annotate dataset.py @ 146:8173e196e291

Trying to make CacheDataSet work
author Yoshua Bengio <bengioy@iro.umontreal.ca>
date Mon, 12 May 2008 15:50:28 -0400
parents ceae4de18981
children 39bb21348fdf
rev   line source
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2 from lookup_list import LookupList
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3 Example = LookupList
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4 from misc import unique_elements_list_intersection
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5 from string import join
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6 from sys import maxint
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7 import numpy
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759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
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9 class AbstractFunction (Exception): """Derived class must override this function"""
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10 class NotImplementedYet (NotImplementedError): """Work in progress, this should eventually be implemented"""
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12 class AttributesHolder(object):
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13 def __init__(self): pass
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14
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15 def attributeNames(self):
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16 raise AbstractFunction()
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18 def setAttributes(self,attribute_names,attribute_values,make_copies=False):
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19 """
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20 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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21 """
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22 if len(attribute_names)==1 and not (isinstance(attribute_values,list) or isinstance(attribute_values,tuple) ):
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23 attribute_values = [attribute_values]
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24 if make_copies:
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25 for name,value in zip(attribute_names,attribute_values):
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26 self.__setattr__(name,copy.deepcopy(value))
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27 else:
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28 for name,value in zip(attribute_names,attribute_values):
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29 self.__setattr__(name,value)
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32 class DataSet(AttributesHolder):
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33 """A virtual base class for datasets.
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34
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35 A DataSet can be seen as a generalization of a matrix, meant to be used in conjunction
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36 with learning algorithms (for training and testing them): rows/records are called examples, and
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37 columns/attributes are called fields. The field value for a particular example can be an arbitrary
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38 python object, which depends on the particular dataset.
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39
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40 We call a DataSet a 'stream' when its length is unbounded (otherwise its __len__ method
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41 should return sys.maxint).
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42
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43 A DataSet is a generator of iterators; these iterators can run through the
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44 examples or the fields in a variety of ways. A DataSet need not necessarily have a finite
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45 or known length, so this class can be used to interface to a 'stream' which
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46 feeds on-line learning (however, as noted below, some operations are not
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47 feasible or not recommanded on streams).
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49 To iterate over examples, there are several possibilities:
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50 - for example in dataset:
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51 - for val1,val2,... in dataset:
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52 - for example in dataset(field1, field2,field3, ...):
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53 - for val1,val2,val3 in dataset(field1, field2,field3):
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54 - for minibatch in dataset.minibatches([field1, field2, ...],minibatch_size=N):
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55 - for mini1,mini2,mini3 in dataset.minibatches([field1, field2, field3], minibatch_size=N):
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56 Each of these is documented below. All of these iterators are expected
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57 to provide, in addition to the usual 'next()' method, a 'next_index()' method
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58 which returns a non-negative integer pointing to the position of the next
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59 example that will be returned by 'next()' (or of the first example in the
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60 next minibatch returned). This is important because these iterators
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61 can wrap around the dataset in order to do multiple passes through it,
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62 in possibly unregular ways if the minibatch size is not a divisor of the
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63 dataset length.
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65 To iterate over fields, one can do
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66 - for field in dataset.fields():
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67 for field_value in field: # iterate over the values associated to that field for all the dataset examples
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68 - for field in dataset(field1,field2,...).fields() to select a subset of fields
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69 - for field in dataset.fields(field1,field2,...) to select a subset of fields
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70 and each of these fields is iterable over the examples:
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71 - for field_examples in dataset.fields():
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72 for example_value in field_examples:
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73 ...
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74 but when the dataset is a stream (unbounded length), it is not recommanded to do
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75 such things because the underlying dataset may refuse to access the different fields in
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76 an unsynchronized ways. Hence the fields() method is illegal for streams, by default.
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77 The result of fields() is a L{DataSetFields} object, which iterates over fields,
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78 and whose elements are iterable over examples. A DataSetFields object can
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79 be turned back into a DataSet with its examples() method::
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80 dataset2 = dataset1.fields().examples()
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81 and dataset2 should behave exactly like dataset1 (in fact by default dataset2==dataset1).
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82
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83 Note: Fields are not mutually exclusive, i.e. two fields can overlap in their actual content.
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84
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85 Note: The content of a field can be of any type. Field values can also be 'missing'
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86 (e.g. to handle semi-supervised learning), and in the case of numeric (numpy array)
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87 fields (i.e. an ArrayFieldsDataSet), NaN plays the role of a missing value.
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88 What about non-numeric values? None.
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89
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90 Dataset elements can be indexed and sub-datasets (with a subset
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91 of examples) can be extracted. These operations are not supported
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92 by default in the case of streams.
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93
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94 - dataset[:n] returns a dataset with the n first examples.
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95
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96 - dataset[i1:i2:s] returns a dataset with the examples i1,i1+s,...i2-s.
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97
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98 - dataset[i] returns an Example.
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99
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100 - dataset[[i1,i2,...in]] returns a dataset with examples i1,i2,...in.
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101
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102 - dataset[fieldname] an iterable over the values of the field fieldname across
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103 the dataset (the iterable is obtained by default by calling valuesVStack
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104 over the values for individual examples).
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105
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106 - dataset.<property> returns the value of a property associated with
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107 the name <property>. The following properties should be supported:
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108 - 'description': a textual description or name for the dataset
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109 - 'fieldtypes': a list of types (one per field)
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110 A DataSet may have other attributes that it makes visible to other objects. These are
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111 used to store information that is not example-wise but global to the dataset.
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112 The list of names of these attributes is given by the attribute_names() method.
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113
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114 Datasets can be concatenated either vertically (increasing the length) or
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115 horizontally (augmenting the set of fields), if they are compatible, using
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116 the following operations (with the same basic semantics as numpy.hstack
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117 and numpy.vstack):
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118
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119 - dataset1 | dataset2 | dataset3 == dataset.hstack([dataset1,dataset2,dataset3])
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120
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121 creates a new dataset whose list of fields is the concatenation of the list of
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122 fields of the argument datasets. This only works if they all have the same length.
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123
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124 - dataset1 & dataset2 & dataset3 == dataset.vstack([dataset1,dataset2,dataset3])
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125
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126 creates a new dataset that concatenates the examples from the argument datasets
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127 (and whose length is the sum of the length of the argument datasets). This only
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128 works if they all have the same fields.
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129
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130 According to the same logic, and viewing a DataSetFields object associated to
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131 a DataSet as a kind of transpose of it, fields1 & fields2 concatenates fields of
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132 a DataSetFields fields1 and fields2, and fields1 | fields2 concatenates their
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133 examples.
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134
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135 A dataset can hold arbitrary key-value pairs that may be used to access meta-data
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136 or other properties of the dataset or associated with the dataset or the result
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137 of a computation stored in a dataset. These can be accessed through the [key] syntax
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138 when key is a string (or more specifically, neither an integer, a slice, nor a list).
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139
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140 A DataSet sub-class should always redefine the following methods:
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141 - __len__ if it is not a stream
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142 - fieldNames
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143 - minibatches_nowrap (called by DataSet.minibatches())
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144 - valuesHStack
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145 - valuesVStack
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146 For efficiency of implementation, a sub-class might also want to redefine
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147 - hasFields
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148 - __getitem__ may not be feasible with some streams
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149 - __iter__
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150 A sub-class should also append attributes to self._attribute_names
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151 (the default value returned by attributeNames()).
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152 By convention, attributes not in attributeNames() should have a name
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153 starting with an underscore.
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154 @todo enforce/test that convention!
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155 """
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156
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157 numpy_vstack = lambda fieldname,values: numpy.vstack(values)
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158 numpy_hstack = lambda fieldnames,values: numpy.hstack(values)
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159
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160 def __init__(self,description=None,fieldtypes=None):
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161 if description is None:
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162 # by default return "<DataSetType>(<SuperClass1>,<SuperClass2>,...)"
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163 description = type(self).__name__ + " ( " + join([x.__name__ for x in type(self).__bases__]) + " )"
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164 self.description=description
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165 self.fieldtypes=fieldtypes
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166 self._attribute_names = ["description"]
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167 if fieldtypes:
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168 self._attribute_names.append("fieldtypes")
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169
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170 def attributeNames(self): return self._attribute_names
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171
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172 class MinibatchToSingleExampleIterator(object):
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173 """
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174 Converts the result of minibatch iterator with minibatch_size==1 into
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175 single-example values in the result. Therefore the result of
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176 iterating on the dataset itself gives a sequence of single examples
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177 (whereas the result of iterating over minibatches gives in each
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178 Example field an iterable object over the individual examples in
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179 the minibatch).
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180 """
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181 def __init__(self, minibatch_iterator):
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182 self.minibatch_iterator = minibatch_iterator
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183 self.minibatch = None
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184 def __iter__(self): #makes for loop work
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185 return self
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186 def next(self):
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187 size1_minibatch = self.minibatch_iterator.next()
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188 if not self.minibatch:
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189 self.minibatch = Example(size1_minibatch.keys(),[value[0] for value in size1_minibatch.values()])
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190 else:
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191 self.minibatch._values = [value[0] for value in size1_minibatch.values()]
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192 return self.minibatch
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193
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194 def next_index(self):
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195 return self.minibatch_iterator.next_index()
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196
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197 def __iter__(self):
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198 """Supports the syntax "for i in dataset: ..."
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199
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200 Using this syntax, "i" will be an Example instance (or equivalent) with
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201 all the fields of DataSet self. Every field of "i" will give access to
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202 a field of a single example. Fields should be accessible via
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203 i["fielname"] or i[3] (in the order defined by the elements of the
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204 Example returned by this iterator), but the derived class is free
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205 to accept any type of identifier, and add extra functionality to the iterator.
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206
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207 The default implementation calls the minibatches iterator and extracts the first example of each field.
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208 """
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209 return DataSet.MinibatchToSingleExampleIterator(self.minibatches(None, minibatch_size = 1))
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210
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211
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212 class MinibatchWrapAroundIterator(object):
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213 """
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214 An iterator for minibatches that handles the case where we need to wrap around the
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215 dataset because n_batches*minibatch_size > len(dataset). It is constructed from
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216 a dataset that provides a minibatch iterator that does not need to handle that problem.
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217 This class is a utility for dataset subclass writers, so that they do not have to handle
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218 this issue multiple times, nor check that fieldnames are valid, nor handle the
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219 empty fieldnames (meaning 'use all the fields').
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220 """
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221 def __init__(self,dataset,fieldnames,minibatch_size,n_batches,offset):
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222 self.dataset=dataset
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223 self.fieldnames=fieldnames
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224 self.minibatch_size=minibatch_size
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225 self.n_batches=n_batches
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226 self.n_batches_done=0
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227 self.next_row=offset
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228 self.offset=offset
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229 self.L=len(dataset)
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230 assert offset+minibatch_size<=self.L
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231 ds_nbatches = (self.L-self.next_row)/self.minibatch_size
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232 if n_batches is not None:
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233 ds_nbatches = min(n_batches,ds_nbatches)
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234 if fieldnames:
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235 assert dataset.hasFields(*fieldnames)
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236 else:
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237 self.fieldnames=dataset.fieldNames()
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238 self.iterator = self.dataset.minibatches_nowrap(self.fieldnames,self.minibatch_size,
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239 ds_nbatches,self.next_row)
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240
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241 def __iter__(self):
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242 return self
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243
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244 def next_index(self):
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245 return self.next_row
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246
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247 def next(self):
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248 if self.n_batches and self.n_batches_done==self.n_batches:
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249 raise StopIteration
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250 elif not self.n_batches and self.next_row ==self.L:
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251 raise StopIteration
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252 upper = self.next_row+self.minibatch_size
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253 if upper <=self.L:
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254 minibatch = self.iterator.next()
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255 else:
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256 if not self.n_batches:
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257 upper=min(upper, self.L)
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258 # if their is not a fixed number of batch, we continue to the end of the dataset.
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259 # this can create a minibatch that is smaller then the minibatch_size
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260 assert (self.L-self.next_row)<=self.minibatch_size
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261 minibatch = self.dataset.minibatches_nowrap(self.fieldnames,self.L-self.next_row,1,self.next_row).next()
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262 else:
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263 # we must concatenate (vstack) the bottom and top parts of our minibatch
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264 # first get the beginning of our minibatch (top of dataset)
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265 first_part = self.dataset.minibatches_nowrap(self.fieldnames,self.L-self.next_row,1,self.next_row).next()
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266 second_part = self.dataset.minibatches_nowrap(self.fieldnames,upper-self.L,1,0).next()
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267 minibatch = Example(self.fieldnames,
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268 [self.dataset.valuesVStack(name,[first_part[name],second_part[name]])
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269 for name in self.fieldnames])
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270 self.next_row=upper
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271 self.n_batches_done+=1
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272 if upper >= self.L and self.n_batches:
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273 self.next_row -= self.L
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274 ds_nbatches = (self.L-self.next_row)/self.minibatch_size
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275 if self.n_batches is not None:
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276 ds_nbatches = min(self.n_batches,ds_nbatches)
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277 self.iterator = self.dataset.minibatches_nowrap(self.fieldnames,self.minibatch_size,
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278 ds_nbatches,self.next_row)
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279 return DataSetFields(MinibatchDataSet(minibatch,self.dataset.valuesVStack,
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280 self.dataset.valuesHStack),
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281 minibatch.keys())
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282
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283
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284 minibatches_fieldnames = None
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285 minibatches_minibatch_size = 1
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286 minibatches_n_batches = None
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287 def minibatches(self,
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288 fieldnames = minibatches_fieldnames,
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289 minibatch_size = minibatches_minibatch_size,
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290 n_batches = minibatches_n_batches,
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291 offset = 0):
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292 """
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293 Return an iterator that supports three forms of syntax:
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294
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295 for i in dataset.minibatches(None,**kwargs): ...
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296
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297 for i in dataset.minibatches([f1, f2, f3],**kwargs): ...
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298
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299 for i1, i2, i3 in dataset.minibatches([f1, f2, f3],**kwargs): ...
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300
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301 Using the first two syntaxes, "i" will be an indexable object, such as a list,
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302 tuple, or Example instance. In both cases, i[k] is a list-like container
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303 of a batch of current examples. In the second case, i[0] is
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304 list-like container of the f1 field of a batch current examples, i[1] is
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305 a list-like container of the f2 field, etc.
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306
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307 Using the first syntax, all the fields will be returned in "i".
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308 Using the third syntax, i1, i2, i3 will be list-like containers of the
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309 f1, f2, and f3 fields of a batch of examples on each loop iteration.
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310
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311 The minibatches iterator is expected to return upon each call to next()
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312 a DataSetFields object, which is a LookupList (indexed by the field names) whose
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313 elements are iterable and indexable over the minibatch examples, and which keeps a pointer to
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314 a sub-dataset that can be used to iterate over the individual examples
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315 in the minibatch. Hence a minibatch can be converted back to a regular
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316 dataset or its fields can be looked at individually (and possibly iterated over).
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317
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318 PARAMETERS
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319 - fieldnames (list of any type, default None):
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320 The loop variables i1, i2, i3 (in the example above) should contain the
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321 f1, f2, and f3 fields of the current batch of examples. If None, the
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322 derived class can choose a default, e.g. all fields.
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323
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324 - minibatch_size (integer, default 1)
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325 On every iteration, the variables i1, i2, i3 will have
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326 exactly minibatch_size elements. e.g. len(i1) == minibatch_size
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327
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328 - n_batches (integer, default None)
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329 The iterator will loop exactly this many times, and then stop. If None,
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330 the derived class can choose a default. If (-1), then the returned
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331 iterator should support looping indefinitely.
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332
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333 - offset (integer, default 0)
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334 The iterator will start at example 'offset' in the dataset, rather than the default.
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335
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336 Note: A list-like container is something like a tuple, list, numpy.ndarray or
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337 any other object that supports integer indexing and slicing.
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338
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339 """
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340 return DataSet.MinibatchWrapAroundIterator(self,fieldnames,minibatch_size,n_batches,offset)
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341
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342 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
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343 """
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344 This is the minibatches iterator generator that sub-classes must define.
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345 It does not need to worry about wrapping around multiple times across the dataset,
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346 as this is handled by MinibatchWrapAroundIterator when DataSet.minibatches() is called.
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347 The next() method of the returned iterator does not even need to worry about
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348 the termination condition (as StopIteration will be raised by DataSet.minibatches
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349 before an improper call to minibatches_nowrap's next() is made).
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350 That next() method can assert that its next row will always be within [0,len(dataset)).
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351 The iterator returned by minibatches_nowrap does not need to implement
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352 a next_index() method either, as this will be provided by MinibatchWrapAroundIterator.
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353 """
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354 raise AbstractFunction()
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355
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356 def __len__(self):
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357 """
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358 len(dataset) returns the number of examples in the dataset.
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359 By default, a DataSet is a 'stream', i.e. it has an unbounded length (sys.maxint).
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360 Sub-classes which implement finite-length datasets should redefine this method.
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361 Some methods only make sense for finite-length datasets.
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362 """
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363 return maxint
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364
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365 def is_unbounded(self):
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366 """
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367 Tests whether a dataset is unbounded (e.g. a stream).
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368 """
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369 return len(self)==maxint
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370
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371 def hasFields(self,*fieldnames):
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372 """
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373 Return true if the given field name (or field names, if multiple arguments are
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374 given) is recognized by the DataSet (i.e. can be used as a field name in one
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375 of the iterators).
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376
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377 The default implementation may be inefficient (O(# fields in dataset)), as it calls the fieldNames()
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378 method. Many datasets may store their field names in a dictionary, which would allow more efficiency.
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379 """
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380 return len(unique_elements_list_intersection(fieldnames,self.fieldNames()))>0
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381
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382 def fieldNames(self):
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383 """
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384 Return the list of field names that are supported by the iterators,
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385 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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386 """
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
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parents: 16 12
diff changeset
387 raise AbstractFunction()
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parents: 16 12
diff changeset
388
36
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389 def __call__(self,*fieldnames):
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
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parents: 22
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390 """
36
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391 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
392 """
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
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393 assert self.hasFields(*fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
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394 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
395
36
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396 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
397 """
36
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398 Return a DataSetFields object associated with this dataset.
17
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bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
399 """
74
b4159cbdc06b Fixed errors raised by test_dataset
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 73
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400 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
401
2
3fddb1c8f955 Rewrote DataSet interface and created FiniteDataSet interface.
bengioy@bengiomac.local
parents: 1
diff changeset
402 def __getitem__(self,i):
28
541a273bc89f Removed __array__ method from dataset, whose
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parents: 26
diff changeset
403 """
541a273bc89f Removed __array__ method from dataset, whose
bengioy@grenat.iro.umontreal.ca
parents: 26
diff changeset
404 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
405 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
406 dataset[i:j:s] returns the subdataset with examples i,i+2,i+4...,j-2.
541a273bc89f Removed __array__ method from dataset, whose
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parents: 26
diff changeset
407 dataset[[i1,i2,..,in]] returns the subdataset with examples i1,i2,...,in.
41
283e95c15b47 Added ArrayDataSet
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parents: 40
diff changeset
408 dataset['key'] returns a property associated with the given 'key' string.
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
409 If 'key' is a fieldname, then the VStacked field values (iterable over
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
410 field values) for that field is returned. Other keys may be supported
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
411 by different dataset subclasses. The following key names are encouraged:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
412 - 'description': a textual description or name for the dataset
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
413 - '<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
414
39
c682c6e9bf93 Minor edits
bengioy@esprit.iro.umontreal.ca
parents: 38
diff changeset
415 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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416 arbitrary slicing/indexing
36
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417 because they can only iterate through examples one or a minibatch at a time
438440ba0627 Rewriting dataset.py completely
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418 and do not actually store or keep past (or future) examples.
40
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diff changeset
419
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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420 The default implementation of getitem uses the minibatches iterator
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 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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422 always be the most efficient way to obtain the result, especially if
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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423 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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424 """
41
283e95c15b47 Added ArrayDataSet
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425 # check for an index
40
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parents: 39
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426 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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427 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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428 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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429 rows=None
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430 # or a slice
40
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parents: 39
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431 if type(i) is slice:
135
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Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 134
diff changeset
432 if not i.start: i=slice(0,i.stop,i.step)
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parents: 134
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433 if not i.step: i=slice(i.start,i.stop,1)
40
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parents: 39
diff changeset
434 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
435 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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436 rows = range(i.start,i.stop,i.step)
41
283e95c15b47 Added ArrayDataSet
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parents: 40
diff changeset
437 # or a list of indices
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parents: 40
diff changeset
438 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
439 rows = i
41
283e95c15b47 Added ArrayDataSet
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parents: 40
diff changeset
440 if rows is not None:
48
b6730f9a336d Fixing MinibatchDataSet getitem
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parents: 46
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441 examples = [self[row] for row in rows]
b6730f9a336d Fixing MinibatchDataSet getitem
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parents: 46
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442 fields_values = zip(*examples)
45
a5c70dc42972 Test functions for dataset.py
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parents: 44
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443 return MinibatchDataSet(
41
283e95c15b47 Added ArrayDataSet
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parents: 40
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444 Example(self.fieldNames(),[ self.valuesVStack(fieldname,field_values)
283e95c15b47 Added ArrayDataSet
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parents: 40
diff changeset
445 for fieldname,field_values
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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parents: 72
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446 in zip(self.fieldNames(),fields_values)]),
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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447 self.valuesVStack,self.valuesHStack)
41
283e95c15b47 Added ArrayDataSet
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parents: 40
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448 # else check for a fieldname
283e95c15b47 Added ArrayDataSet
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parents: 40
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449 if self.hasFields(i):
283e95c15b47 Added ArrayDataSet
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450 return self.minibatches(fieldnames=[i],minibatch_size=len(self),n_batches=1,offset=0).next()[0]
283e95c15b47 Added ArrayDataSet
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451 # else we are trying to access a property of the dataset
283e95c15b47 Added ArrayDataSet
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parents: 40
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452 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
453 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
454
36
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455 def valuesHStack(self,fieldnames,fieldvalues):
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456 """
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457 Return a value that corresponds to concatenating (horizontally) several field values.
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458 This can be useful to merge some fields. The implementation of this operation is likely
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
459 to involve a copy of the original values. When the values are numpy arrays, the
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
460 result should be numpy.hstack(values). If it makes sense, this operation should
438440ba0627 Rewriting dataset.py completely
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diff changeset
461 work as well when each value corresponds to multiple examples in a minibatch
438440ba0627 Rewriting dataset.py completely
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462 e.g. if each value is a Ni-vector and a minibatch of length L is a LxNi matrix,
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parents: 29
diff changeset
463 then the result should be a Lx(N1+N2+..) matrix equal to numpy.hstack(values).
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464 The default is to use numpy.hstack for numpy.ndarray values, and a list
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465 pointing to the original values for other data types.
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466 """
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467 all_numpy=True
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468 for value in fieldvalues:
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diff changeset
469 if not type(value) is numpy.ndarray:
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470 all_numpy=False
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471 if all_numpy:
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472 return numpy.hstack(fieldvalues)
438440ba0627 Rewriting dataset.py completely
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473 # the default implementation of horizontal stacking is to put values in a list
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474 return fieldvalues
26
672fe4b23032 Fixed dataset errors so that _test_dataset.py works again.
bengioy@grenat.iro.umontreal.ca
parents: 23
diff changeset
475
672fe4b23032 Fixed dataset errors so that _test_dataset.py works again.
bengioy@grenat.iro.umontreal.ca
parents: 23
diff changeset
476
36
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diff changeset
477 def valuesVStack(self,fieldname,values):
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parents: 29
diff changeset
478 """
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
479 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
480 same field. This can be important to build a minibatch out of individual examples. This
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
481 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
482 result should be numpy.vstack(values).
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
483 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
484 pointing to the original values for other data types.
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
485 """
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
486 all_numpy=True
438440ba0627 Rewriting dataset.py completely
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diff changeset
487 for value in values:
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
488 if not type(value) is numpy.ndarray:
438440ba0627 Rewriting dataset.py completely
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diff changeset
489 all_numpy=False
438440ba0627 Rewriting dataset.py completely
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diff changeset
490 if all_numpy:
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
491 return numpy.vstack(values)
438440ba0627 Rewriting dataset.py completely
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diff changeset
492 # the default implementation of vertical stacking is to put values in a list
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parents: 29
diff changeset
493 return values
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
494
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
495 def __or__(self,other):
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diff changeset
496 """
438440ba0627 Rewriting dataset.py completely
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diff changeset
497 dataset1 | dataset2 returns a dataset whose list of fields is the concatenation of the list of
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parents: 29
diff changeset
498 fields of the argument datasets. This only works if they all have the same length.
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parents: 29
diff changeset
499 """
135
0d8e721cc63c Fixed bugs in dataset to make test_mlp.py work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 134
diff changeset
500 return HStackedDataSet([self,other])
3
378b68d5c4ad Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents: 2
diff changeset
501
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
502 def __and__(self,other):
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
503 """
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
504 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
505 (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
506 works if they all have the same fields.
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diff changeset
507 """
135
0d8e721cc63c Fixed bugs in dataset to make test_mlp.py work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 134
diff changeset
508 return VStackedDataSet([self,other])
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
509
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
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diff changeset
510 def hstack(datasets):
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parents: 29
diff changeset
511 """
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
512 hstack(dataset1,dataset2,...) returns dataset1 | datataset2 | ...
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
513 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
514 of the individual datasets.
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
515 """
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
516 assert len(datasets)>0
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
517 if len(datasets)==1:
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
518 return datasets[0]
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
519 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
520
36
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diff changeset
521 def vstack(datasets):
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bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
522 """
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
523 vstack(dataset1,dataset2,...) returns dataset1 & datataset2 & ...
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
524 which is a dataset which iterates first over the examples of dataset1, then
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
525 over those of dataset2, etc.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
526 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
527 assert len(datasets)>0
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
528 if len(datasets)==1:
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
529 return datasets[0]
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
530 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
531
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
532 class FieldsSubsetDataSet(DataSet):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
533 """
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
534 A sub-class of DataSet that selects a subset of the fields.
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
535 """
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
536 def __init__(self,src,fieldnames):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
537 self.src=src
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
538 self.fieldnames=fieldnames
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
539 assert src.hasFields(*fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
540 self.valuesHStack = src.valuesHStack
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
541 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
542
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
543 def __len__(self): return len(self.src)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
544
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
545 def fieldNames(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
546 return self.fieldnames
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
547
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
548 def __iter__(self):
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
549 class FieldsSubsetIterator(object):
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
550 def __init__(self,ds):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
551 self.ds=ds
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
552 self.src_iter=ds.src.__iter__()
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
553 self.example=None
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
554 def __iter__(self): return self
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
555 def next(self):
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
556 complete_example = self.src_iter.next()
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
557 if self.example:
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
558 self.example._values=[complete_example[field]
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
559 for field in self.ds.fieldnames]
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
560 else:
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
561 self.example=Example(self.ds.fieldnames,
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
562 [complete_example[field] for field in self.ds.fieldnames])
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
563 return self.example
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
564 return FieldsSubsetIterator(self)
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
565
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
566 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
567 assert self.hasFields(*fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
568 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
569 def __getitem__(self,i):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
570 return FieldsSubsetDataSet(self.src[i],self.fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
571
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
572
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
573 class DataSetFields(LookupList):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
574 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
575 Although a DataSet iterates over examples (like rows of a matrix), an associated
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
576 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
577 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
578
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
579 To iterate over fields, one can do
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
580 * for fields in dataset.fields()
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
581 * 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
582 * 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
583 and each of these fields is iterable over the examples:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
584 * for field_examples in dataset.fields():
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
585 for example_value in field_examples:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
586 ...
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
587 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
588 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
589 an unsynchronized ways. Hence the fields() method is illegal for streams, by default.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
590 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
591 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
592 be turned back into a DataSet with its examples() method:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
593 dataset2 = dataset1.fields().examples()
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
594 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
595
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 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
597 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
598 the examples.
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
599 """
74
b4159cbdc06b Fixed errors raised by test_dataset
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 73
diff changeset
600 def __init__(self,dataset,fieldnames):
65
d48eba49a2f4 fixed the infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 64
diff changeset
601 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
602 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
603 fieldnames=dataset.fieldNames()
65
d48eba49a2f4 fixed the infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 64
diff changeset
604 elif not fieldnames==dataset.fieldNames():
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
605 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
606 assert dataset.hasFields(*fieldnames)
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
607 self.dataset=dataset
66
dde1fb1b63ba fixed test and removed print
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 65
diff changeset
608
64
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
609 if isinstance(dataset,MinibatchDataSet):
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
610 LookupList.__init__(self,fieldnames,list(dataset._fields))
65
d48eba49a2f4 fixed the infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 64
diff changeset
611 elif isinstance(original_dataset,MinibatchDataSet):
d48eba49a2f4 fixed the infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 64
diff changeset
612 LookupList.__init__(self,fieldnames,
d48eba49a2f4 fixed the infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 64
diff changeset
613 [original_dataset._fields[field]
d48eba49a2f4 fixed the infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 64
diff changeset
614 for field in fieldnames])
64
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
615 else:
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
616 minibatch_iterator = dataset.minibatches(fieldnames,
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
617 minibatch_size=len(dataset),
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
618 n_batches=1)
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
619 minibatch=minibatch_iterator.next()
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
620 LookupList.__init__(self,fieldnames,minibatch)
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
621
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
622 def examples(self):
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
623 return self.dataset
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
624
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
625 def __or__(self,other):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
626 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
627 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
628 of the list of examples of DataSetFields fields1 and fields2.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
629 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
630 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
631
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
632 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
633 """
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
634 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
635 of the fields of DataSetFields fields1 and fields2.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
636 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
637 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
638
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
639
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
640 class MinibatchDataSet(DataSet):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
641 """
85
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 83
diff changeset
642 Turn a LookupList of same-length (iterable) fields into an example-iterable dataset.
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
643 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
644 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
645 def __init__(self,fields_lookuplist,values_vstack=DataSet().valuesVStack,
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
646 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
647 """
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
648 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
649 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
650 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
651 """
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
652 self._fields=fields_lookuplist
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
653 assert len(fields_lookuplist)>0
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
654 self.length=len(fields_lookuplist[0])
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
655 for field in fields_lookuplist[1:]:
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
656 assert self.length==len(field)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
657 self.values_vstack=values_vstack
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
658 self.values_hstack=values_hstack
3
378b68d5c4ad Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents: 2
diff changeset
659
378b68d5c4ad Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents: 2
diff changeset
660 def __len__(self):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
661 return self.length
28
541a273bc89f Removed __array__ method from dataset, whose
bengioy@grenat.iro.umontreal.ca
parents: 26
diff changeset
662
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
663 def __getitem__(self,i):
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
664 if type(i) in (slice,list):
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
665 return DataSetFields(MinibatchDataSet(
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
666 Example(self._fields.keys(),[field[i] for field in self._fields])),self.fieldNames())
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
667 if type(i) is int:
85
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 83
diff changeset
668 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
669 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
670 return self._fields[i]
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
671 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
672 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
673
29
46c5c90019c2 Changed apply_function so that it propagates methods of the source.
bengioy@grenat.iro.umontreal.ca
parents: 28
diff changeset
674 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
675 return self._fields.keys()
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
676
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
677 def hasFields(self,*fieldnames):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
678 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
679 if fieldname not in self._fields.keys():
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
680 return False
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
681 return True
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
682
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
683 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
684 class Iterator(object):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
685 def __init__(self,ds):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
686 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
687 self.next_example=offset
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
688 assert minibatch_size > 0
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
689 if offset+minibatch_size > ds.length:
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
690 raise NotImplementedError()
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
691 def __iter__(self):
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
692 return self
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
693 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
694 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
695 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
696 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
697 [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
698 for field in self.ds._fields])
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
699 self.next_example+=minibatch_size
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
700 return minibatch
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
701
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
702 return Iterator(self)
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
703
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
704 def valuesVStack(self,fieldname,fieldvalues):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
705 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
706
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
707 def valuesHStack(self,fieldnames,fieldvalues):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
708 return self.values_hstack(fieldnames,fieldvalues)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
709
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
710 class HStackedDataSet(DataSet):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
711 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
712 A DataSet that wraps several datasets and shows a view that includes all their fields,
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
713 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
714
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
715 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
716 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
717 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
718
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
719 TODO: automatically detect a chain of stacked datasets due to A | B | C | D ...
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
720 """
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
721 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
722 DataSet.__init__(self,description,field_types)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
723 self.datasets=datasets
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
724 self.accept_nonunique_names=accept_nonunique_names
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
725 self.fieldname2dataset={}
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
726
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
727 def rename_field(fieldname,dataset,i):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
728 if hasattr(dataset,"__name__"):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
729 return dataset.__name__ + "." + fieldname
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
730 return fieldname+"."+str(i)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
731
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
732 # 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
733 self.length=None
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
734 names_to_change=[]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
735 for i in xrange(len(datasets)):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
736 dataset = datasets[i]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
737 length=len(dataset)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
738 if self.length:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
739 assert self.length==length
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
740 else:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
741 self.length=length
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
742 for fieldname in dataset.fieldNames():
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
743 if fieldname in self.fieldname2dataset: # name conflict!
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
744 if accept_nonunique_names:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
745 fieldname=rename_field(fieldname,dataset,i)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
746 names2change.append((fieldname,i))
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
747 else:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
748 raise ValueError("Incompatible datasets: non-unique field name = "+fieldname)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
749 self.fieldname2dataset[fieldname]=i
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
750 for fieldname,i in names_to_change:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
751 del self.fieldname2dataset[fieldname]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
752 self.fieldname2dataset[rename_field(fieldname,self.datasets[i],i)]=i
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
753
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
754 def hasFields(self,*fieldnames):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
755 for fieldname in fieldnames:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
756 if not fieldname in self.fieldname2dataset:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
757 return False
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
758 return True
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
759
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
760 def fieldNames(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
761 return self.fieldname2dataset.keys()
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
762
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
763 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
764
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
765 class HStackedIterator(object):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
766 def __init__(self,hsds,iterators):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
767 self.hsds=hsds
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
768 self.iterators=iterators
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
769 def __iter__(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
770 return self
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
771 def next(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
772 # concatenate all the fields of the minibatches
140
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 136
diff changeset
773 l=LookupList()
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 136
diff changeset
774 for iter in self.iterators:
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 136
diff changeset
775 l.append_lookuplist(iter.next())
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 136
diff changeset
776 return l
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
777
125
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 123
diff changeset
778 assert self.hasFields(*fieldnames)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
779 # 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
780 # and construct corresponding minibatch iterators
140
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 136
diff changeset
781 if fieldnames and fieldnames!=self.fieldNames():
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
782 datasets=set([])
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
783 fields_in_dataset=dict([(dataset,[]) for dataset in datasets])
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
784 for fieldname in fieldnames:
136
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 125
diff changeset
785 dataset=self.datasets[self.fieldname2dataset[fieldname]]
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
786 datasets.add(dataset)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
787 fields_in_dataset[dataset].append(fieldname)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
788 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
789 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
790 for dataset in datasets]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
791 else:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
792 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
793 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
794 return HStackedIterator(self,iterators)
36
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
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
797 def valuesVStack(self,fieldname,fieldvalues):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
798 return self.datasets[self.fieldname2dataset[fieldname]].valuesVStack(fieldname,fieldvalues)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
799
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
800 def valuesHStack(self,fieldnames,fieldvalues):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
801 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
802 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
803 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
804 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
805 all the fieldnames are of the same sub-dataset.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
806 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
807 return self.datasets[self.fieldname2dataset[fieldnames[0]]].valuesHStack(fieldnames,fieldvalues)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
808
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
809 class VStackedDataSet(DataSet):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
810 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
811 A DataSet that wraps several datasets and shows a view that includes all their examples,
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
812 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
813 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
814
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
815 TODO: automatically detect a chain of stacked datasets due to A + B + C + D ...
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
816 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
817 def __init__(self,datasets):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
818 self.datasets=datasets
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
819 self.length=0
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
820 self.index2dataset={}
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
821 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
822 fieldnames = datasets[-1].fieldNames()
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
823 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
824 # 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
825 # 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
826 for dataset,k in enumerate(datasets[0:-1]):
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
827 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
828 L=len(dataset)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
829 for i in xrange(L):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
830 self.index2dataset[self.length+i]=k
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
831 self.datasets_start_row.append(self.length)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
832 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
833 assert dataset.fieldNames()==fieldnames
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
834 self.datasets_start_row.append(self.length)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
835 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
836 # 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
837 # 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
838 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
839 # 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
840 # TODO
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
841 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
842
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
843 def __len__(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
844 return self.length
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
845
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
846 def fieldNames(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
847 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
848
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
849 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
850 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
851
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
852 def locate_row(self,row):
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
853 """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
854 dataset_index = self.index2dataset[row]
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
855 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
856 return dataset_index, row_within_dataset
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
857
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
858 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
859
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
860 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
861 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
862 self.vsds=vsds
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
863 self.next_row=offset
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
864 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
865 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
866 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
867
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
868 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
869 L=len(dataset)
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
870 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
871 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
872 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
873 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
874 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
875 n_left_in_mb=minibatch_size-L
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
876 ds_nbatches=1
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
877 else:
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
878 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
879 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
880 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
881
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
882 def move_to_next_dataset(self):
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
883 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
884 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
885 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
886 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
887 else:
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
888 self.next_dataset_index +=1
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
889 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
890 self.next_dataset_index = 0
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
891 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
892 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
893
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
894 def __iter__(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
895 return self
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
896
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
897 def next(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
898 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
899 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
900 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
901 extra_mb = []
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
902 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
903 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
904 extra_mb.append(self.next_iterator.next())
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
905 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
906 [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
907 [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
908 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
909
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
910 self.next_row+=minibatch_size
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
911 self.next_dataset_row+=minibatch_size
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
912 if self.next_row+minibatch_size>len(dataset):
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
913 self.move_to_next_dataset()
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
914 return examples
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
915 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
916
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
917 class ArrayFieldsDataSet(DataSet):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
918 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
919 Virtual super-class of datasets whose field values are numpy array,
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
920 thus defining valuesHStack and valuesVStack for sub-classes.
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
921 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
922 def __init__(self,description=None,field_types=None):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
923 DataSet.__init__(self,description,field_types)
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
924 def valuesHStack(self,fieldnames,fieldvalues):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
925 """Concatenate field values horizontally, e.g. two vectors
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
926 become a longer vector, two matrices become a wider matrix, etc."""
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
927 return numpy.hstack(fieldvalues)
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
928 def valuesVStack(self,fieldname,values):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
929 """Concatenate field values vertically, e.g. two vectors
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
930 become a two-row matrix, two matrices become a longer matrix, etc."""
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
931 return numpy.vstack(values)
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
932
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
933 class ArrayDataSet(ArrayFieldsDataSet):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
934 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
935 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
936 whose first axis iterates over examples, second axis determines fields.
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
937 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
938 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
939 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
940
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
941 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
942 """
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
943 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
944 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
945 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
946 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
947 """
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
948 self.data=data_array
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
949 self.fields_columns=fields_columns
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
950
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
951 # check consistency and complete slices definitions
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
952 for fieldname, fieldcolumns in self.fields_columns.items():
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
953 if type(fieldcolumns) is int:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
954 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
955 self.fields_columns[fieldname]=[fieldcolumns]
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
956 elif type(fieldcolumns) is slice:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
957 start,step=None,None
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
958 if not fieldcolumns.start:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
959 start=0
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
960 if not fieldcolumns.step:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
961 step=1
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
962 if start or step:
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
963 self.fields_columns[fieldname]=slice(start,fieldcolumns.stop,step)
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
964 elif hasattr(fieldcolumns,"__iter__"): # something like a list
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
965 for i in fieldcolumns:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
966 assert i>=0 and i<data_array.shape[1]
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
967
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
968 def fieldNames(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
969 return self.fields_columns.keys()
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
970
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
971 def __len__(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
972 return len(self.data)
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
973
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
974 def __getitem__(self,key):
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
975 """More efficient implementation than the default __getitem__"""
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
976 fieldnames=self.fields_columns.keys()
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
977 if type(key) is int:
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
978 return Example(fieldnames,
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
979 [self.data[key,self.fields_columns[f]] for f in fieldnames])
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
980 if type(key) is slice:
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
981 return MinibatchDataSet(Example(fieldnames,
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
982 [self.data[key,self.fields_columns[f]] for f in fieldnames]))
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
983 if type(key) is list:
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
984 for i in range(len(key)):
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
985 if self.hasFields(key[i]):
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
986 key[i]=self.fields_columns[key[i]]
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
987 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
988 #we must separate differently for list as numpy
128
ee5507af2c60 minor edits
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 125
diff changeset
989 # 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
990 # 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
991 [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
992 if isinstance(self.fields_columns[f],list) else
128
ee5507af2c60 minor edits
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 125
diff changeset
993 self.data[key,self.fields_columns[f]] for f in fieldnames]),
ee5507af2c60 minor edits
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 125
diff changeset
994
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
995 self.valuesVStack,self.valuesHStack)
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
996
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
997 # else check for a fieldname
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
998 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
999 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
1000 # else we are trying to access a property of the dataset
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1001 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
1002 return self.__dict__[key]
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1003
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1004
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1005 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
1006 class ArrayDataSetIterator(object):
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1007 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
1008 if fieldnames is None: fieldnames = dataset.fieldNames()
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
1009 # 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
1010 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
1011 self.dataset=dataset
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1012 self.minibatch_size=minibatch_size
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1013 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
1014 assert offset+minibatch_size<=len(dataset.data)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1015 self.current=offset
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1016 def __iter__(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1017 return self
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1018 def next(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1019 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
1020 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
1021 self.current+=self.minibatch_size
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
1022 return self.minibatch
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1023
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
1024 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
1025
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1026
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1027 class CachedDataSet(DataSet):
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1028 """
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1029 Wrap a dataset whose values are computationally expensive to obtain
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1030 (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
1031 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
1032 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
1033
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1034 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
1035 (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
1036 first access.
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1037
77
1e2bb5bad636 toying with different ways to implement learners
bengioy@bengiomac.local
parents: 74
diff changeset
1038 @todo when cache_all_upon_construction create mini-batches that are as
1e2bb5bad636 toying with different ways to implement learners
bengioy@bengiomac.local
parents: 74
diff changeset
1039 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
1040
1e2bb5bad636 toying with different ways to implement learners
bengioy@bengiomac.local
parents: 74
diff changeset
1041 @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
1042 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
1043 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
1044 """
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1045 def __init__(self,source_dataset,cache_all_upon_construction=False):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1046 self.source_dataset=source_dataset
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1047 self.cache_all_upon_construction=cache_all_upon_construction
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()
8173e196e291 Trying to make CacheDataSet work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 144
diff changeset
1054 self.cached_examples = zip(*fields_values)
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1055 else:
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1056 self.cached_examples = []
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
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1072 def next(self):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1073 upper = self.current+minibatch_size
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1074 cache_len = len(self.dataset.cached_examples)
135
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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
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1077 for example in self.dataset.source_dataset[cache_len:upper]:
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diff changeset
1078 self.dataset.cached_examples.append(example)
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diff changeset
1079 all_fields_minibatch = Example(self.dataset.fieldNames(),
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diff changeset
1080 self.dataset.cached_examples[self.current:self.current+minibatch_size])
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diff changeset
1081 if self.dataset.fieldNames()==fieldnames:
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1082 return all_fields_minibatch
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diff changeset
1083 return Example(fieldnames,[all_fields_minibatch[name] for name in fieldnames])
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diff changeset
1084 return CacheIterator(self)
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diff changeset
1085
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diff changeset
1086
57
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
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diff changeset
1087 class ApplyFunctionDataSet(DataSet):
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1088 """
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
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diff changeset
1089 A dataset that contains as fields the results of applying a given function
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1090 example-wise or minibatch-wise to all the fields of an input dataset.
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
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parents: 56
diff changeset
1091 The output of the function should be an iterable (e.g. a list or a LookupList)
73
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diff changeset
1092 over the resulting values.
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diff changeset
1093
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diff changeset
1094 In minibatch mode, the function is expected to work on minibatches (takes
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diff changeset
1095 a minibatch in input and returns a minibatch in output). More precisely,
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diff changeset
1096 it means that each element of the input or output list should be iterable
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diff changeset
1097 and indexable over the individual example values (typically these
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diff changeset
1098 elements will be numpy arrays). All of the elements in the input and
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diff changeset
1099 output lists should have the same length, which is the length of the
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diff changeset
1100 minibatch.
57
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
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diff changeset
1101
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1102 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
1103 To avoid re-doing computation, wrap this dataset inside a CachedDataSet.
73
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diff changeset
1104
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diff changeset
1105 If the values_{h,v}stack functions are not provided, then
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1106 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
1107 """
73
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diff changeset
1108 def __init__(self,input_dataset,function,output_names,minibatch_mode=True,
74
b4159cbdc06b Fixed errors raised by test_dataset
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parents: 73
diff changeset
1109 values_hstack=None,values_vstack=None,
73
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diff changeset
1110 description=None,fieldtypes=None):
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diff changeset
1111 """
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diff changeset
1112 Constructor takes an input dataset that has as many fields as the function
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diff changeset
1113 expects as inputs. The resulting dataset has as many fields as the function
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diff changeset
1114 produces as outputs, and that should correspond to the number of output names
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diff changeset
1115 (provided in a list).
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diff changeset
1116
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1117 Note that the expected semantics of the function differs in minibatch mode
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diff changeset
1118 (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
1119 documented in the class comment).
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1120 """
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diff changeset
1121 self.input_dataset=input_dataset
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diff changeset
1122 self.function=function
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diff changeset
1123 self.output_names=output_names
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diff changeset
1124 self.minibatch_mode=minibatch_mode
134
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diff changeset
1125 DataSet.__init__(self,description,fieldtypes)
73
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diff changeset
1126 self.valuesHStack = values_hstack if values_hstack else input_dataset.valuesHStack
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parents: 72
diff changeset
1127 self.valuesVStack = values_vstack if values_vstack else input_dataset.valuesVStack
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parents: 72
diff changeset
1128
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diff changeset
1129 def __len__(self):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1130 return len(self.input_dataset)
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diff changeset
1131
134
3f4e5c9bdc5e Fixes to ApplyFunctionDataSet and other things to make learner and mlp work
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diff changeset
1132 def fieldNames(self):
73
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diff changeset
1133 return self.output_names
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1134
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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parents: 72
diff changeset
1135 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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parents: 72
diff changeset
1136 class ApplyFunctionIterator(object):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1137 def __init__(self,output_dataset):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1138 self.input_dataset=output_dataset.input_dataset
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diff changeset
1139 self.output_dataset=output_dataset
134
3f4e5c9bdc5e Fixes to ApplyFunctionDataSet and other things to make learner and mlp work
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parents: 132
diff changeset
1140 self.input_iterator=self.input_dataset.minibatches(minibatch_size=minibatch_size,
3f4e5c9bdc5e Fixes to ApplyFunctionDataSet and other things to make learner and mlp work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 132
diff changeset
1141 n_batches=n_batches,offset=offset).__iter__()
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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parents: 72
diff changeset
1142
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1143 def __iter__(self): return self
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1144
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1145 def next(self):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1146 function_inputs = self.input_iterator.next()
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1147 all_output_names = self.output_dataset.output_names
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diff changeset
1148 if self.output_dataset.minibatch_mode:
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
1149 function_outputs = self.output_dataset.function(*function_inputs)
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1150 else:
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1151 input_examples = zip(*function_inputs)
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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parents: 72
diff changeset
1152 output_examples = [self.output_dataset.function(input_example)
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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parents: 72
diff changeset
1153 for input_example in input_examples]
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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parents: 72
diff changeset
1154 function_outputs = [self.output_dataset.valuesVStack(name,values)
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1155 for name,values in zip(all_output_names,
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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parents: 72
diff changeset
1156 zip(*output_examples))]
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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parents: 72
diff changeset
1157 all_outputs = Example(all_output_names,function_outputs)
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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parents: 72
diff changeset
1158 if fieldnames==all_output_names:
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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parents: 72
diff changeset
1159 return all_outputs
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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parents: 72
diff changeset
1160 return Example(fieldnames,[all_outputs[name] for name in fieldnames])
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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parents: 72
diff changeset
1161
134
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diff changeset
1162 return ApplyFunctionIterator(self)
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1163
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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parents: 72
diff changeset
1164 def __iter__(self): # only implemented for increased efficiency
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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parents: 72
diff changeset
1165 class ApplyFunctionSingleExampleIterator(object):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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parents: 72
diff changeset
1166 def __init__(self,output_dataset):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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parents: 72
diff changeset
1167 self.current=0
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diff changeset
1168 self.output_dataset=output_dataset
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parents: 72
diff changeset
1169 self.input_iterator=output_dataset.input_dataset.__iter__()
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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parents: 72
diff changeset
1170 def __iter__(self): return self
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parents: 72
diff changeset
1171 def next(self):
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parents: 72
diff changeset
1172 function_inputs = self.input_iterator.next()
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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parents: 72
diff changeset
1173 if self.output_dataset.minibatch_mode:
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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parents: 72
diff changeset
1174 function_outputs = [output[0] for output in self.output_dataset.function(function_inputs)]
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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parents: 72
diff changeset
1175 else:
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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parents: 72
diff changeset
1176 function_outputs = self.output_dataset.function(function_inputs)
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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parents: 72
diff changeset
1177 return Example(self.output_dataset.output_names,function_outputs)
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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parents: 72
diff changeset
1178 return ApplyFunctionSingleExampleIterator(self)
57
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1179
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1180
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1181 def supervised_learning_dataset(src_dataset,input_fields,target_fields,weight_field=None):
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1182 """
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1183 Wraps an arbitrary DataSet into one for supervised learning tasks by forcing the
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1184 user to define a set of fields as the 'input' field and a set of fields
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1185 as the 'target' field. Optionally, a single weight_field can also be defined.
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1186 """
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1187 args = ((input_fields,'input'),(output_fields,'target'))
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1188 if weight_field: args+=(([weight_field],'weight'))
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
1189 return src_dataset.merge_fields(*args)
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1190
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1191
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1192
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1193