875 def __init__(self,hsds,iterators):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
876 self.hsds=hsds
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
877 self.iterators=iterators
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
878 def __iter__(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
879 return self
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
880 def next(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
881 # concatenate all the fields of the minibatches
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
882 l=Example()
140
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 136
diff changeset
883 for iter in self.iterators:
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 136
diff changeset
884 l.append_lookuplist(iter.next())
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 136
diff changeset
885 return l
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
886
125
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 123
diff changeset
887 assert self.hasFields(*fieldnames)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
888 # 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
889 # and construct corresponding minibatch iterators
140
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 136
diff changeset
890 if fieldnames and fieldnames!=self.fieldNames():
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
891 datasets=set([])
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
892 fields_in_dataset=dict([(dataset,[]) for dataset in datasets])
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
893 for fieldname in fieldnames:
136
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 125
diff changeset
894 dataset=self.datasets[self.fieldname2dataset[fieldname]]
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
895 datasets.add(dataset)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
896 fields_in_dataset[dataset].append(fieldname)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
897 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
898 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
899 for dataset in datasets]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
900 else:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
901 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
902 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
903 return HStackedIterator(self,iterators)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
904
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
905
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
906 def untested_valuesVStack(self,fieldname,fieldvalues):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
907 return self.datasets[self.fieldname2dataset[fieldname]].valuesVStack(fieldname,fieldvalues)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
908
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
909 def untested_valuesHStack(self,fieldnames,fieldvalues):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
910 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
911 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
912 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
913 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
914 all the fieldnames are of the same sub-dataset.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
915 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
916 return self.datasets[self.fieldname2dataset[fieldnames[0]]].valuesHStack(fieldnames,fieldvalues)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
917
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
918 class VStackedDataSet(DataSet):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
919 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
920 A L{DataSet} that wraps several datasets and shows a view that includes all their examples,
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
921 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
922 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
923
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
924 @todo: automatically detect a chain of stacked datasets due to A + B + C + D ...
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
925 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
926 def __init__(self,datasets):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
927 self.datasets=datasets
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
928 self.length=0
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
929 self.index2dataset={}
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
930 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
931 fieldnames = datasets[-1].fieldNames()
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
932 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
933 # 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
934 # 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
935 for dataset,k in enumerate(datasets[0:-1]):
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
936 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
937 L=len(dataset)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
938 for i in xrange(L):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
939 self.index2dataset[self.length+i]=k
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
940 self.datasets_start_row.append(self.length)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
941 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
942 assert dataset.fieldNames()==fieldnames
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
943 self.datasets_start_row.append(self.length)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
944 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
945 # 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
946 # 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
947 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
948 # 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
949 # TODO
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
950 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
951
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
952 def __len__(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
953 return self.length
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
954
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
955 def fieldNames(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
956 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
957
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
958 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
959 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
960
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
961 def locate_row(self,row):
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
962 """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
963 dataset_index = self.index2dataset[row]
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
964 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
965 return dataset_index, row_within_dataset
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
966
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
967 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
968
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
969 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
970 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
971 self.vsds=vsds
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
972 self.next_row=offset
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
973 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
974 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
975 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
976
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
977 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
978 L=len(dataset)
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
979 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
980 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
981 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
982 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
983 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
984 n_left_in_mb=minibatch_size-L
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
985 ds_nbatches=1
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
986 else:
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
987 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
988 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
989 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
990
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
991 def move_to_next_dataset(self):
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
992 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
993 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
994 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
995 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
996 else:
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
997 self.next_dataset_index +=1
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
998 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
999 self.next_dataset_index = 0
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1000 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
1001 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
1002
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1003 def __iter__(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1004 return self
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1005
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1006 def next(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1007 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
1008 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
1009 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
1010 extra_mb = []
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1011 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
1012 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
1013 extra_mb.append(self.next_iterator.next())
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1014 mb = Example(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
1015 [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
1016 [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
1017 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
1018
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1019 self.next_row+=minibatch_size
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1020 self.next_dataset_row+=minibatch_size
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1021 if self.next_row+minibatch_size>len(dataset):
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1022 self.move_to_next_dataset()
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
1023 return examples
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
1024 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
1025
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1026 class ArrayFieldsDataSet(DataSet):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1027 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1028 Virtual super-class of datasets whose field values are numpy array,
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1029 thus defining valuesHStack and valuesVStack for sub-classes.
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1030 """
268
3f1cd8897fda reverting dataset
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 266
diff changeset
1031 def __init__(self,description=None,field_types=None):
3f1cd8897fda reverting dataset
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 266
diff changeset
1032 DataSet.__init__(self,description,field_types)
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1033 def untested_valuesHStack(self,fieldnames,fieldvalues):
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1034 """Concatenate field values horizontally, e.g. two vectors
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1035 become a longer vector, two matrices become a wider matrix, etc."""
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1036 return numpy.hstack(fieldvalues)
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1037 def untested_valuesVStack(self,fieldname,values):
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1038 """Concatenate field values vertically, e.g. two vectors
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1039 become a two-row matrix, two matrices become a longer matrix, etc."""
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1040 return numpy.vstack(values)
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1041
316
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1042
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1043
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1044 class NArraysDataSet(ArrayFieldsDataSet) :
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1045 """
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1046 An NArraysDataSet stores fields that are numpy tensor, whose first axis
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1047 iterates over examples. It's a generalization of ArrayDataSet.
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1048 """
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1049 #@TODO not completely implemented yet
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1050 def __init__(self, data_arrays, fieldnames, **kwargs) :
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1051 """
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1052 Construct an NArraysDataSet from a list of numpy tensor (data_arrays) and a list
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1053 of fieldnames. The number of arrays must be the same as the number of
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1054 fieldnames. Each set of numpy tensor must have the same first dimension (first
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1055 axis) corresponding to the number of examples.
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1056
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1057 Every tensor is treated as a numpy matrix (using numpy.asmatrix)
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1058 """
318
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1059 ArrayFieldsDataSet.__init__(self,**kwargs)
316
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1060 assert len(data_arrays) == len(fieldnames)
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1061 assert len(fieldnames) > 0
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1062 num_examples = numpy.asmatrix(data_arrays[0]).shape[0]
318
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1063 for k in range(len(data_arrays)) :
316
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1064 assert numpy.asmatrix(data_arrays[k]).shape[0] == num_examples
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1065 self._fieldnames = fieldnames
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1066 self._datas = []
318
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1067 for k in range(len(data_arrays)) :
316
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1068 self._datas.append( numpy.asmatrix(data_arrays[k]) )
318
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1069 #raise NotImplemented
316
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1070
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1071
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1072 def __len__(self) :
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1073 """
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1074 Length of the dataset is based on the first array = data_arrays[0], using its shape
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1075 """
318
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1076 return self._datas[0].shape[0]
316
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1077
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1078 def fieldNames(self) :
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1079 """
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1080 Returns the fieldnames as set in self.__init__
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1081 """
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1082 return self._fieldnames
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1083
318
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1084 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1085 cursor = Example(fieldnames,[0]*len(fieldnames))
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1086 fieldnames = self.fieldNames() if fieldnames is None else fieldnames
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1087 for n in xrange(n_batches):
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1088 if offset == len(self):
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1089 break
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1090 for f in range(len(cursor._names)) :
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1091 idx = self._fieldnames.index(cursor._names[f])
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1092 assert idx >= 0
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1093 sub_data = self._datas[f][offset : offset+minibatch_size]
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1094 cursor._values[f] = sub_data
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1095 offset += len(sub_data) #can be less than minibatch_size at end
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1096 yield cursor
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1097
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1098 #return ArrayDataSetIterator(self,fieldnames,minibatch_size,n_batches,offset)
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1099
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1100
316
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1101
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1102
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1103 class ArrayDataSet(ArrayFieldsDataSet):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1104 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1105 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
1106 whose first axis iterates over examples, second axis determines fields.
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1107 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
1108 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
1109 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1110
188
f01ac276c6fb added __contains__ to Dataset, added parent constructor call to ArrayDataSet
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 171
diff changeset
1111 def __init__(self, data_array, fields_columns, **kwargs):
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1112 """
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1113 Construct an ArrayDataSet from the underlying numpy array (data) and
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1114 a map (fields_columns) from fieldnames to field columns. The columns of a field are specified
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1115 using the standard arguments for indexing/slicing: integer for a column index,
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1116 slice for an interval of columns (with possible stride), or iterable of column indices.
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1117 """
188
f01ac276c6fb added __contains__ to Dataset, added parent constructor call to ArrayDataSet
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 171
diff changeset
1118 ArrayFieldsDataSet.__init__(self, **kwargs)
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1119 self.data=data_array
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1120 self.fields_columns=fields_columns
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1121
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1122 # check consistency and complete slices definitions
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1123 for fieldname, fieldcolumns in self.fields_columns.items():
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1124 if type(fieldcolumns) is int:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1125 assert fieldcolumns>=0 and fieldcolumns<data_array.shape[1]
268
3f1cd8897fda reverting dataset
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 266
diff changeset
1126 if 1:
227
17c5d080964b reinstating changeset 216 clobbered accidentally by 218
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 223
diff changeset
1127 #I changed this because it didn't make sense to me,
17c5d080964b reinstating changeset 216 clobbered accidentally by 218
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 223
diff changeset
1128 # and it made it more difficult to write my learner.
17c5d080964b reinstating changeset 216 clobbered accidentally by 218
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 223
diff changeset
1129 # If it breaks stuff, let's talk about it.
17c5d080964b reinstating changeset 216 clobbered accidentally by 218
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 223
diff changeset
1130 # - James 22/05/2008
17c5d080964b reinstating changeset 216 clobbered accidentally by 218
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 223
diff changeset
1131 self.fields_columns[fieldname]=[fieldcolumns]
17c5d080964b reinstating changeset 216 clobbered accidentally by 218
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 223
diff changeset
1132 else:
17c5d080964b reinstating changeset 216 clobbered accidentally by 218
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 223
diff changeset
1133 self.fields_columns[fieldname]=fieldcolumns
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1134 elif type(fieldcolumns) is slice:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1135 start,step=None,None
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1136 if not fieldcolumns.start:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1137 start=0
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1138 if not fieldcolumns.step:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1139 step=1
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1140 if start or step:
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1141 self.fields_columns[fieldname]=slice(start,fieldcolumns.stop,step)
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1142 elif hasattr(fieldcolumns,"__iter__"): # something like a list
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1143 for i in fieldcolumns:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1144 assert i>=0 and i<data_array.shape[1]
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1145
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1146 def fieldNames(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1147 return self.fields_columns.keys()
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1148
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1149 def __len__(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1150 return len(self.data)
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1151
316
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1152 def __getitem__(self,key):
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1153 """More efficient implementation than the default __getitem__"""
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1154 fieldnames=self.fields_columns.keys()
243
c8f19a9eb10f Optimisation in ArrayDataSet::__getitem__
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 242
diff changeset
1155 values=self.fields_columns.values()
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1156 if type(key) is int:
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1157 return Example(fieldnames,
243
c8f19a9eb10f Optimisation in ArrayDataSet::__getitem__
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 242
diff changeset
1158 [self.data[key,col] for col in values])
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1159 if type(key) is slice:
316
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1160 return Example(fieldnames,[self.data[key,col] for col in values])
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1161 if type(key) is list:
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1162 for i in range(len(key)):
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1163 if self.hasFields(key[i]):
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1164 key[i]=self.fields_columns[key[i]]
316
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1165 return Example(fieldnames,
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1166 #we must separate differently for list as numpy
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1167 # doesn't support self.data[[i1,...],[i2,...]]
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1168 # when their is more then two i1 and i2
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1169 [self.data[key,:][:,col]
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1170 if isinstance(col,list) else
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1171 self.data[key,col] for col in values])
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1172
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1173 # else check for a fieldname
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1174 if self.hasFields(key):
105
8c0a1b11b007 bugfix, we keep all the line, but only a some columns
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 101
diff changeset
1175 return self.data[:,self.fields_columns[key]]
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1176 # else we are trying to access a property of the dataset
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1177 assert key in self.__dict__ # else it means we are trying to access a non-existing property
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1178 return self.__dict__[key]
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1179
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1180 def dontuse__iter__(self):
270
1cafd495098c code cleanup and small optimisation
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 254
diff changeset
1181 class ArrayDataSetIteratorIter(object):
1cafd495098c code cleanup and small optimisation
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 254
diff changeset
1182 def __init__(self,dataset,fieldnames):
228
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1183 if fieldnames is None: fieldnames = dataset.fieldNames()
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1184 # store the resulting minibatch in a lookup-list of values
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1185 self.minibatch = Example(fieldnames,[0]*len(fieldnames))
228
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1186 self.dataset=dataset
270
1cafd495098c code cleanup and small optimisation
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 254
diff changeset
1187 self.current=0
238
ae1d85aca858 optimization in ArrayDataSet::__iter__
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 235
diff changeset
1188 self.columns = [self.dataset.fields_columns[f]
ae1d85aca858 optimization in ArrayDataSet::__iter__
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 235
diff changeset
1189 for f in self.minibatch._names]
270
1cafd495098c code cleanup and small optimisation
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 254
diff changeset
1190 self.l = self.dataset.data.shape[0]
228
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1191 def __iter__(self):
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1192 return self
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1193 def next(self):
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1194 #@todo: we suppose that we need to stop only when minibatch_size == 1.
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1195 # Otherwise, MinibatchWrapAroundIterator do it.
270
1cafd495098c code cleanup and small optimisation
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 254
diff changeset
1196 if self.current>=self.l:
228
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1197 raise StopIteration
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1198 sub_data = self.dataset.data[self.current]
238
ae1d85aca858 optimization in ArrayDataSet::__iter__
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 235
diff changeset
1199 self.minibatch._values = [sub_data[c] for c in self.columns]
ae1d85aca858 optimization in ArrayDataSet::__iter__
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 235
diff changeset
1200
270
1cafd495098c code cleanup and small optimisation
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 254
diff changeset
1201 self.current+=1
228
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1202 return self.minibatch
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1203
270
1cafd495098c code cleanup and small optimisation
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 254
diff changeset
1204 return ArrayDataSetIteratorIter(self,self.fieldNames())
228
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1205
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1206 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1207 cursor = Example(fieldnames,[0]*len(fieldnames))
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1208 fieldnames = self.fieldNames() if fieldnames is None else fieldnames
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1209 for n in xrange(n_batches):
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1210 if offset == len(self):
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1211 break
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1212 sub_data = self.data[offset : offset+minibatch_size]
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1213 offset += len(sub_data) #can be less than minibatch_size at end
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1214 cursor._values = [sub_data[:,self.fields_columns[f]] for f in cursor._names]
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1215 yield cursor
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1216
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1217 #return ArrayDataSetIterator(self,fieldnames,minibatch_size,n_batches,offset)
57
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1218
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1219
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1220 class CachedDataSet(DataSet):
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1221 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1222 Wrap a L{DataSet} whose values are computationally expensive to obtain
57
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1223 (e.g. because they involve some computation, or disk access),
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1224 so that repeated accesses to the same example are done cheaply,
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1225 by caching every example value that has been accessed at least once.
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1226
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1227 Optionally, for finite-length dataset, all the values can be computed
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1228 (and cached) upon construction of the CachedDataSet, rather at the
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1229 first access.
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1230
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1231 @todo: when cache_all_upon_construction create mini-batches that are as
77
1e2bb5bad636 toying with different ways to implement learners
bengioy@bengiomac.local
parents: 74
diff changeset
1232 large as possible but not so large as to fill up memory.
1e2bb5bad636 toying with different ways to implement learners
bengioy@bengiomac.local
parents: 74
diff changeset
1233
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1234 @todo: add disk-buffering capability, so that when the cache becomes too
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1235 big for memory, we cache things on disk, trying to keep in memory only
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1236 the record most likely to be accessed next.
57
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1237 """
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1238 def __init__(self,source_dataset,cache_all_upon_construction=False):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1239 self.source_dataset=source_dataset
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1240 self.cache_all_upon_construction=cache_all_upon_construction
152
3f627e844cba Fixes in CacheDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 151
diff changeset
1241 self.cached_examples = []
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1242 if cache_all_upon_construction:
77
1e2bb5bad636 toying with different ways to implement learners
bengioy@bengiomac.local
parents: 74
diff changeset
1243 # this potentially brings all the source examples
1e2bb5bad636 toying with different ways to implement learners
bengioy@bengiomac.local
parents: 74
diff changeset
1244 # into memory at once, which may be too much
1e2bb5bad636 toying with different ways to implement learners
bengioy@bengiomac.local
parents: 74
diff changeset
1245 # the work could possibly be done by minibatches
1e2bb5bad636 toying with different ways to implement learners
bengioy@bengiomac.local
parents: 74
diff changeset
1246 # that are as large as possible but no more than what memory allows.
146
8173e196e291 Trying to make CacheDataSet work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 144
diff changeset
1247 fields_values = source_dataset.minibatches(minibatch_size=len(source_dataset)).__iter__().next()
152
3f627e844cba Fixes in CacheDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 151
diff changeset
1248 assert all([len(self)==len(field_values) for field_values in fields_values])
3f627e844cba Fixes in CacheDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 151
diff changeset
1249 for example in fields_values.examples():
171
895b4b60f5e8 bugfix. Otherwise the example was writed over and not a new one was returned
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 167
diff changeset
1250 self.cached_examples.append(copy.copy(example))
57
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1251
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1252 self.fieldNames = source_dataset.fieldNames
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1253 self.hasFields = source_dataset.hasFields
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1254 self.valuesHStack = source_dataset.valuesHStack
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1255 self.valuesVStack = source_dataset.valuesVStack
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1256
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1257 def __len__(self):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1258 return len(self.source_dataset)
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1259
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1260 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1261 class CacheIterator(object):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1262 def __init__(self,dataset):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1263 self.dataset=dataset
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1264 self.current=offset
254
8ec867d12428 optimication in CachedDataSet.minibatches_nowrap
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 253
diff changeset
1265 self.all_fields = self.dataset.fieldNames()==fieldnames
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1266 def __iter__(self): return self
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1267 def next(self):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1268 upper = self.current+minibatch_size
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1269 cache_len = len(self.dataset.cached_examples)
135
0d8e721cc63c Fixed bugs in dataset to make test_mlp.py work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 134
diff changeset
1270 if upper>cache_len: # whole minibatch is not already in cache
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1271 # cache everything from current length to upper
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1272 for example in self.dataset.source_dataset[cache_len:upper]:
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1273 self.dataset.cached_examples.append(example)
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1274 all_fields_minibatch = Example(self.dataset.fieldNames(),
152
3f627e844cba Fixes in CacheDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 151
diff changeset
1275 zip(*self.dataset.cached_examples[self.current:self.current+minibatch_size]))
163
d7d67651d67c bugfix, we should advence by the minibatch size.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 159
diff changeset
1276 self.current+=minibatch_size
254
8ec867d12428 optimication in CachedDataSet.minibatches_nowrap
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 253
diff changeset
1277 if self.all_fields:
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1278 return all_fields_minibatch
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1279 return Example(fieldnames,[all_fields_minibatch[name] for name in fieldnames])
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1280 return CacheIterator(self)
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1281
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1282 def dontuse__getitem__(self,i):
153
71107b0ac860 optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 151
diff changeset
1283 if type(i)==int and len(self.cached_examples)>i:
71107b0ac860 optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 151
diff changeset
1284 return self.cached_examples[i]
71107b0ac860 optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 151
diff changeset
1285 else:
251
7e6edee187e3 optimization of CachedDataSet__getitem__
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 243
diff changeset
1286 return self.source_dataset[i]
252
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1287
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1288 def __iter__(self):
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1289 class CacheIteratorIter(object):
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1290 def __init__(self,dataset):
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1291 self.dataset=dataset
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1292 self.l = len(dataset)
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1293 self.current = 0
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1294 self.fieldnames = self.dataset.fieldNames()
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1295 self.example = Example(self.fieldnames,[0]*len(self.fieldnames))
252
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1296 def __iter__(self): return self
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1297 def next(self):
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1298 if self.current>=self.l:
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1299 raise StopIteration
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1300 cache_len = len(self.dataset.cached_examples)
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1301 if self.current>=cache_len: # whole minibatch is not already in cache
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1302 # cache everything from current length to upper
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1303 self.dataset.cached_examples.append(
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1304 self.dataset.source_dataset[self.current])
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1305 self.example._values = self.dataset.cached_examples[self.current]
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1306 self.current+=1
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1307 return self.example
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1308
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1309 return CacheIteratorIter(self)
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1310
57
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1311 class ApplyFunctionDataSet(DataSet):
290
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1312 """
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parents: 274
diff changeset
1313 A L{DataSet} that contains as fields the results of applying a
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1314 given function example-wise or minibatch-wise to all the fields of
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1315 an input dataset. The output of the function should be an iterable
296
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1316 (e.g. a list or a LookupList) over the resulting values.
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1317
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parents: 274
diff changeset
1318 The function take as input the fields of the dataset, not the examples.
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1319
290
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1320 In minibatch mode, the function is expected to work on minibatches
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1321 (takes a minibatch in input and returns a minibatch in output). More
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1322 precisely, it means that each element of the input or output list
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parents: 274
diff changeset
1323 should be iterable and indexable over the individual example values
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parents: 274
diff changeset
1324 (typically these elements will be numpy arrays). All of the elements
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diff changeset
1325 in the input and output lists should have the same length, which is
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1326 the length of the minibatch.
57
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1327
290
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diff changeset
1328 The function is applied each time an example or a minibatch is accessed.
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1329 To avoid re-doing computation, wrap this dataset inside a CachedDataSet.
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1330
290
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parents: 274
diff changeset
1331 If the values_{h,v}stack functions are not provided, then
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1332 the input_dataset.values{H,V}Stack functions are used by default.
296
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1333
290
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diff changeset
1334 """
296
f5d33f9c0b9c ApplyFunctionDataSet passing
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parents: 293
diff changeset
1335
290
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diff changeset
1336 def __init__(self,input_dataset,function,output_names,minibatch_mode=True,
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1337 values_hstack=None,values_vstack=None,
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parents: 274
diff changeset
1338 description=None,fieldtypes=None):
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parents: 274
diff changeset
1339 """
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parents: 274
diff changeset
1340 Constructor takes an input dataset that has as many fields as the function
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1341 expects as inputs. The resulting dataset has as many fields as the function
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1342 produces as outputs, and that should correspond to the number of output names
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1343 (provided in a list).
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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parents: 72
diff changeset
1344
290
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diff changeset
1345 Note that the expected semantics of the function differs in minibatch mode
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1346 (it takes minibatches of inputs and produces minibatches of outputs, as
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1347 documented in the class comment).
211
bd728c83faff in __get__, problem if the i.stop was None, i being the slice, added one line replacing None by the len(self)
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 203
diff changeset
1348
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1349 TBM: are filedtypes the old field types (from input_dataset) or the new ones
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1350 (for the new dataset created)?
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1351 """
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1352 self.input_dataset=input_dataset
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parents: 274
diff changeset
1353 self.function=function
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parents: 274
diff changeset
1354 self.output_names=output_names
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parents: 274
diff changeset
1355 self.minibatch_mode=minibatch_mode
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diff changeset
1356 DataSet.__init__(self,description,fieldtypes)
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parents: 274
diff changeset
1357 self.valuesHStack = values_hstack if values_hstack else input_dataset.valuesHStack
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1358 self.valuesVStack = values_vstack if values_vstack else input_dataset.valuesVStack
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1359
290
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diff changeset
1360 def __len__(self):
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parents: 274
diff changeset
1361 return len(self.input_dataset)
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1362
290
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parents: 274
diff changeset
1363 def fieldNames(self):
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1364 return self.output_names
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1365
290
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1366 def minibatches_nowrap(self, fieldnames, *args, **kwargs):
296
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1367 all_input_fieldNames = self.input_dataset.fieldNames()
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1368 mbnw = self.input_dataset.minibatches_nowrap
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1369
296
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1370 for input_fields in mbnw(all_input_fieldNames, *args, **kwargs):
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1371 if self.minibatch_mode:
296
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1372 all_output_fields = self.function(*input_fields)
290
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1373 else:
296
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1374 input_examples = zip(*input_fields) #makes so that [i] means example i
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1375 output_examples = [self.function(*input_example)
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parents: 274
diff changeset
1376 for input_example in input_examples]
296
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1377 all_output_fields = zip(*output_examples)
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1378
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1379 all_outputs = Example(self.output_names, all_output_fields)
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1380 #print 'input_fields', input_fields
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1381 #print 'all_outputs', all_outputs
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1382 if fieldnames==self.output_names:
293
4bfdda107a17 still merging
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 292
diff changeset
1383 rval = all_outputs
290
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1384 else:
293
4bfdda107a17 still merging
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 292
diff changeset
1385 rval = Example(fieldnames,[all_outputs[name] for name in fieldnames])
296
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1386 #print 'rval', rval
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1387 #print '--------'
293
4bfdda107a17 still merging
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 292
diff changeset
1388 yield rval
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1389
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1390 def untested__iter__(self): # only implemented for increased efficiency
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1391 class ApplyFunctionSingleExampleIterator(object):
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1392 def __init__(self,output_dataset):
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1393 self.current=0
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1394 self.output_dataset=output_dataset
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1395 self.input_iterator=output_dataset.input_dataset.__iter__()
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James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1396 def __iter__(self): return self
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1397 def next(self):
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1398 if self.output_dataset.minibatch_mode:
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1399 function_inputs = [[input] for input in self.input_iterator.next()]
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1400 outputs = self.output_dataset.function(*function_inputs)
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1401 assert all([hasattr(output,'__iter__') for output in outputs])
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1402 function_outputs = [output[0] for output in outputs]
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1403 else:
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parents: 274
diff changeset
1404 function_inputs = self.input_iterator.next()
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1405 function_outputs = self.output_dataset.function(*function_inputs)
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1406 return Example(self.output_dataset.output_names,function_outputs)
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1407 return ApplyFunctionSingleExampleIterator(self)
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1408
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1409 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
1410 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1411 Wraps an arbitrary L{DataSet} into one for supervised learning tasks
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1412 by forcing the user to define a set of fields as the 'input' field
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1413 and a set of fields as the 'target' field. Optionally, a single
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1414 weight_field can also be defined.
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1415 """
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1416 args = ((input_fields,'input'),(output_fields,'target'))
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1417 if weight_field: args+=(([weight_field],'weight'))
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
1418 return src_dataset.merge_fields(*args)
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1419
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1420
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1421
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1422