annotate dataset.py @ 198:136f78559138

bugfix
author Frederic Bastien <bastienf@iro.umontreal.ca>
date Tue, 13 May 2008 16:02:32 -0400
parents 96d891448107
children 1400fa04dfab
rev   line source
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2 from lookup_list import LookupList
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3 Example = LookupList
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4 from misc import unique_elements_list_intersection
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5 from string import join
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6 from sys import maxint
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7 import numpy, copy
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9 from exceptions import *
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11 class AttributesHolder(object):
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12 def __init__(self): pass
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14 def attributeNames(self):
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15 raise AbstractFunction()
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17 def setAttributes(self,attribute_names,attribute_values,make_copies=False):
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18 """
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19 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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20 """
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21 if len(attribute_names)==1 and not (isinstance(attribute_values,list) or isinstance(attribute_values,tuple) ):
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22 attribute_values = [attribute_values]
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23 if make_copies:
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24 for name,value in zip(attribute_names,attribute_values):
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25 self.__setattr__(name,copy.deepcopy(value))
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26 else:
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27 for name,value in zip(attribute_names,attribute_values):
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28 self.__setattr__(name,value)
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31 class DataSet(AttributesHolder):
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32 """A virtual base class for datasets.
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33
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34 A DataSet can be seen as a generalization of a matrix, meant to be used in conjunction
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35 with learning algorithms (for training and testing them): rows/records are called examples, and
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36 columns/attributes are called fields. The field value for a particular example can be an arbitrary
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37 python object, which depends on the particular dataset.
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38
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39 We call a DataSet a 'stream' when its length is unbounded (otherwise its __len__ method
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40 should return sys.maxint).
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42 A DataSet is a generator of iterators; these iterators can run through the
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43 examples or the fields in a variety of ways. A DataSet need not necessarily have a finite
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44 or known length, so this class can be used to interface to a 'stream' which
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45 feeds on-line learning (however, as noted below, some operations are not
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46 feasible or not recommanded on streams).
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48 To iterate over examples, there are several possibilities:
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49 - for example in dataset:
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50 - for val1,val2,... in dataset:
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51 - for example in dataset(field1, field2,field3, ...):
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52 - for val1,val2,val3 in dataset(field1, field2,field3):
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53 - for minibatch in dataset.minibatches([field1, field2, ...],minibatch_size=N):
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54 - for mini1,mini2,mini3 in dataset.minibatches([field1, field2, field3], minibatch_size=N):
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55 Each of these is documented below. All of these iterators are expected
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56 to provide, in addition to the usual 'next()' method, a 'next_index()' method
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57 which returns a non-negative integer pointing to the position of the next
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58 example that will be returned by 'next()' (or of the first example in the
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59 next minibatch returned). This is important because these iterators
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60 can wrap around the dataset in order to do multiple passes through it,
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61 in possibly unregular ways if the minibatch size is not a divisor of the
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62 dataset length.
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64 To iterate over fields, one can do
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65 - for field in dataset.fields():
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66 for field_value in field: # iterate over the values associated to that field for all the dataset examples
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67 - for field in dataset(field1,field2,...).fields() to select a subset of fields
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68 - for field in dataset.fields(field1,field2,...) to select a subset of fields
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69 and each of these fields is iterable over the examples:
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70 - for field_examples in dataset.fields():
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71 for example_value in field_examples:
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72 ...
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73 but when the dataset is a stream (unbounded length), it is not recommanded to do
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74 such things because the underlying dataset may refuse to access the different fields in
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75 an unsynchronized ways. Hence the fields() method is illegal for streams, by default.
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76 The result of fields() is a L{DataSetFields} object, which iterates over fields,
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77 and whose elements are iterable over examples. A DataSetFields object can
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78 be turned back into a DataSet with its examples() method::
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79 dataset2 = dataset1.fields().examples()
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80 and dataset2 should behave exactly like dataset1 (in fact by default dataset2==dataset1).
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81
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82 Note: Fields are not mutually exclusive, i.e. two fields can overlap in their actual content.
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83
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84 Note: The content of a field can be of any type. Field values can also be 'missing'
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85 (e.g. to handle semi-supervised learning), and in the case of numeric (numpy array)
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86 fields (i.e. an ArrayFieldsDataSet), NaN plays the role of a missing value.
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87 What about non-numeric values? None.
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88
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89 Dataset elements can be indexed and sub-datasets (with a subset
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90 of examples) can be extracted. These operations are not supported
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91 by default in the case of streams.
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92
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93 - dataset[:n] returns a dataset with the n first examples.
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94
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95 - dataset[i1:i2:s] returns a dataset with the examples i1,i1+s,...i2-s.
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96
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97 - dataset[i] returns an Example.
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98
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99 - dataset[[i1,i2,...in]] returns a dataset with examples i1,i2,...in.
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100
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101 - dataset[fieldname] an iterable over the values of the field fieldname across
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102 the dataset (the iterable is obtained by default by calling valuesVStack
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103 over the values for individual examples).
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104
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105 - dataset.<property> returns the value of a property associated with
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106 the name <property>. The following properties should be supported:
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107 - 'description': a textual description or name for the dataset
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108 - 'fieldtypes': a list of types (one per field)
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109 A DataSet may have other attributes that it makes visible to other objects. These are
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110 used to store information that is not example-wise but global to the dataset.
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111 The list of names of these attributes is given by the attribute_names() method.
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112
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113 Datasets can be concatenated either vertically (increasing the length) or
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114 horizontally (augmenting the set of fields), if they are compatible, using
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115 the following operations (with the same basic semantics as numpy.hstack
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116 and numpy.vstack):
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117
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118 - dataset1 | dataset2 | dataset3 == dataset.hstack([dataset1,dataset2,dataset3])
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119
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120 creates a new dataset whose list of fields is the concatenation of the list of
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121 fields of the argument datasets. This only works if they all have the same length.
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122
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123 - dataset1 & dataset2 & dataset3 == dataset.vstack([dataset1,dataset2,dataset3])
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124
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125 creates a new dataset that concatenates the examples from the argument datasets
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126 (and whose length is the sum of the length of the argument datasets). This only
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127 works if they all have the same fields.
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128
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129 According to the same logic, and viewing a DataSetFields object associated to
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130 a DataSet as a kind of transpose of it, fields1 & fields2 concatenates fields of
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131 a DataSetFields fields1 and fields2, and fields1 | fields2 concatenates their
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132 examples.
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133
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134 A dataset can hold arbitrary key-value pairs that may be used to access meta-data
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135 or other properties of the dataset or associated with the dataset or the result
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136 of a computation stored in a dataset. These can be accessed through the [key] syntax
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137 when key is a string (or more specifically, neither an integer, a slice, nor a list).
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138
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139 A DataSet sub-class should always redefine the following methods:
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140 - __len__ if it is not a stream
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141 - fieldNames
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142 - minibatches_nowrap (called by DataSet.minibatches())
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143 - valuesHStack
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144 - valuesVStack
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145 For efficiency of implementation, a sub-class might also want to redefine
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146 - hasFields
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147 - __getitem__ may not be feasible with some streams
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148 - __iter__
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149 A sub-class should also append attributes to self._attribute_names
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150 (the default value returned by attributeNames()).
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151 By convention, attributes not in attributeNames() should have a name
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152 starting with an underscore.
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153 @todo enforce/test that convention!
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154 """
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155
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156 numpy_vstack = lambda fieldname,values: numpy.vstack(values)
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157 numpy_hstack = lambda fieldnames,values: numpy.hstack(values)
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158
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159 def __init__(self,description=None,fieldtypes=None):
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160 if description is None:
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161 # by default return "<DataSetType>(<SuperClass1>,<SuperClass2>,...)"
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162 description = type(self).__name__ + " ( " + join([x.__name__ for x in type(self).__bases__]) + " )"
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163 self.description=description
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164 self.fieldtypes=fieldtypes
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165 self._attribute_names = ["description"]
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166 if fieldtypes:
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167 self._attribute_names.append("fieldtypes")
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168
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169 def attributeNames(self): return self._attribute_names
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170
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171 class MinibatchToSingleExampleIterator(object):
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172 """
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173 Converts the result of minibatch iterator with minibatch_size==1 into
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174 single-example values in the result. Therefore the result of
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175 iterating on the dataset itself gives a sequence of single examples
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176 (whereas the result of iterating over minibatches gives in each
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177 Example field an iterable object over the individual examples in
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178 the minibatch).
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179 """
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180 def __init__(self, minibatch_iterator):
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181 self.minibatch_iterator = minibatch_iterator
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182 self.minibatch = None
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183 def __iter__(self): #makes for loop work
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184 return self
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185 def next(self):
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186 size1_minibatch = self.minibatch_iterator.next()
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187 if not self.minibatch:
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188 self.minibatch = Example(size1_minibatch.keys(),[value[0] for value in size1_minibatch.values()])
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189 else:
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190 self.minibatch._values = [value[0] for value in size1_minibatch.values()]
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191 return self.minibatch
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192
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193 def next_index(self):
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194 return self.minibatch_iterator.next_index()
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195
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196 def __iter__(self):
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197 """Supports the syntax "for i in dataset: ..."
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198
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199 Using this syntax, "i" will be an Example instance (or equivalent) with
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200 all the fields of DataSet self. Every field of "i" will give access to
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201 a field of a single example. Fields should be accessible via
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202 i["fielname"] or i[3] (in the order defined by the elements of the
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203 Example returned by this iterator), but the derived class is free
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204 to accept any type of identifier, and add extra functionality to the iterator.
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205
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206 The default implementation calls the minibatches iterator and extracts the first example of each field.
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207 """
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208 return DataSet.MinibatchToSingleExampleIterator(self.minibatches(None, minibatch_size = 1))
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209
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210
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211 class MinibatchWrapAroundIterator(object):
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212 """
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213 An iterator for minibatches that handles the case where we need to wrap around the
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214 dataset because n_batches*minibatch_size > len(dataset). It is constructed from
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215 a dataset that provides a minibatch iterator that does not need to handle that problem.
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216 This class is a utility for dataset subclass writers, so that they do not have to handle
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217 this issue multiple times, nor check that fieldnames are valid, nor handle the
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218 empty fieldnames (meaning 'use all the fields').
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219 """
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220 def __init__(self,dataset,fieldnames,minibatch_size,n_batches,offset):
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221 self.dataset=dataset
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222 self.fieldnames=fieldnames
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223 self.minibatch_size=minibatch_size
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224 self.n_batches=n_batches
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225 self.n_batches_done=0
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226 self.next_row=offset
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227 self.offset=offset
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228 self.L=len(dataset)
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229 assert offset+minibatch_size<=self.L
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230 ds_nbatches = (self.L-self.next_row)/self.minibatch_size
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231 if n_batches is not None:
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232 ds_nbatches = min(n_batches,ds_nbatches)
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233 if fieldnames:
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234 assert dataset.hasFields(*fieldnames)
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235 else:
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236 self.fieldnames=dataset.fieldNames()
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237 self.iterator = self.dataset.minibatches_nowrap(self.fieldnames,self.minibatch_size,
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238 ds_nbatches,self.next_row)
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239
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240 def __iter__(self):
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241 return self
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242
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243 def next_index(self):
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244 return self.next_row
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245
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246 def next(self):
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247 if self.n_batches and self.n_batches_done==self.n_batches:
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248 raise StopIteration
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249 elif not self.n_batches and self.next_row ==self.L:
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250 raise StopIteration
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251 upper = self.next_row+self.minibatch_size
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252 if upper <=self.L:
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253 minibatch = self.iterator.next()
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254 else:
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255 if not self.n_batches:
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256 upper=min(upper, self.L)
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257 # if their is not a fixed number of batch, we continue to the end of the dataset.
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258 # this can create a minibatch that is smaller then the minibatch_size
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259 assert (self.L-self.next_row)<=self.minibatch_size
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260 minibatch = self.dataset.minibatches_nowrap(self.fieldnames,self.L-self.next_row,1,self.next_row).next()
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261 else:
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262 # we must concatenate (vstack) the bottom and top parts of our minibatch
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263 # first get the beginning of our minibatch (top of dataset)
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264 first_part = self.dataset.minibatches_nowrap(self.fieldnames,self.L-self.next_row,1,self.next_row).next()
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265 second_part = self.dataset.minibatches_nowrap(self.fieldnames,upper-self.L,1,0).next()
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266 minibatch = Example(self.fieldnames,
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267 [self.dataset.valuesVStack(name,[first_part[name],second_part[name]])
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268 for name in self.fieldnames])
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269 self.next_row=upper
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270 self.n_batches_done+=1
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271 if upper >= self.L and self.n_batches:
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272 self.next_row -= self.L
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273 ds_nbatches = (self.L-self.next_row)/self.minibatch_size
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274 if self.n_batches is not None:
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275 ds_nbatches = min(self.n_batches,ds_nbatches)
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276 self.iterator = self.dataset.minibatches_nowrap(self.fieldnames,self.minibatch_size,
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277 ds_nbatches,self.next_row)
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278 return DataSetFields(MinibatchDataSet(minibatch,self.dataset.valuesVStack,
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279 self.dataset.valuesHStack),
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280 minibatch.keys())
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281
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282
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283 minibatches_fieldnames = None
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284 minibatches_minibatch_size = 1
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285 minibatches_n_batches = None
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286 def minibatches(self,
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287 fieldnames = minibatches_fieldnames,
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288 minibatch_size = minibatches_minibatch_size,
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289 n_batches = minibatches_n_batches,
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290 offset = 0):
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291 """
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292 Return an iterator that supports three forms of syntax:
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293
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294 for i in dataset.minibatches(None,**kwargs): ...
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295
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296 for i in dataset.minibatches([f1, f2, f3],**kwargs): ...
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297
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298 for i1, i2, i3 in dataset.minibatches([f1, f2, f3],**kwargs): ...
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299
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300 Using the first two syntaxes, "i" will be an indexable object, such as a list,
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301 tuple, or Example instance. In both cases, i[k] is a list-like container
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302 of a batch of current examples. In the second case, i[0] is
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303 list-like container of the f1 field of a batch current examples, i[1] is
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304 a list-like container of the f2 field, etc.
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305
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306 Using the first syntax, all the fields will be returned in "i".
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307 Using the third syntax, i1, i2, i3 will be list-like containers of the
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308 f1, f2, and f3 fields of a batch of examples on each loop iteration.
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309
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310 The minibatches iterator is expected to return upon each call to next()
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311 a DataSetFields object, which is a LookupList (indexed by the field names) whose
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312 elements are iterable and indexable over the minibatch examples, and which keeps a pointer to
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313 a sub-dataset that can be used to iterate over the individual examples
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314 in the minibatch. Hence a minibatch can be converted back to a regular
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315 dataset or its fields can be looked at individually (and possibly iterated over).
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316
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317 PARAMETERS
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318 - fieldnames (list of any type, default None):
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319 The loop variables i1, i2, i3 (in the example above) should contain the
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320 f1, f2, and f3 fields of the current batch of examples. If None, the
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321 derived class can choose a default, e.g. all fields.
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322
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323 - minibatch_size (integer, default 1)
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324 On every iteration, the variables i1, i2, i3 will have
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325 exactly minibatch_size elements. e.g. len(i1) == minibatch_size
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326
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327 - n_batches (integer, default None)
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328 The iterator will loop exactly this many times, and then stop. If None,
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329 the derived class can choose a default. If (-1), then the returned
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330 iterator should support looping indefinitely.
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331
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332 - offset (integer, default 0)
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333 The iterator will start at example 'offset' in the dataset, rather than the default.
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334
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335 Note: A list-like container is something like a tuple, list, numpy.ndarray or
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336 any other object that supports integer indexing and slicing.
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337
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338 """
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339 return DataSet.MinibatchWrapAroundIterator(self,fieldnames,minibatch_size,n_batches,offset)
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340
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341 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
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342 """
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343 This is the minibatches iterator generator that sub-classes must define.
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344 It does not need to worry about wrapping around multiple times across the dataset,
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345 as this is handled by MinibatchWrapAroundIterator when DataSet.minibatches() is called.
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346 The next() method of the returned iterator does not even need to worry about
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347 the termination condition (as StopIteration will be raised by DataSet.minibatches
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348 before an improper call to minibatches_nowrap's next() is made).
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349 That next() method can assert that its next row will always be within [0,len(dataset)).
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350 The iterator returned by minibatches_nowrap does not need to implement
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351 a next_index() method either, as this will be provided by MinibatchWrapAroundIterator.
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352 """
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353 raise AbstractFunction()
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354
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355 def __len__(self):
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356 """
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357 len(dataset) returns the number of examples in the dataset.
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358 By default, a DataSet is a 'stream', i.e. it has an unbounded length (sys.maxint).
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359 Sub-classes which implement finite-length datasets should redefine this method.
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360 Some methods only make sense for finite-length datasets.
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361 """
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362 return maxint
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363
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364 def is_unbounded(self):
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365 """
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366 Tests whether a dataset is unbounded (e.g. a stream).
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367 """
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368 return len(self)==maxint
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369
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370 def hasFields(self,*fieldnames):
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371 """
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372 Return true if the given field name (or field names, if multiple arguments are
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373 given) is recognized by the DataSet (i.e. can be used as a field name in one
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374 of the iterators).
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375
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376 The default implementation may be inefficient (O(# fields in dataset)), as it calls the fieldNames()
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377 method. Many datasets may store their field names in a dictionary, which would allow more efficiency.
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378 """
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379 return len(unique_elements_list_intersection(fieldnames,self.fieldNames()))>0
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380
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381 def fieldNames(self):
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382 """
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383 Return the list of field names that are supported by the iterators,
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parents: 29
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384 and for which hasFields(fieldname) would return True.
11
be128b9127c8 Debugged (to the extent of my tests) the new version of dataset
bengioy@esprit.iro.umontreal.ca
parents: 9
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385 """
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
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parents: 16 12
diff changeset
386 raise AbstractFunction()
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bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
387
36
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388 def __call__(self,*fieldnames):
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
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parents: 22
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389 """
36
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390 Return a dataset that sees only the fields whose name are specified.
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
391 """
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
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392 assert self.hasFields(*fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
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393 return self.fields(*fieldnames).examples()
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
394
36
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395 def fields(self,*fieldnames):
29
46c5c90019c2 Changed apply_function so that it propagates methods of the source.
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parents: 28
diff changeset
396 """
36
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397 Return a DataSetFields object associated with this dataset.
17
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bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
398 """
74
b4159cbdc06b Fixed errors raised by test_dataset
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 73
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399 return DataSetFields(self,fieldnames)
11
be128b9127c8 Debugged (to the extent of my tests) the new version of dataset
bengioy@esprit.iro.umontreal.ca
parents: 9
diff changeset
400
2
3fddb1c8f955 Rewrote DataSet interface and created FiniteDataSet interface.
bengioy@bengiomac.local
parents: 1
diff changeset
401 def __getitem__(self,i):
28
541a273bc89f Removed __array__ method from dataset, whose
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parents: 26
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402 """
541a273bc89f Removed __array__ method from dataset, whose
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parents: 26
diff changeset
403 dataset[i] returns the (i+1)-th example of the dataset.
541a273bc89f Removed __array__ method from dataset, whose
bengioy@grenat.iro.umontreal.ca
parents: 26
diff changeset
404 dataset[i:j] returns the subdataset with examples i,i+1,...,j-1.
541a273bc89f Removed __array__ method from dataset, whose
bengioy@grenat.iro.umontreal.ca
parents: 26
diff changeset
405 dataset[i:j:s] returns the subdataset with examples i,i+2,i+4...,j-2.
541a273bc89f Removed __array__ method from dataset, whose
bengioy@grenat.iro.umontreal.ca
parents: 26
diff changeset
406 dataset[[i1,i2,..,in]] returns the subdataset with examples i1,i2,...,in.
41
283e95c15b47 Added ArrayDataSet
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parents: 40
diff changeset
407 dataset['key'] returns a property associated with the given 'key' string.
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
408 If 'key' is a fieldname, then the VStacked field values (iterable over
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
409 field values) for that field is returned. Other keys may be supported
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
410 by different dataset subclasses. The following key names are encouraged:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
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411 - 'description': a textual description or name for the dataset
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
412 - '<fieldname>.type': a type name or value for a given <fieldname>
1
2cd82666b9a7 Added statscollector and started writing dataset and learner.
bengioy@esprit.iro.umontreal.ca
parents: 0
diff changeset
413
39
c682c6e9bf93 Minor edits
bengioy@esprit.iro.umontreal.ca
parents: 38
diff changeset
414 Note that some stream datasets may be unable to implement random access, i.e.
c682c6e9bf93 Minor edits
bengioy@esprit.iro.umontreal.ca
parents: 38
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415 arbitrary slicing/indexing
36
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416 because they can only iterate through examples one or a minibatch at a time
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417 and do not actually store or keep past (or future) examples.
40
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418
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
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419 The default implementation of getitem uses the minibatches iterator
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parents: 39
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420 to obtain one example, one slice, or a list of examples. It may not
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
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parents: 39
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421 always be the most efficient way to obtain the result, especially if
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parents: 39
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422 the data are actually stored in a memory array.
28
541a273bc89f Removed __array__ method from dataset, whose
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parents: 26
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423 """
41
283e95c15b47 Added ArrayDataSet
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424 # check for an index
40
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parents: 39
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425 if type(i) is int:
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
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parents: 39
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426 return DataSet.MinibatchToSingleExampleIterator(
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
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parents: 39
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427 self.minibatches(minibatch_size=1,n_batches=1,offset=i)).next()
41
283e95c15b47 Added ArrayDataSet
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parents: 40
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428 rows=None
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429 # or a slice
40
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parents: 39
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430 if type(i) is slice:
135
0d8e721cc63c Fixed bugs in dataset to make test_mlp.py work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 134
diff changeset
431 if not i.start: i=slice(0,i.stop,i.step)
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parents: 134
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432 if not i.step: i=slice(i.start,i.stop,1)
40
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parents: 39
diff changeset
433 if i.step is 1:
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
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parents: 39
diff changeset
434 return self.minibatches(minibatch_size=i.stop-i.start,n_batches=1,offset=i.start).next().examples()
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
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parents: 39
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435 rows = range(i.start,i.stop,i.step)
41
283e95c15b47 Added ArrayDataSet
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parents: 40
diff changeset
436 # or a list of indices
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parents: 40
diff changeset
437 elif type(i) is list:
40
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
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parents: 39
diff changeset
438 rows = i
41
283e95c15b47 Added ArrayDataSet
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parents: 40
diff changeset
439 if rows is not None:
48
b6730f9a336d Fixing MinibatchDataSet getitem
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parents: 46
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440 examples = [self[row] for row in rows]
b6730f9a336d Fixing MinibatchDataSet getitem
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parents: 46
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441 fields_values = zip(*examples)
45
a5c70dc42972 Test functions for dataset.py
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parents: 44
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442 return MinibatchDataSet(
41
283e95c15b47 Added ArrayDataSet
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parents: 40
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443 Example(self.fieldNames(),[ self.valuesVStack(fieldname,field_values)
283e95c15b47 Added ArrayDataSet
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parents: 40
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444 for fieldname,field_values
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
445 in zip(self.fieldNames(),fields_values)]),
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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446 self.valuesVStack,self.valuesHStack)
41
283e95c15b47 Added ArrayDataSet
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parents: 40
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447 # else check for a fieldname
283e95c15b47 Added ArrayDataSet
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parents: 40
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448 if self.hasFields(i):
283e95c15b47 Added ArrayDataSet
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parents: 40
diff changeset
449 return self.minibatches(fieldnames=[i],minibatch_size=len(self),n_batches=1,offset=0).next()[0]
283e95c15b47 Added ArrayDataSet
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parents: 40
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450 # else we are trying to access a property of the dataset
283e95c15b47 Added ArrayDataSet
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451 assert i in self.__dict__ # else it means we are trying to access a non-existing property
283e95c15b47 Added ArrayDataSet
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parents: 40
diff changeset
452 return self.__dict__[i]
22
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
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parents: 20
diff changeset
453
36
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454 def valuesHStack(self,fieldnames,fieldvalues):
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455 """
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456 Return a value that corresponds to concatenating (horizontally) several field values.
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457 This can be useful to merge some fields. The implementation of this operation is likely
438440ba0627 Rewriting dataset.py completely
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diff changeset
458 to involve a copy of the original values. When the values are numpy arrays, the
438440ba0627 Rewriting dataset.py completely
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diff changeset
459 result should be numpy.hstack(values). If it makes sense, this operation should
438440ba0627 Rewriting dataset.py completely
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diff changeset
460 work as well when each value corresponds to multiple examples in a minibatch
438440ba0627 Rewriting dataset.py completely
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461 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
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462 then the result should be a Lx(N1+N2+..) matrix equal to numpy.hstack(values).
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463 The default is to use numpy.hstack for numpy.ndarray values, and a list
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464 pointing to the original values for other data types.
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465 """
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466 all_numpy=True
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467 for value in fieldvalues:
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468 if not type(value) is numpy.ndarray:
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469 all_numpy=False
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470 if all_numpy:
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471 return numpy.hstack(fieldvalues)
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472 # the default implementation of horizontal stacking is to put values in a list
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473 return fieldvalues
26
672fe4b23032 Fixed dataset errors so that _test_dataset.py works again.
bengioy@grenat.iro.umontreal.ca
parents: 23
diff changeset
474
672fe4b23032 Fixed dataset errors so that _test_dataset.py works again.
bengioy@grenat.iro.umontreal.ca
parents: 23
diff changeset
475
36
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diff changeset
476 def valuesVStack(self,fieldname,values):
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parents: 29
diff changeset
477 """
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
478 Return a value that corresponds to concatenating (vertically) several values of the
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
479 same field. This can be important to build a minibatch out of individual examples. This
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
480 is likely to involve a copy of the original values. When the values are numpy arrays, the
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
481 result should be numpy.vstack(values).
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
482 The default is to use numpy.vstack for numpy.ndarray values, and a list
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
483 pointing to the original values for other data types.
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
484 """
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
485 all_numpy=True
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
486 for value in values:
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
487 if not type(value) is numpy.ndarray:
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
488 all_numpy=False
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diff changeset
489 if all_numpy:
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diff changeset
490 return numpy.vstack(values)
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
491 # the default implementation of vertical stacking is to put values in a list
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parents: 29
diff changeset
492 return values
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
493
36
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parents: 29
diff changeset
494 def __or__(self,other):
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diff changeset
495 """
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diff changeset
496 dataset1 | dataset2 returns a dataset whose list of fields is the concatenation of the list of
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parents: 29
diff changeset
497 fields of the argument datasets. This only works if they all have the same length.
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parents: 29
diff changeset
498 """
135
0d8e721cc63c Fixed bugs in dataset to make test_mlp.py work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 134
diff changeset
499 return HStackedDataSet([self,other])
3
378b68d5c4ad Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents: 2
diff changeset
500
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
501 def __and__(self,other):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
502 """
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
503 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
504 (and whose length is the sum of the length of the argument datasets). This only
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
505 works if they all have the same fields.
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parents: 29
diff changeset
506 """
135
0d8e721cc63c Fixed bugs in dataset to make test_mlp.py work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 134
diff changeset
507 return VStackedDataSet([self,other])
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
508
36
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diff changeset
509 def hstack(datasets):
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parents: 29
diff changeset
510 """
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
511 hstack(dataset1,dataset2,...) returns dataset1 | datataset2 | ...
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
512 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
513 of the individual datasets.
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
514 """
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parents: 29
diff changeset
515 assert len(datasets)>0
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
516 if len(datasets)==1:
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parents: 29
diff changeset
517 return datasets[0]
438440ba0627 Rewriting dataset.py completely
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diff changeset
518 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
519
36
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diff changeset
520 def vstack(datasets):
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bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
521 """
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
522 vstack(dataset1,dataset2,...) returns dataset1 & datataset2 & ...
36
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parents: 29
diff changeset
523 which is a dataset which iterates first over the examples of dataset1, then
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
524 over those of dataset2, etc.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
525 """
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
526 assert len(datasets)>0
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parents: 29
diff changeset
527 if len(datasets)==1:
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parents: 29
diff changeset
528 return datasets[0]
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
529 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
530
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
531 class FieldsSubsetDataSet(DataSet):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
532 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
533 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
534 """
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
535 def __init__(self,src,fieldnames):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
536 self.src=src
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
537 self.fieldnames=fieldnames
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
538 assert src.hasFields(*fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
539 self.valuesHStack = src.valuesHStack
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
540 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
541
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
542 def __len__(self): return len(self.src)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
543
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
544 def fieldNames(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
545 return self.fieldnames
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
546
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
547 def __iter__(self):
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
548 class FieldsSubsetIterator(object):
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
549 def __init__(self,ds):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
550 self.ds=ds
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
551 self.src_iter=ds.src.__iter__()
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
552 self.example=None
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
553 def __iter__(self): return self
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
554 def next(self):
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
555 complete_example = self.src_iter.next()
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
556 if self.example:
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
557 self.example._values=[complete_example[field]
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
558 for field in self.ds.fieldnames]
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
559 else:
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
560 self.example=Example(self.ds.fieldnames,
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
561 [complete_example[field] for field in self.ds.fieldnames])
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
562 return self.example
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
563 return FieldsSubsetIterator(self)
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
564
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
565 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
566 assert self.hasFields(*fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
567 return self.src.minibatches_nowrap(fieldnames,minibatch_size,n_batches,offset)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
568 def __getitem__(self,i):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
569 return FieldsSubsetDataSet(self.src[i],self.fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
570
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
571
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
572 class DataSetFields(LookupList):
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
573 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
574 Although a L{DataSet} iterates over examples (like rows of a matrix), an associated
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
575 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
576 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
577
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
578 To iterate over fields, one can do
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
579 * for fields in dataset.fields()
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
580 * 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
581 * 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
582 and each of these fields is iterable over the examples:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
583 * for field_examples in dataset.fields():
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
584 for example_value in field_examples:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
585 ...
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
586 but when the dataset is a stream (unbounded length), it is not recommanded to do
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
587 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
588 an unsynchronized ways. Hence the fields() method is illegal for streams, by default.
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
589 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
590 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
591 be turned back into a DataSet with its examples() method:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
592 dataset2 = dataset1.fields().examples()
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
593 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
594
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
595 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
596 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
597 the examples.
36
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parents: 29
diff changeset
598 """
74
b4159cbdc06b Fixed errors raised by test_dataset
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 73
diff changeset
599 def __init__(self,dataset,fieldnames):
65
d48eba49a2f4 fixed the infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 64
diff changeset
600 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
601 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
602 fieldnames=dataset.fieldNames()
65
d48eba49a2f4 fixed the infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 64
diff changeset
603 elif not fieldnames==dataset.fieldNames():
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
604 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
605 assert dataset.hasFields(*fieldnames)
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
606 self.dataset=dataset
66
dde1fb1b63ba fixed test and removed print
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 65
diff changeset
607
64
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
608 if isinstance(dataset,MinibatchDataSet):
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
609 LookupList.__init__(self,fieldnames,list(dataset._fields))
65
d48eba49a2f4 fixed the infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 64
diff changeset
610 elif isinstance(original_dataset,MinibatchDataSet):
d48eba49a2f4 fixed the infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 64
diff changeset
611 LookupList.__init__(self,fieldnames,
d48eba49a2f4 fixed the infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 64
diff changeset
612 [original_dataset._fields[field]
d48eba49a2f4 fixed the infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 64
diff changeset
613 for field in fieldnames])
64
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
614 else:
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
615 minibatch_iterator = dataset.minibatches(fieldnames,
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
616 minibatch_size=len(dataset),
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
617 n_batches=1)
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
618 minibatch=minibatch_iterator.next()
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
619 LookupList.__init__(self,fieldnames,minibatch)
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
620
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
621 def examples(self):
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
622 return self.dataset
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
623
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
624 def __or__(self,other):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
625 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
626 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
627 of the list of examples of DataSetFields fields1 and fields2.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
628 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
629 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
630
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
631 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
632 """
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
633 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
634 of the fields of DataSetFields fields1 and fields2.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
635 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
636 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
637
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
638
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
639 class MinibatchDataSet(DataSet):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
640 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
641 Turn a L{LookupList} of same-length (iterable) fields into an example-iterable dataset.
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
642 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
643 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
644 def __init__(self,fields_lookuplist,values_vstack=DataSet().valuesVStack,
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
645 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
646 """
36
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parents: 29
diff changeset
647 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
648 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
649 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
650 """
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
651 self._fields=fields_lookuplist
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
652 assert len(fields_lookuplist)>0
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
653 self.length=len(fields_lookuplist[0])
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
654 for field in fields_lookuplist[1:]:
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
655 assert self.length==len(field)
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
656 self.values_vstack=values_vstack
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
657 self.values_hstack=values_hstack
3
378b68d5c4ad Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents: 2
diff changeset
658
378b68d5c4ad Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents: 2
diff changeset
659 def __len__(self):
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
660 return self.length
28
541a273bc89f Removed __array__ method from dataset, whose
bengioy@grenat.iro.umontreal.ca
parents: 26
diff changeset
661
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
662 def __getitem__(self,i):
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
663 if type(i) in (slice,list):
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
664 return DataSetFields(MinibatchDataSet(
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
665 Example(self._fields.keys(),[field[i] for field in self._fields])),self.fieldNames())
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
666 if type(i) is int:
85
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 83
diff changeset
667 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
668 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
669 return self._fields[i]
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
670 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
671 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
672
29
46c5c90019c2 Changed apply_function so that it propagates methods of the source.
bengioy@grenat.iro.umontreal.ca
parents: 28
diff changeset
673 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
674 return self._fields.keys()
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
675
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
676 def hasFields(self,*fieldnames):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
677 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
678 if fieldname not in self._fields.keys():
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
679 return False
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
680 return True
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
681
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
682 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
683 class Iterator(object):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
684 def __init__(self,ds):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
685 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
686 self.next_example=offset
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
687 assert minibatch_size > 0
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
688 if offset+minibatch_size > ds.length:
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
689 raise NotImplementedError()
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
690 def __iter__(self):
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
691 return self
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
692 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
693 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
694 assert upper<=self.ds.length
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
695 minibatch = Example(self.ds._fields.keys(),
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
696 [field[self.next_example:upper]
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
697 for field in self.ds._fields])
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
698 self.next_example+=minibatch_size
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
699 return minibatch
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
700
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
701 return Iterator(self)
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
702
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
703 def valuesVStack(self,fieldname,fieldvalues):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
704 return self.values_vstack(fieldname,fieldvalues)
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
705
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
706 def valuesHStack(self,fieldnames,fieldvalues):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
707 return self.values_hstack(fieldnames,fieldvalues)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
708
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
709 class HStackedDataSet(DataSet):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
710 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
711 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
712 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
713
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
714 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
715 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
716 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
717
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
718 @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
719 """
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
720 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
721 DataSet.__init__(self,description,field_types)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
722 self.datasets=datasets
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
723 self.accept_nonunique_names=accept_nonunique_names
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
724 self.fieldname2dataset={}
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
725
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
726 def rename_field(fieldname,dataset,i):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
727 if hasattr(dataset,"__name__"):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
728 return dataset.__name__ + "." + fieldname
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
729 return fieldname+"."+str(i)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
730
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
731 # 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
732 self.length=None
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
733 names_to_change=[]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
734 for i in xrange(len(datasets)):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
735 dataset = datasets[i]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
736 length=len(dataset)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
737 if self.length:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
738 assert self.length==length
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
739 else:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
740 self.length=length
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
741 for fieldname in dataset.fieldNames():
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
742 if fieldname in self.fieldname2dataset: # name conflict!
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
743 if accept_nonunique_names:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
744 fieldname=rename_field(fieldname,dataset,i)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
745 names2change.append((fieldname,i))
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
746 else:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
747 raise ValueError("Incompatible datasets: non-unique field name = "+fieldname)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
748 self.fieldname2dataset[fieldname]=i
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
749 for fieldname,i in names_to_change:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
750 del self.fieldname2dataset[fieldname]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
751 self.fieldname2dataset[rename_field(fieldname,self.datasets[i],i)]=i
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
752
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
753 def hasFields(self,*fieldnames):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
754 for fieldname in fieldnames:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
755 if not fieldname in self.fieldname2dataset:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
756 return False
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
757 return True
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
758
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
759 def fieldNames(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
760 return self.fieldname2dataset.keys()
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
761
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
762 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
763
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
764 class HStackedIterator(object):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
765 def __init__(self,hsds,iterators):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
766 self.hsds=hsds
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
767 self.iterators=iterators
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
768 def __iter__(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
769 return self
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
770 def next(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
771 # concatenate all the fields of the minibatches
140
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 136
diff changeset
772 l=LookupList()
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 136
diff changeset
773 for iter in self.iterators:
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 136
diff changeset
774 l.append_lookuplist(iter.next())
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 136
diff changeset
775 return l
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
776
125
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 123
diff changeset
777 assert self.hasFields(*fieldnames)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
778 # 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
779 # and construct corresponding minibatch iterators
140
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 136
diff changeset
780 if fieldnames and fieldnames!=self.fieldNames():
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
781 datasets=set([])
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
782 fields_in_dataset=dict([(dataset,[]) for dataset in datasets])
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
783 for fieldname in fieldnames:
136
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 125
diff changeset
784 dataset=self.datasets[self.fieldname2dataset[fieldname]]
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
785 datasets.add(dataset)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
786 fields_in_dataset[dataset].append(fieldname)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
787 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
788 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
789 for dataset in datasets]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
790 else:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
791 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
792 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
793 return HStackedIterator(self,iterators)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
794
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
795
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
796 def valuesVStack(self,fieldname,fieldvalues):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
797 return self.datasets[self.fieldname2dataset[fieldname]].valuesVStack(fieldname,fieldvalues)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
798
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
799 def valuesHStack(self,fieldnames,fieldvalues):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
800 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
801 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
802 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
803 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
804 all the fieldnames are of the same sub-dataset.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
805 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
806 return self.datasets[self.fieldname2dataset[fieldnames[0]]].valuesHStack(fieldnames,fieldvalues)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
807
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
808 class VStackedDataSet(DataSet):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
809 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
810 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
811 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
812 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
813
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
814 @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
815 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
816 def __init__(self,datasets):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
817 self.datasets=datasets
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
818 self.length=0
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
819 self.index2dataset={}
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
820 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
821 fieldnames = datasets[-1].fieldNames()
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
822 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
823 # 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
824 # 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
825 for dataset,k in enumerate(datasets[0:-1]):
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
826 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
827 L=len(dataset)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
828 for i in xrange(L):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
829 self.index2dataset[self.length+i]=k
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
830 self.datasets_start_row.append(self.length)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
831 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
832 assert dataset.fieldNames()==fieldnames
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
833 self.datasets_start_row.append(self.length)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
834 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
835 # 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
836 # 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
837 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
838 # 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
839 # TODO
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
840 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
841
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
842 def __len__(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
843 return self.length
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
844
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
845 def fieldNames(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
846 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
847
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
848 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
849 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
850
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
851 def locate_row(self,row):
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
852 """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
853 dataset_index = self.index2dataset[row]
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
854 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
855 return dataset_index, row_within_dataset
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
856
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
857 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
858
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
859 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
860 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
861 self.vsds=vsds
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
862 self.next_row=offset
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
863 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
864 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
865 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
866
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
867 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
868 L=len(dataset)
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
869 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
870 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
871 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
872 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
873 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
874 n_left_in_mb=minibatch_size-L
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
875 ds_nbatches=1
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
876 else:
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
877 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
878 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
879 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
880
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
881 def move_to_next_dataset(self):
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
882 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
883 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
884 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
885 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
886 else:
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
887 self.next_dataset_index +=1
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
888 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
889 self.next_dataset_index = 0
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
890 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
891 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
892
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
893 def __iter__(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
894 return self
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
895
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
896 def next(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
897 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
898 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
899 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
900 extra_mb = []
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
901 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
902 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
903 extra_mb.append(self.next_iterator.next())
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
904 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
905 [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
906 [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
907 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
908
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
909 self.next_row+=minibatch_size
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
910 self.next_dataset_row+=minibatch_size
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
911 if self.next_row+minibatch_size>len(dataset):
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
912 self.move_to_next_dataset()
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
913 return examples
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
914 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
915
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
916 class ArrayFieldsDataSet(DataSet):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
917 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
918 Virtual super-class of datasets whose field values are numpy array,
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
919 thus defining valuesHStack and valuesVStack for sub-classes.
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
920 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
921 def __init__(self,description=None,field_types=None):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
922 DataSet.__init__(self,description,field_types)
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
923 def valuesHStack(self,fieldnames,fieldvalues):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
924 """Concatenate field values horizontally, e.g. two vectors
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
925 become a longer vector, two matrices become a wider matrix, etc."""
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
926 return numpy.hstack(fieldvalues)
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
927 def valuesVStack(self,fieldname,values):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
928 """Concatenate field values vertically, e.g. two vectors
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
929 become a two-row matrix, two matrices become a longer matrix, etc."""
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
930 return numpy.vstack(values)
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
931
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
932 class ArrayDataSet(ArrayFieldsDataSet):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
933 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
934 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
935 whose first axis iterates over examples, second axis determines fields.
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
936 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
937 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
938 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
939
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
940 def __init__(self, data_array, fields_columns):
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
941 """
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
942 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
943 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
944 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
945 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
946 """
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
947 self.data=data_array
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
948 self.fields_columns=fields_columns
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
949
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
950 # check consistency and complete slices definitions
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
951 for fieldname, fieldcolumns in self.fields_columns.items():
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
952 if type(fieldcolumns) is int:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
953 assert fieldcolumns>=0 and fieldcolumns<data_array.shape[1]
99
a8da709eb6a9 in ArrayDataSet.__init__ if a columns is an index, we change it to be a list that containt only this index. This way, we remove the special case where the columns is an index for all subsequent call.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 98
diff changeset
954 self.fields_columns[fieldname]=[fieldcolumns]
41
283e95c15b47 Added ArrayDataSet
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parents: 40
diff changeset
955 elif type(fieldcolumns) is slice:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
956 start,step=None,None
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
957 if not fieldcolumns.start:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
958 start=0
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
959 if not fieldcolumns.step:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
960 step=1
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
961 if start or step:
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
962 self.fields_columns[fieldname]=slice(start,fieldcolumns.stop,step)
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
963 elif hasattr(fieldcolumns,"__iter__"): # something like a list
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
964 for i in fieldcolumns:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
965 assert i>=0 and i<data_array.shape[1]
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
966
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
967 def fieldNames(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
968 return self.fields_columns.keys()
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
969
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
970 def __len__(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
971 return len(self.data)
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
972
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
973 def __getitem__(self,key):
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
974 """More efficient implementation than the default __getitem__"""
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
975 fieldnames=self.fields_columns.keys()
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
976 if type(key) is int:
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
977 return Example(fieldnames,
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
978 [self.data[key,self.fields_columns[f]] for f in fieldnames])
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
979 if type(key) is slice:
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
980 return MinibatchDataSet(Example(fieldnames,
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
981 [self.data[key,self.fields_columns[f]] for f in fieldnames]))
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
982 if type(key) is list:
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
983 for i in range(len(key)):
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
984 if self.hasFields(key[i]):
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
985 key[i]=self.fields_columns[key[i]]
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
986 return MinibatchDataSet(Example(fieldnames,
88
6749d18e11c8 bugfix as numpy numpy don't support self.data[[i1,...],[i2,...]] when their is more then two i1 and i2
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 85
diff changeset
987 #we must separate differently for list as numpy
128
ee5507af2c60 minor edits
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 125
diff changeset
988 # doesn't support self.data[[i1,...],[i2,...]]
88
6749d18e11c8 bugfix as numpy numpy don't support self.data[[i1,...],[i2,...]] when their is more then two i1 and i2
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 85
diff changeset
989 # when their is more then two i1 and i2
6749d18e11c8 bugfix as numpy numpy don't support self.data[[i1,...],[i2,...]] when their is more then two i1 and i2
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 85
diff changeset
990 [self.data[key,:][:,self.fields_columns[f]]
6749d18e11c8 bugfix as numpy numpy don't support self.data[[i1,...],[i2,...]] when their is more then two i1 and i2
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 85
diff changeset
991 if isinstance(self.fields_columns[f],list) else
128
ee5507af2c60 minor edits
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 125
diff changeset
992 self.data[key,self.fields_columns[f]] for f in fieldnames]),
ee5507af2c60 minor edits
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 125
diff changeset
993
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
994 self.valuesVStack,self.valuesHStack)
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
995
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
996 # else check for a fieldname
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
997 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
998 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
999 # else we are trying to access a property of the dataset
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1000 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
1001 return self.__dict__[key]
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1002
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1003
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1004 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
1005 class ArrayDataSetIterator(object):
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1006 def __init__(self,dataset,fieldnames,minibatch_size,n_batches,offset):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1007 if fieldnames is None: fieldnames = dataset.fieldNames()
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
1008 # store the resulting minibatch in a lookup-list of values
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
1009 self.minibatch = LookupList(fieldnames,[0]*len(fieldnames))
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1010 self.dataset=dataset
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1011 self.minibatch_size=minibatch_size
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1012 assert offset>=0 and offset<len(dataset.data)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1013 assert offset+minibatch_size<=len(dataset.data)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1014 self.current=offset
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1015 def __iter__(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1016 return self
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1017 def next(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1018 sub_data = self.dataset.data[self.current:self.current+self.minibatch_size]
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
1019 self.minibatch._values = [sub_data[:,self.dataset.fields_columns[f]] for f in self.minibatch._names]
43
e92244f30116 Corrected iterator logic errors
bengioy@grenat.iro.umontreal.ca
parents: 42
diff changeset
1020 self.current+=self.minibatch_size
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
1021 return self.minibatch
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1022
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
1023 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
1024
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1025
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1026 class CachedDataSet(DataSet):
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1027 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1028 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
1029 (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
1030 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
1031 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
1032
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1033 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
1034 (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
1035 first access.
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1036
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1037 @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
1038 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
1039
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1040 @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
1041 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
1042 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
1043 """
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1044 def __init__(self,source_dataset,cache_all_upon_construction=False):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1045 self.source_dataset=source_dataset
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1046 self.cache_all_upon_construction=cache_all_upon_construction
152
3f627e844cba Fixes in CacheDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 151
diff changeset
1047 self.cached_examples = []
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1048 if cache_all_upon_construction:
77
1e2bb5bad636 toying with different ways to implement learners
bengioy@bengiomac.local
parents: 74
diff changeset
1049 # this potentially brings all the source examples
1e2bb5bad636 toying with different ways to implement learners
bengioy@bengiomac.local
parents: 74
diff changeset
1050 # into memory at once, which may be too much
1e2bb5bad636 toying with different ways to implement learners
bengioy@bengiomac.local
parents: 74
diff changeset
1051 # the work could possibly be done by minibatches
1e2bb5bad636 toying with different ways to implement learners
bengioy@bengiomac.local
parents: 74
diff changeset
1052 # 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
1053 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
1054 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
1055 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
1056 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
1057
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1058 self.fieldNames = source_dataset.fieldNames
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1059 self.hasFields = source_dataset.hasFields
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1060 self.valuesHStack = source_dataset.valuesHStack
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1061 self.valuesVStack = source_dataset.valuesVStack
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1062
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1063 def __len__(self):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1064 return len(self.source_dataset)
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1065
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1066 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1067 class CacheIterator(object):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1068 def __init__(self,dataset):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1069 self.dataset=dataset
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1070 self.current=offset
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1071 def __iter__(self): return self
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diff changeset
1072 def next(self):
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parents: 72
diff changeset
1073 upper = self.current+minibatch_size
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diff changeset
1074 cache_len = len(self.dataset.cached_examples)
135
0d8e721cc63c Fixed bugs in dataset to make test_mlp.py work
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diff changeset
1075 if upper>cache_len: # whole minibatch is not already in cache
73
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diff changeset
1076 # cache everything from current length to upper
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diff changeset
1077 for example in self.dataset.source_dataset[cache_len:upper]:
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parents: 72
diff changeset
1078 self.dataset.cached_examples.append(example)
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diff changeset
1079 all_fields_minibatch = Example(self.dataset.fieldNames(),
152
3f627e844cba Fixes in CacheDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 151
diff changeset
1080 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
1081 self.current+=minibatch_size
73
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diff changeset
1082 if self.dataset.fieldNames()==fieldnames:
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diff changeset
1083 return all_fields_minibatch
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diff changeset
1084 return Example(fieldnames,[all_fields_minibatch[name] for name in fieldnames])
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diff changeset
1085 return CacheIterator(self)
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diff changeset
1086
153
71107b0ac860 optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 151
diff changeset
1087 def __getitem__(self,i):
71107b0ac860 optimization
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diff changeset
1088 if type(i)==int and len(self.cached_examples)>i:
71107b0ac860 optimization
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parents: 151
diff changeset
1089 return self.cached_examples[i]
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Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 151
diff changeset
1090 else:
71107b0ac860 optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 151
diff changeset
1091 return DataSet.__getitem__(self,i)
73
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diff changeset
1092
57
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1093 class ApplyFunctionDataSet(DataSet):
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
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diff changeset
1094 """
167
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diff changeset
1095 A L{DataSet} that contains as fields the results of applying a
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Joseph Turian <turian@gmail.com>
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diff changeset
1096 given function example-wise or minibatch-wise to all the fields of
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Joseph Turian <turian@gmail.com>
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diff changeset
1097 an input dataset. The output of the function should be an iterable
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Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1098 (e.g. a list or a LookupList) over the resulting values.
197
96d891448107 more explicit comment
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 196
diff changeset
1099
96d891448107 more explicit comment
Frederic Bastien <bastienf@iro.umontreal.ca>
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diff changeset
1100 The function take as input the fields of the dataset, not the examples.
73
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diff changeset
1101
167
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Joseph Turian <turian@gmail.com>
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diff changeset
1102 In minibatch mode, the function is expected to work on minibatches
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diff changeset
1103 (takes a minibatch in input and returns a minibatch in output). More
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1104 precisely, it means that each element of the input or output list
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Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1105 should be iterable and indexable over the individual example values
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diff changeset
1106 (typically these elements will be numpy arrays). All of the elements
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Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1107 in the input and output lists should have the same length, which is
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diff changeset
1108 the length of the minibatch.
57
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
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diff changeset
1109
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parents: 56
diff changeset
1110 The function is applied each time an example or a minibatch is accessed.
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1111 To avoid re-doing computation, wrap this dataset inside a CachedDataSet.
73
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diff changeset
1112
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diff changeset
1113 If the values_{h,v}stack functions are not provided, then
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1114 the input_dataset.values{H,V}Stack functions are used by default.
57
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
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diff changeset
1115 """
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1116 def __init__(self,input_dataset,function,output_names,minibatch_mode=True,
74
b4159cbdc06b Fixed errors raised by test_dataset
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 73
diff changeset
1117 values_hstack=None,values_vstack=None,
73
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diff changeset
1118 description=None,fieldtypes=None):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1119 """
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diff changeset
1120 Constructor takes an input dataset that has as many fields as the function
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diff changeset
1121 expects as inputs. The resulting dataset has as many fields as the function
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diff changeset
1122 produces as outputs, and that should correspond to the number of output names
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parents: 72
diff changeset
1123 (provided in a list).
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1124
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1125 Note that the expected semantics of the function differs in minibatch mode
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parents: 72
diff changeset
1126 (it takes minibatches of inputs and produces minibatches of outputs, as
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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parents: 72
diff changeset
1127 documented in the class comment).
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1128 """
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diff changeset
1129 self.input_dataset=input_dataset
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diff changeset
1130 self.function=function
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diff changeset
1131 self.output_names=output_names
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diff changeset
1132 self.minibatch_mode=minibatch_mode
134
3f4e5c9bdc5e Fixes to ApplyFunctionDataSet and other things to make learner and mlp work
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diff changeset
1133 DataSet.__init__(self,description,fieldtypes)
73
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diff changeset
1134 self.valuesHStack = values_hstack if values_hstack else input_dataset.valuesHStack
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diff changeset
1135 self.valuesVStack = values_vstack if values_vstack else input_dataset.valuesVStack
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parents: 72
diff changeset
1136
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1137 def __len__(self):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1138 return len(self.input_dataset)
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diff changeset
1139
134
3f4e5c9bdc5e Fixes to ApplyFunctionDataSet and other things to make learner and mlp work
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diff changeset
1140 def fieldNames(self):
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1141 return self.output_names
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diff changeset
1142
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1143 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1144 class ApplyFunctionIterator(object):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1145 def __init__(self,output_dataset):
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diff changeset
1146 self.input_dataset=output_dataset.input_dataset
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diff changeset
1147 self.output_dataset=output_dataset
134
3f4e5c9bdc5e Fixes to ApplyFunctionDataSet and other things to make learner and mlp work
Yoshua Bengio <bengioy@iro.umontreal.ca>
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diff changeset
1148 self.input_iterator=self.input_dataset.minibatches(minibatch_size=minibatch_size,
3f4e5c9bdc5e Fixes to ApplyFunctionDataSet and other things to make learner and mlp work
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diff changeset
1149 n_batches=n_batches,offset=offset).__iter__()
73
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diff changeset
1150
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1151 def __iter__(self): return self
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1152
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1153 def next(self):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1154 function_inputs = self.input_iterator.next()
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1155 all_output_names = self.output_dataset.output_names
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diff changeset
1156 if self.output_dataset.minibatch_mode:
134
3f4e5c9bdc5e Fixes to ApplyFunctionDataSet and other things to make learner and mlp work
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diff changeset
1157 function_outputs = self.output_dataset.function(*function_inputs)
73
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diff changeset
1158 else:
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1159 input_examples = zip(*function_inputs)
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1160 output_examples = [self.output_dataset.function(input_example)
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diff changeset
1161 for input_example in input_examples]
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1162 function_outputs = [self.output_dataset.valuesVStack(name,values)
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diff changeset
1163 for name,values in zip(all_output_names,
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diff changeset
1164 zip(*output_examples))]
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diff changeset
1165 all_outputs = Example(all_output_names,function_outputs)
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1166 if fieldnames==all_output_names:
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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parents: 72
diff changeset
1167 return all_outputs
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1168 return Example(fieldnames,[all_outputs[name] for name in fieldnames])
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diff changeset
1169
134
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diff changeset
1170 return ApplyFunctionIterator(self)
73
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diff changeset
1171
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diff changeset
1172 def __iter__(self): # only implemented for increased efficiency
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diff changeset
1173 class ApplyFunctionSingleExampleIterator(object):
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diff changeset
1174 def __init__(self,output_dataset):
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diff changeset
1175 self.current=0
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diff changeset
1176 self.output_dataset=output_dataset
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diff changeset
1177 self.input_iterator=output_dataset.input_dataset.__iter__()
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diff changeset
1178 def __iter__(self): return self
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diff changeset
1179 def next(self):
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diff changeset
1180 function_inputs = self.input_iterator.next()
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diff changeset
1181 if self.output_dataset.minibatch_mode:
198
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diff changeset
1182 function_outputs = self.output_dataset.function(*function_inputs)
73
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diff changeset
1183 else:
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diff changeset
1184 function_outputs = self.output_dataset.function(function_inputs)
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diff changeset
1185 return Example(self.output_dataset.output_names,function_outputs)
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diff changeset
1186 return ApplyFunctionSingleExampleIterator(self)
57
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
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parents: 56
diff changeset
1187
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1188
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1189 def supervised_learning_dataset(src_dataset,input_fields,target_fields,weight_field=None):
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
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parents: 22
diff changeset
1190 """
167
4803cb76e26b Updated documentation
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diff changeset
1191 Wraps an arbitrary L{DataSet} into one for supervised learning tasks
4803cb76e26b Updated documentation
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parents: 166
diff changeset
1192 by forcing the user to define a set of fields as the 'input' field
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parents: 166
diff changeset
1193 and a set of fields as the 'target' field. Optionally, a single
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parents: 166
diff changeset
1194 weight_field can also be defined.
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
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parents: 22
diff changeset
1195 """
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
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parents: 22
diff changeset
1196 args = ((input_fields,'input'),(output_fields,'target'))
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
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parents: 22
diff changeset
1197 if weight_field: args+=(([weight_field],'weight'))
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
1198 return src_dataset.merge_fields(*args)
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
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parents: 22
diff changeset
1199
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
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parents: 22
diff changeset
1200
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
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parents: 22
diff changeset
1201
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
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parents: 22
diff changeset
1202