annotate dataset.py @ 338:7d4792fc28ae

Automated merge with ssh://projects@lgcm.iro.umontreal.ca/hg/pylearn
author Frederic Bastien <bastienf@iro.umontreal.ca>
date Mon, 16 Jun 2008 17:17:50 -0400
parents 5e38ed2b3a75 0ce6e62ac6e5
children d96be0eba3cc
rev   line source
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1
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2 from lookup_list import LookupList as Example
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3 from misc import unique_elements_list_intersection
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4 from string import join
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5 from sys import maxint
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6 import numpy, copy
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8 from exceptions import *
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9
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10 class AttributesHolder(object):
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11 def __init__(self): pass
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12
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13 def attributeNames(self):
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14 raise AbstractFunction()
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15
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16 def setAttributes(self,attribute_names,attribute_values,make_copies=False):
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17 """
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18 Allow the attribute_values to not be a list (but a single value) if the attribute_names is of length 1.
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19 """
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20 if len(attribute_names)==1 and not (isinstance(attribute_values,list) or isinstance(attribute_values,tuple) ):
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21 attribute_values = [attribute_values]
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22 if make_copies:
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23 for name,value in zip(attribute_names,attribute_values):
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24 self.__setattr__(name,copy.deepcopy(value))
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25 else:
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26 for name,value in zip(attribute_names,attribute_values):
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27 self.__setattr__(name,value)
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29 def getAttributes(self,attribute_names=None, return_copy=False):
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30 """
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31 Return all (if attribute_names=None, in the order of attributeNames()) or a specified subset of attributes.
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32 """
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33 if attribute_names is None:
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34 attribute_names = self.attributeNames()
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35 if return_copy:
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36 return [copy.copy(self.__getattribute__(name)) for name in attribute_names]
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37 else:
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38 return [self.__getattribute__(name) for name in attribute_names]
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39
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40 class DataSet(AttributesHolder):
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41 """A virtual base class for datasets.
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42
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43 A DataSet can be seen as a generalization of a matrix, meant to be used in conjunction
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44 with learning algorithms (for training and testing them): rows/records are called examples, and
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45 columns/attributes are called fields. The field value for a particular example can be an arbitrary
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46 python object, which depends on the particular dataset.
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47
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48 We call a DataSet a 'stream' when its length is unbounded (in which case its __len__ method
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49 should return sys.maxint).
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50
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51 A DataSet is a generator of iterators; these iterators can run through the
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52 examples or the fields in a variety of ways. A DataSet need not necessarily have a finite
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53 or known length, so this class can be used to interface to a 'stream' which
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54 feeds on-line learning (however, as noted below, some operations are not
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55 feasible or not recommended on streams).
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56
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57 To iterate over examples, there are several possibilities:
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58 - for example in dataset:
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59 - for val1,val2,... in dataset:
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60 - for example in dataset(field1, field2,field3, ...):
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61 - for val1,val2,val3 in dataset(field1, field2,field3):
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62 - for minibatch in dataset.minibatches([field1, field2, ...],minibatch_size=N):
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63 - for mini1,mini2,mini3 in dataset.minibatches([field1, field2, field3], minibatch_size=N):
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64 Each of these is documented below. All of these iterators are expected
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65 to provide, in addition to the usual 'next()' method, a 'next_index()' method
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66 which returns a non-negative integer pointing to the position of the next
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67 example that will be returned by 'next()' (or of the first example in the
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68 next minibatch returned). This is important because these iterators
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69 can wrap around the dataset in order to do multiple passes through it,
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70 in possibly unregular ways if the minibatch size is not a divisor of the
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71 dataset length.
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73 To iterate over fields, one can do
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74 - for field in dataset.fields():
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75 for field_value in field: # iterate over the values associated to that field for all the dataset examples
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76 - for field in dataset(field1,field2,...).fields() to select a subset of fields
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77 - for field in dataset.fields(field1,field2,...) to select a subset of fields
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78 and each of these fields is iterable over the examples:
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79 - for field_examples in dataset.fields():
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80 for example_value in field_examples:
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81 ...
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82 but when the dataset is a stream (unbounded length), it is not recommended to do
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83 such things because the underlying dataset may refuse to access the different fields in
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84 an unsynchronized ways. Hence the fields() method is illegal for streams, by default.
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85 The result of fields() is a L{DataSetFields} object, which iterates over fields,
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86 and whose elements are iterable over examples. A DataSetFields object can
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87 be turned back into a DataSet with its examples() method::
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88 dataset2 = dataset1.fields().examples()
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89 and dataset2 should behave exactly like dataset1 (in fact by default dataset2==dataset1).
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90
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91 Note: Fields are not mutually exclusive, i.e. two fields can overlap in their actual content.
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92
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93 Note: The content of a field can be of any type. Field values can also be 'missing'
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94 (e.g. to handle semi-supervised learning), and in the case of numeric (numpy array)
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95 fields (i.e. an ArrayFieldsDataSet), NaN plays the role of a missing value.
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96 What about non-numeric values? None.
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97
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98 Dataset elements can be indexed and sub-datasets (with a subset
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99 of examples) can be extracted. These operations are not supported
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100 by default in the case of streams.
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101
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102 - dataset[:n] returns an Example with the n first examples.
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103
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104 - dataset[i1:i2:s] returns an Example with the examples i1,i1+s,...i2-s.
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105
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106 - dataset[i] returns an Example.
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107
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108 - dataset[[i1,i2,...in]] returns a. Example with examples i1,i2,...in.
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109
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110 A similar command gives you a DataSet instead of Examples :
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111
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112 - dataset.subset[:n] returns a DataSet with the n first examples.
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113
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114 - dataset.subset[i1:i2:s] returns a DataSet with the examples i1,i1+s,...i2-s.
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115
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116 - dataset.subset[i] returns a DataSet.
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117
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118 - dataset.subset[[i1,i2,...in]] returns a DataSet with examples i1,i2,...in.
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119
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120
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121 - dataset.<property> returns the value of a property associated with
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122 the name <property>. The following properties should be supported:
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123 - 'description': a textual description or name for the dataset
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124 - 'fieldtypes': a list of types (one per field)
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125 A DataSet may have other attributes that it makes visible to other objects. These are
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126 used to store information that is not example-wise but global to the dataset.
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127 The list of names of these attributes is given by the attribute_names() method.
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128
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129 Datasets can be concatenated either vertically (increasing the length) or
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130 horizontally (augmenting the set of fields), if they are compatible, using
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131 the following operations (with the same basic semantics as numpy.hstack
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132 and numpy.vstack):
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133
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134 - dataset1 | dataset2 | dataset3 == dataset.hstack([dataset1,dataset2,dataset3])
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135
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136 creates a new dataset whose list of fields is the concatenation of the list of
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137 fields of the argument datasets. This only works if they all have the same length.
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138
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139 - dataset1 & dataset2 & dataset3 == dataset.vstack([dataset1,dataset2,dataset3])
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140
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141 creates a new dataset that concatenates the examples from the argument datasets
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142 (and whose length is the sum of the length of the argument datasets). This only
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143 works if they all have the same fields.
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144
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145 According to the same logic, and viewing a DataSetFields object associated to
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146 a DataSet as a kind of transpose of it, fields1 & fields2 concatenates fields of
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147 a DataSetFields fields1 and fields2, and fields1 | fields2 concatenates their
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148 examples.
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149
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150 A dataset can hold arbitrary key-value pairs that may be used to access meta-data
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151 or other properties of the dataset or associated with the dataset or the result
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152 of a computation stored in a dataset. These can be accessed through the [key] syntax
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153 when key is a string (or more specifically, neither an integer, a slice, nor a list).
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154
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155 A DataSet sub-class should always redefine the following methods:
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156 - __len__ if it is not a stream
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157 - fieldNames
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158 - minibatches_nowrap (called by DataSet.minibatches())
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159 For efficiency of implementation, a sub-class might also want to redefine
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160 - valuesHStack
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161 - valuesVStack
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162 - hasFields
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163 - __getitem__ may not be feasible with some streams
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164 - __iter__
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165 A sub-class should also append attributes to self._attribute_names
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166 (the default value returned by attributeNames()).
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167 By convention, attributes not in attributeNames() should have a name
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168 starting with an underscore.
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169 @todo enforce/test that convention!
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170 """
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171
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172 numpy_vstack = lambda fieldname,values: numpy.vstack(values)
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173 numpy_hstack = lambda fieldnames,values: numpy.hstack(values)
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174
292
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175 def __init__(self, description=None, fieldnames=None, fieldtypes=None):
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176 """
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177 @type fieldnames: list of strings
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178 @type fieldtypes: list of python types, same length as fieldnames
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179 @type description: string
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180 @param description: description/name for this dataset
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181 """
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182 def default_desc():
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183 return type(self).__name__ \
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184 + " ( " + join([x.__name__ for x in type(self).__bases__]) + " )"
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185
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186 #self.fieldnames = fieldnames
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187
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188 self.fieldtypes = fieldtypes if fieldtypes is not None \
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189 else [None]*1 #len(fieldnames)
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190
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191 self.description = default_desc() if description is None \
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192 else description
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193 self._attribute_names = ["description"]
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194
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195
292
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196 attributeNames = property(lambda self: copy.copy(self._attribute_names))
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197
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198 def __contains__(self, fieldname):
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199 return (fieldname in self.fieldNames()) \
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200 or (fieldname in self.attributeNames())
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201
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202 def __iter__(self):
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203 """Supports the syntax "for i in dataset: ..."
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204
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205 Using this syntax, "i" will be an Example instance (or equivalent) with
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206 all the fields of DataSet self. Every field of "i" will give access to
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207 a field of a single example. Fields should be accessible via
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208 i["fielname"] or i[3] (in the order defined by the elements of the
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209 Example returned by this iterator), but the derived class is free
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210 to accept any type of identifier, and add extra functionality to the iterator.
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211
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212 The default implementation calls the minibatches iterator and extracts the first example of each field.
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213 """
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214 return DataSet.MinibatchToSingleExampleIterator(self.minibatches(None, minibatch_size = 1))
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215
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216 def __len__(self):
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217 """
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218 len(dataset) returns the number of examples in the dataset.
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219 By default, a DataSet is a 'stream', i.e. it has an unbounded length (sys.maxint).
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220 Sub-classes which implement finite-length datasets should redefine this method.
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221 Some methods only make sense for finite-length datasets.
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222 """
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223 return None
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224
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225
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226 class MinibatchToSingleExampleIterator(object):
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227 """
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228 Converts the result of minibatch iterator with minibatch_size==1 into
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229 single-example values in the result. Therefore the result of
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230 iterating on the dataset itself gives a sequence of single examples
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231 (whereas the result of iterating over minibatches gives in each
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232 Example field an iterable object over the individual examples in
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233 the minibatch).
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234 """
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235 def __init__(self, minibatch_iterator):
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236 self.minibatch_iterator = minibatch_iterator
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237 self.minibatch = None
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238 def __iter__(self): #makes for loop work
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239 return self
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240 def next(self):
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241 size1_minibatch = self.minibatch_iterator.next()
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242 if not self.minibatch:
329
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243 names = size1_minibatch.keys()
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244 # next lines are a hack, but there was problem when we were getting [array(327)] for instance
332
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245 try:
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246 values = [value[0] for value in size1_minibatch.values()]
332
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247 except :
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248 values = [value for value in size1_minibatch.values()]
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249 self.minibatch = Example(names,values)
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250 else:
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251 self.minibatch._values = [value[0] for value in size1_minibatch.values()]
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252 return self.minibatch
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253
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254 def next_index(self):
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255 return self.minibatch_iterator.next_index()
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256
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257 class MinibatchWrapAroundIterator(object):
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258 """
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259 An iterator for minibatches that handles the case where we need to wrap around the
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260 dataset because n_batches*minibatch_size > len(dataset). It is constructed from
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261 a dataset that provides a minibatch iterator that does not need to handle that problem.
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262 This class is a utility for dataset subclass writers, so that they do not have to handle
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263 this issue multiple times, nor check that fieldnames are valid, nor handle the
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264 empty fieldnames (meaning 'use all the fields').
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265 """
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266 def __init__(self,dataset,fieldnames,minibatch_size,n_batches,offset):
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267 self.dataset=dataset
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268 self.fieldnames=fieldnames
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269 self.minibatch_size=minibatch_size
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270 self.n_batches=n_batches
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271 self.n_batches_done=0
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272 self.next_row=offset
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273 self.L=len(dataset)
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274 self.offset=offset % self.L
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275 ds_nbatches = (self.L-self.next_row)/self.minibatch_size
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276 if n_batches is not None:
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277 ds_nbatches = min(n_batches,ds_nbatches)
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278 if fieldnames:
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279 assert dataset.hasFields(*fieldnames)
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280 else:
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281 self.fieldnames=dataset.fieldNames()
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282 self.iterator = self.dataset.minibatches_nowrap(self.fieldnames,self.minibatch_size, ds_nbatches,self.next_row)
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283
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284 def __iter__(self):
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285 return self
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286
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287 def next_index(self):
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288 return self.next_row
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289
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290 def next(self):
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291 if self.n_batches and self.n_batches_done==self.n_batches:
37
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292 raise StopIteration
101
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293 elif not self.n_batches and self.next_row ==self.L:
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294 raise StopIteration
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295 upper = self.next_row+self.minibatch_size
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296 if upper <=self.L:
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297 minibatch = self.iterator.next()
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298 else:
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299 if not self.n_batches:
101
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300 upper=min(upper, self.L)
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301 # if their is not a fixed number of batch, we continue to the end of the dataset.
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302 # this can create a minibatch that is smaller then the minibatch_size
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303 assert (self.L-self.next_row)<=self.minibatch_size
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304 minibatch = self.dataset.minibatches_nowrap(self.fieldnames,self.L-self.next_row,1,self.next_row).next()
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305 else:
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306 # we must concatenate (vstack) the bottom and top parts of our minibatch
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307 # first get the beginning of our minibatch (top of dataset)
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308 first_part = self.dataset.minibatches_nowrap(self.fieldnames,self.L-self.next_row,1,self.next_row).next()
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309 second_part = self.dataset.minibatches_nowrap(self.fieldnames,upper-self.L,1,0).next()
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310 minibatch = Example(self.fieldnames,
268
3f1cd8897fda reverting dataset
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311 [self.dataset.valuesVStack(name,[first_part[name],second_part[name]])
101
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312 for name in self.fieldnames])
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313 self.next_row=upper
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314 self.n_batches_done+=1
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315 if upper >= self.L and self.n_batches:
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316 self.next_row -= self.L
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317 ds_nbatches = (self.L-self.next_row)/self.minibatch_size
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318 if self.n_batches is not None:
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319 ds_nbatches = min(self.n_batches,ds_nbatches)
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320 self.iterator = self.dataset.minibatches_nowrap(self.fieldnames,self.minibatch_size,
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321 ds_nbatches,self.next_row)
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69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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322 return DataSetFields(MinibatchDataSet(minibatch,self.dataset.valuesVStack,
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diff changeset
323 self.dataset.valuesHStack),
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b4159cbdc06b Fixed errors raised by test_dataset
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324 minibatch.keys())
37
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325
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326
17
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327 minibatches_fieldnames = None
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328 minibatches_minibatch_size = 1
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329 minibatches_n_batches = None
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330 def minibatches(self,
37
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331 fieldnames = minibatches_fieldnames,
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332 minibatch_size = minibatches_minibatch_size,
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333 n_batches = minibatches_n_batches,
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334 offset = 0):
6
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335 """
36
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336 Return an iterator that supports three forms of syntax:
22
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337
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338 for i in dataset.minibatches(None,**kwargs): ...
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diff changeset
339
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340 for i in dataset.minibatches([f1, f2, f3],**kwargs): ...
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341
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342 for i1, i2, i3 in dataset.minibatches([f1, f2, f3],**kwargs): ...
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343
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344 Using the first two syntaxes, "i" will be an indexable object, such as a list,
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345 tuple, or Example instance. In both cases, i[k] is a list-like container
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346 of a batch of current examples. In the second case, i[0] is
17
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347 list-like container of the f1 field of a batch current examples, i[1] is
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348 a list-like container of the f2 field, etc.
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349
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350 Using the first syntax, all the fields will be returned in "i".
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351 Using the third syntax, i1, i2, i3 will be list-like containers of the
17
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352 f1, f2, and f3 fields of a batch of examples on each loop iteration.
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diff changeset
353
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354 The minibatches iterator is expected to return upon each call to next()
290
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355 a DataSetFields object, which is a Example (indexed by the field names) whose
80
Frederic Bastien <bastienf@iro.umontreal.ca>
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diff changeset
356 elements are iterable and indexable over the minibatch examples, and which keeps a pointer to
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357 a sub-dataset that can be used to iterate over the individual examples
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358 in the minibatch. Hence a minibatch can be converted back to a regular
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359 dataset or its fields can be looked at individually (and possibly iterated over).
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360
17
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diff changeset
361 PARAMETERS
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362 - fieldnames (list of any type, default None):
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363 The loop variables i1, i2, i3 (in the example above) should contain the
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364 f1, f2, and f3 fields of the current batch of examples. If None, the
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365 derived class can choose a default, e.g. all fields.
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diff changeset
366
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367 - minibatch_size (integer, default 1)
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368 On every iteration, the variables i1, i2, i3 will have
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369 exactly minibatch_size elements. e.g. len(i1) == minibatch_size
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diff changeset
370
331
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371 @DEPRECATED n_batches : not used anywhere
17
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372 - n_batches (integer, default None)
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373 The iterator will loop exactly this many times, and then stop. If None,
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374 the derived class can choose a default. If (-1), then the returned
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diff changeset
375 iterator should support looping indefinitely.
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diff changeset
376
37
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377 - offset (integer, default 0)
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378 The iterator will start at example 'offset' in the dataset, rather than the default.
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379
17
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380 Note: A list-like container is something like a tuple, list, numpy.ndarray or
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381 any other object that supports integer indexing and slicing.
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diff changeset
382
331
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383 @ATTENTION: now minibatches returns minibatches_nowrap, which is supposed to return complete
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384 batches only, raise StopIteration
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diff changeset
385
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386 """
331
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diff changeset
387 #return DataSet.MinibatchWrapAroundIterator(self,fieldnames,minibatch_size,n_batches,offset)\
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diff changeset
388 assert offset >= 0
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Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 330
diff changeset
389 assert offset < len(self)
334
a0f150a33b0f debug in an assert of minibatches
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 332
diff changeset
390 assert offset + minibatch_size -1 < len(self)
337
5e38ed2b3a75 debugging when fieldnames = None, now -> fieldnames = fieldNames()
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 335
diff changeset
391 if fieldnames == None :
5e38ed2b3a75 debugging when fieldnames = None, now -> fieldnames = fieldNames()
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 335
diff changeset
392 fieldnames = self.fieldNames()
335
89d88807e958 sorry for all the debugging, this push should be the good one (and damn you *self*)
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 334
diff changeset
393 return self.minibatches_nowrap(fieldnames,minibatch_size,n_batches,offset)
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
394
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
395 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
396 """
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
397 This is the minibatches iterator generator that sub-classes must define.
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
398 It does not need to worry about wrapping around multiple times across the dataset,
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
399 as this is handled by MinibatchWrapAroundIterator when DataSet.minibatches() is called.
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
400 The next() method of the returned iterator does not even need to worry about
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
401 the termination condition (as StopIteration will be raised by DataSet.minibatches
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
402 before an improper call to minibatches_nowrap's next() is made).
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
403 That next() method can assert that its next row will always be within [0,len(dataset)).
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bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
404 The iterator returned by minibatches_nowrap does not need to implement
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
405 a next_index() method either, as this will be provided by MinibatchWrapAroundIterator.
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bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
406 """
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
407 raise AbstractFunction()
22
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
408
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
409 def is_unbounded(self):
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
410 """
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
411 Tests whether a dataset is unbounded (e.g. a stream).
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
412 """
123
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 110
diff changeset
413 return len(self)==maxint
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
414
26
672fe4b23032 Fixed dataset errors so that _test_dataset.py works again.
bengioy@grenat.iro.umontreal.ca
parents: 23
diff changeset
415 def hasFields(self,*fieldnames):
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
416 """
22
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
417 Return true if the given field name (or field names, if multiple arguments are
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
418 given) is recognized by the DataSet (i.e. can be used as a field name in one
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
419 of the iterators).
29
46c5c90019c2 Changed apply_function so that it propagates methods of the source.
bengioy@grenat.iro.umontreal.ca
parents: 28
diff changeset
420
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
421 The default implementation may be inefficient (O(# fields in dataset)), as it calls the fieldNames()
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
422 method. Many datasets may store their field names in a dictionary, which would allow more efficiency.
11
be128b9127c8 Debugged (to the extent of my tests) the new version of dataset
bengioy@esprit.iro.umontreal.ca
parents: 9
diff changeset
423 """
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
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424 return len(unique_elements_list_intersection(fieldnames,self.fieldNames()))>0
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parents: 29
diff changeset
425
438440ba0627 Rewriting dataset.py completely
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parents: 29
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426 def fieldNames(self):
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
427 """
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parents: 29
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428 Return the list of field names that are supported by the iterators,
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parents: 29
diff changeset
429 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
diff changeset
430 """
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
431 raise AbstractFunction()
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bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
432
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
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433 def __call__(self,*fieldnames):
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
434 """
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
435 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
436 """
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
437 assert self.hasFields(*fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
438 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
439
36
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parents: 29
diff changeset
440 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
441 """
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
442 Return a DataSetFields object associated with this dataset.
17
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bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
443 """
74
b4159cbdc06b Fixed errors raised by test_dataset
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 73
diff changeset
444 return DataSetFields(self,fieldnames)
11
be128b9127c8 Debugged (to the extent of my tests) the new version of dataset
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parents: 9
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445
269
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446 def getitem_key(self, fieldname):
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447 """A not-so-well thought-out place to put code that used to be in
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parents: 268
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448 getitem.
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parents: 268
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449 """
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parents: 268
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450 #removing as per discussion June 4. --JSB
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451
fdce496c3b56 deprecating __getitem__[fieldname] syntax
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452 i = fieldname
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parents: 268
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453 # else check for a fieldname
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parents: 268
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454 if self.hasFields(i):
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parents: 268
diff changeset
455 return self.minibatches(fieldnames=[i],minibatch_size=len(self),n_batches=1,offset=0).next()[0]
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parents: 268
diff changeset
456 # else we are trying to access a property of the dataset
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parents: 268
diff changeset
457 assert i in self.__dict__ # else it means we are trying to access a non-existing property
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parents: 268
diff changeset
458 return self.__dict__[i]
fdce496c3b56 deprecating __getitem__[fieldname] syntax
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parents: 268
diff changeset
459
2
3fddb1c8f955 Rewrote DataSet interface and created FiniteDataSet interface.
bengioy@bengiomac.local
parents: 1
diff changeset
460 def __getitem__(self,i):
28
541a273bc89f Removed __array__ method from dataset, whose
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parents: 26
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461 """
290
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parents: 274
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462 @rtype: Example
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463 @returns: single or multiple examples
1
2cd82666b9a7 Added statscollector and started writing dataset and learner.
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parents: 0
diff changeset
464
290
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465 @type i: integer or slice or <iterable> of integers
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diff changeset
466 @param i:
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467 dataset[i] returns the (i+1)-th example of the dataset.
309
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parents: 296
diff changeset
468 dataset[i:j] returns a LookupList with examples i,i+1,...,j-1.
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parents: 296
diff changeset
469 dataset[i:j:s] returns a LookupList with examples i,i+2,i+4...,j-2.
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parents: 296
diff changeset
470 dataset[[i1,i2,..,in]] returns a LookupList with examples i1,i2,...,in.
290
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diff changeset
471
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472 @note:
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parents: 274
diff changeset
473 Some stream datasets may be unable to implement random access, i.e.
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parents: 274
diff changeset
474 arbitrary slicing/indexing because they can only iterate through
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parents: 274
diff changeset
475 examples one or a minibatch at a time and do not actually store or keep
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parents: 274
diff changeset
476 past (or future) examples.
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
477
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
478 The default implementation of getitem uses the minibatches iterator
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
479 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
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
480 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
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
481 the data are actually stored in a memory array.
28
541a273bc89f Removed __array__ method from dataset, whose
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parents: 26
diff changeset
482 """
290
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parents: 274
diff changeset
483
40
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
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parents: 39
diff changeset
484 if type(i) is int:
309
923de30457f0 get item now returns LookupLists
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parents: 296
diff changeset
485 assert i >= 0 # TBM: see if someone complains and want negative i
313
009ce84e9f52 behaviour is now the same as a list in pylearn, so if len(ds) = 10, ds[10] raise an IndexError, same thing for ds[[1,10]], and ds[0:14:1] returns 10 elements
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 310
diff changeset
486 if i >= len(self) :
009ce84e9f52 behaviour is now the same as a list in pylearn, so if len(ds) = 10, ds[10] raise an IndexError, same thing for ds[[1,10]], and ds[0:14:1] returns 10 elements
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 310
diff changeset
487 raise IndexError
290
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diff changeset
488 i_batch = self.minibatches_nowrap(self.fieldNames(),
293
4bfdda107a17 still merging
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parents: 292
diff changeset
489 minibatch_size=1, n_batches=1, offset=i)
290
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parents: 274
diff changeset
490 return DataSet.MinibatchToSingleExampleIterator(i_batch).next()
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parents: 274
diff changeset
491
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diff changeset
492 #if i is a contiguous slice
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diff changeset
493 if type(i) is slice and (i.step in (None, 1)):
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diff changeset
494 offset = 0 if i.start is None else i.start
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diff changeset
495 upper_bound = len(self) if i.stop is None else i.stop
313
009ce84e9f52 behaviour is now the same as a list in pylearn, so if len(ds) = 10, ds[10] raise an IndexError, same thing for ds[[1,10]], and ds[0:14:1] returns 10 elements
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parents: 310
diff changeset
496 upper_bound = min(len(self) , upper_bound)
309
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parents: 296
diff changeset
497 #return MinibatchDataSet(self.minibatches_nowrap(self.fieldNames(),
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parents: 296
diff changeset
498 # minibatch_size=upper_bound - offset,
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parents: 296
diff changeset
499 # n_batches=1,
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Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 296
diff changeset
500 # offset=offset).next())
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Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 296
diff changeset
501 # now returns a LookupList
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diff changeset
502 return self.minibatches_nowrap(self.fieldNames(),
290
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diff changeset
503 minibatch_size=upper_bound - offset,
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504 n_batches=1,
309
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diff changeset
505 offset=offset).next()
290
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506
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parents: 274
diff changeset
507 # if slice has a step param, convert it to list and handle it with the
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diff changeset
508 # list code
40
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parents: 39
diff changeset
509 if type(i) is slice:
290
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diff changeset
510 offset = 0 if i.start is None else i.start
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diff changeset
511 upper_bound = len(self) if i.stop is None else i.stop
314
105b54ac8260 bug fixed concerning the slicing, now ds[0:len(ds) + 1000 : 2] is accepted, same a python list
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 313
diff changeset
512 upper_bound = min(len(self) , upper_bound)
290
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diff changeset
513 i = list(range(offset, upper_bound, i.step))
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diff changeset
514
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diff changeset
515 # handle tuples, arrays, lists
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diff changeset
516 if hasattr(i, '__getitem__'):
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diff changeset
517 for idx in i:
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diff changeset
518 #dis-allow nested slices
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parents: 274
diff changeset
519 if not isinstance(idx, int):
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diff changeset
520 raise TypeError(idx)
313
009ce84e9f52 behaviour is now the same as a list in pylearn, so if len(ds) = 10, ds[10] raise an IndexError, same thing for ds[[1,10]], and ds[0:14:1] returns 10 elements
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 310
diff changeset
521 if idx >= len(self) :
009ce84e9f52 behaviour is now the same as a list in pylearn, so if len(ds) = 10, ds[10] raise an IndexError, same thing for ds[[1,10]], and ds[0:14:1] returns 10 elements
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 310
diff changeset
522 raise IndexError
290
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diff changeset
523 # call back into self.__getitem__
9b533cc7874a trying to get default implemenations to work
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diff changeset
524 examples = [self.minibatches_nowrap(self.fieldNames(),
293
4bfdda107a17 still merging
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diff changeset
525 minibatch_size=1, n_batches=1, offset=ii).next()
290
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diff changeset
526 for ii in i]
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diff changeset
527 # re-index the fields in each example by field instead of by example
9b533cc7874a trying to get default implemenations to work
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diff changeset
528 field_values = [[] for blah in self.fieldNames()]
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parents: 274
diff changeset
529 for e in examples:
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parents: 274
diff changeset
530 for f,v in zip(field_values, e):
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James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
531 f.append(v)
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
532 #build them into a LookupList (a.ka. Example)
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
533 zz = zip(self.fieldNames(),field_values)
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parents: 274
diff changeset
534 vst = [self.valuesVStack(fieldname,field_values) for fieldname,field_values in zz]
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
535 example = Example(self.fieldNames(), vst)
309
923de30457f0 get item now returns LookupLists
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 296
diff changeset
536 #return MinibatchDataSet(example, self.valuesVStack, self.valuesHStack)
923de30457f0 get item now returns LookupLists
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 296
diff changeset
537 # now returns a LookupList
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Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 296
diff changeset
538 return example
923de30457f0 get item now returns LookupLists
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 296
diff changeset
539
923de30457f0 get item now returns LookupLists
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 296
diff changeset
540 # what in the world is i?
269
fdce496c3b56 deprecating __getitem__[fieldname] syntax
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 268
diff changeset
541 raise TypeError(i, type(i))
22
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
542
310
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
543
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
544 """
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
545 Enables the call dataset.subset[a:b:c] that will return a DataSet
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
546 around the examples returned by __getitem__(slice(a,b,c))
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
547
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
548 @SEE DataSet.__getsubset(self)
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
549 """
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
550 subset = property(lambda s : s.__getsubset(),doc="returns a subset as a DataSet")
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
551
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
552
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
553 def __getsubset(self) :
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
554 """
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
555 Enables the call data.subset[a:b:c], returns a DataSet.
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
556 Default implementation is a simple wrap around __getitem__() using MinibatchDataSet.
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
557
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
558 @RETURN DataSet
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
559 @SEE DataSet.subset = property(lambda s : s.__getsubset())
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
560 """
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
561 _self = self
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
562 class GetSliceReturnsDataSet(object) :
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
563 def __getitem__(self,slice) :
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
564 return MinibatchDataSet(_self.__getitem__(slice))
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
565 return GetSliceReturnsDataSet()
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
566
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
567
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
568
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
569 def valuesHStack(self,fieldnames,fieldvalues):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
570 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
571 Return a value that corresponds to concatenating (horizontally) several field values.
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bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
572 This can be useful to merge some fields. The implementation of this operation is likely
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
573 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
574 result should be numpy.hstack(values). If it makes sense, this operation should
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
575 work as well when each value corresponds to multiple examples in a minibatch
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
576 e.g. if each value is a Ni-vector and a minibatch of length L is a LxNi matrix,
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
577 then the result should be a Lx(N1+N2+..) matrix equal to numpy.hstack(values).
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
578 The default is to use numpy.hstack for numpy.ndarray values, and a list
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
579 pointing to the original values for other data types.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
580 """
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bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
581 all_numpy=True
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
582 for value in fieldvalues:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
583 if not type(value) is numpy.ndarray:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
584 all_numpy=False
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
585 if all_numpy:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
586 return numpy.hstack(fieldvalues)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
587 # the default implementation of horizontal stacking is to put values in a list
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
588 return fieldvalues
26
672fe4b23032 Fixed dataset errors so that _test_dataset.py works again.
bengioy@grenat.iro.umontreal.ca
parents: 23
diff changeset
589
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
590 def valuesVStack(self,fieldname,values):
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
591 """
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
592 @param fieldname: the name of the field from which the values were taken
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
593 @type fieldname: any type
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
594
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
595 @param values: bits near the beginning or end of the dataset
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
596 @type values: list of minibatches (returned by minibatch_nowrap)
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
597
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
598 @return: the concatenation (stacking) of the values
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
599 @rtype: something suitable as a minibatch field
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
600 """
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
601 rval = []
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
602 for v in values:
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
603 rval.extend(v)
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
604 return rval
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
605
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
606 def __or__(self,other):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
607 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
608 dataset1 | dataset2 returns a dataset whose list of fields is the concatenation of the list of
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bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
609 fields of the argument datasets. This only works if they all have the same length.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
610 """
135
0d8e721cc63c Fixed bugs in dataset to make test_mlp.py work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 134
diff changeset
611 return HStackedDataSet([self,other])
3
378b68d5c4ad Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents: 2
diff changeset
612
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
613 def __and__(self,other):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
614 """
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
615 dataset1 & dataset2 is a dataset that concatenates the examples from the argument datasets
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
616 (and whose length is the sum of the length of the argument datasets). This only
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
617 works if they all have the same fields.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
618 """
135
0d8e721cc63c Fixed bugs in dataset to make test_mlp.py work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 134
diff changeset
619 return VStackedDataSet([self,other])
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
620
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
621 def hstack(datasets):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
622 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
623 hstack(dataset1,dataset2,...) returns dataset1 | datataset2 | ...
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
624 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
625 of the individual datasets.
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 assert len(datasets)>0
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
628 if len(datasets)==1:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
629 return datasets[0]
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
630 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
631
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
632 def vstack(datasets):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
633 """
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
634 vstack(dataset1,dataset2,...) returns dataset1 & datataset2 & ...
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
635 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
636 over those of dataset2, etc.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
637 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
638 assert len(datasets)>0
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
639 if len(datasets)==1:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
640 return datasets[0]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
641 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
642
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
643 class FieldsSubsetDataSet(DataSet):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
644 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
645 A sub-class of L{DataSet} that selects a subset of the fields.
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
646 """
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
647 def __init__(self,src,fieldnames):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
648 self.src=src
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
649 self.fieldnames=fieldnames
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
650 assert src.hasFields(*fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
651 self.valuesHStack = src.valuesHStack
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
652 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
653
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
654 def __len__(self): return len(self.src)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
655
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
656 def fieldNames(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
657 return self.fieldnames
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
658
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
659 def __iter__(self):
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
660 class FieldsSubsetIterator(object):
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
661 def __init__(self,ds):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
662 self.ds=ds
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
663 self.src_iter=ds.src.__iter__()
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
664 self.example=None
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
665 def __iter__(self): return self
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
666 def next(self):
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
667 complete_example = self.src_iter.next()
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
668 if self.example:
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
669 self.example._values=[complete_example[field]
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
670 for field in self.ds.fieldnames]
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
671 else:
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
672 self.example=Example(self.ds.fieldnames,
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
673 [complete_example[field] for field in self.ds.fieldnames])
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
674 return self.example
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
675 return FieldsSubsetIterator(self)
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
676
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
677 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
678 assert self.hasFields(*fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
679 return self.src.minibatches_nowrap(fieldnames,minibatch_size,n_batches,offset)
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
680 def dontuse__getitem__(self,i):
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
681 return FieldsSubsetDataSet(self.src[i],self.fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
682
328
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
683 class RenamedFieldsDataSet(DataSet):
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
684 """
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
685 A sub-class of L{DataSet} that selects and renames a subset of the fields.
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
686 """
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
687 def __init__(self,src,src_fieldnames,new_fieldnames):
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
688 self.src=src
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
689 self.src_fieldnames=src_fieldnames
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
690 self.new_fieldnames=new_fieldnames
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
691 assert src.hasFields(*src_fieldnames)
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
692 assert len(src_fieldnames)==len(new_fieldnames)
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
693 self.valuesHStack = src.valuesHStack
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
694 self.valuesVStack = src.valuesVStack
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
695
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
696 def __len__(self): return len(self.src)
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
697
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
698 def fieldNames(self):
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
699 return self.new_fieldnames
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
700
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
701 def __iter__(self):
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
702 class FieldsSubsetIterator(object):
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
703 def __init__(self,ds):
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
704 self.ds=ds
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
705 self.src_iter=ds.src.__iter__()
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
706 self.example=None
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
707 def __iter__(self): return self
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
708 def next(self):
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
709 complete_example = self.src_iter.next()
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
710 if self.example:
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
711 self.example._values=[complete_example[field]
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
712 for field in self.ds.src_fieldnames]
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
713 else:
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
714 self.example=Example(self.ds.new_fieldnames,
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
715 [complete_example[field]
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
716 for field in self.ds.src_fieldnames])
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
717 return self.example
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
718 return FieldsSubsetIterator(self)
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
719
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
720 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
721 assert self.hasFields(*fieldnames)
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
722 return self.src.minibatches_nowrap(fieldnames,minibatch_size,n_batches,offset)
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
723 def __getitem__(self,i):
333
7d2f7b8fe213 bugfix in RenamedDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 332
diff changeset
724 # return FieldsSubsetDataSet(self.src[i],self.new_fieldnames)
7d2f7b8fe213 bugfix in RenamedDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 332
diff changeset
725 complete_example = self.src[i]
7d2f7b8fe213 bugfix in RenamedDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 332
diff changeset
726 return Example(self.new_fieldnames,
7d2f7b8fe213 bugfix in RenamedDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 332
diff changeset
727 [complete_example[field]
7d2f7b8fe213 bugfix in RenamedDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 332
diff changeset
728 for field in self.src_fieldnames])
7d2f7b8fe213 bugfix in RenamedDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 332
diff changeset
729
328
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
730
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
731
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
732 class DataSetFields(Example):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
733 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
734 Although a L{DataSet} iterates over examples (like rows of a matrix), an associated
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
735 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
736 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
737
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
738 To iterate over fields, one can do
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
739 * for fields in dataset.fields()
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
740 * 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
741 * 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
742 and each of these fields is iterable over the examples:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
743 * for field_examples in dataset.fields():
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
744 for example_value in field_examples:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
745 ...
241
ddb88a8e9fd2 If I understand properly, the length of an unbounded stream is sys.maxint
delallea@opale.iro.umontreal.ca
parents: 231
diff changeset
746 but when the dataset is a stream (unbounded length), it is not recommended to do
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
747 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
748 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
749 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
750 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
751 be turned back into a DataSet with its examples() method:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
752 dataset2 = dataset1.fields().examples()
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
753 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
754
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
755 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
756 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
757 the examples.
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
758 """
74
b4159cbdc06b Fixed errors raised by test_dataset
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 73
diff changeset
759 def __init__(self,dataset,fieldnames):
65
d48eba49a2f4 fixed the infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 64
diff changeset
760 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
761 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
762 fieldnames=dataset.fieldNames()
274
ed70580f2324 bugfix in FieldSubsetDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 273
diff changeset
763 elif not list(fieldnames)==list(dataset.fieldNames()):
ed70580f2324 bugfix in FieldSubsetDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 273
diff changeset
764 #we must cast to list, othersize('x','y')!=['x','y']
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
765 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
766 assert dataset.hasFields(*fieldnames)
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
767 self.dataset=dataset
66
dde1fb1b63ba fixed test and removed print
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 65
diff changeset
768
64
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
769 if isinstance(dataset,MinibatchDataSet):
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
770 Example.__init__(self,fieldnames,list(dataset._fields))
65
d48eba49a2f4 fixed the infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 64
diff changeset
771 elif isinstance(original_dataset,MinibatchDataSet):
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
772 Example.__init__(self,fieldnames,
65
d48eba49a2f4 fixed the infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 64
diff changeset
773 [original_dataset._fields[field]
d48eba49a2f4 fixed the infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 64
diff changeset
774 for field in fieldnames])
64
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
775 else:
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
776 minibatch_iterator = dataset.minibatches(fieldnames,
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
777 minibatch_size=len(dataset),
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
778 n_batches=1)
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
779 minibatch=minibatch_iterator.next()
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
780 Example.__init__(self,fieldnames,minibatch)
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
781
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
782 def examples(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
783 return self.dataset
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
784
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
785 def __or__(self,other):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
786 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
787 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
788 of the list of examples of DataSetFields fields1 and fields2.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
789 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
790 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
791
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
792 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
793 """
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
794 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
795 of the fields of DataSetFields fields1 and fields2.
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 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
798
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
799
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
800 class MinibatchDataSet(DataSet):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
801 """
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
802 Turn a L{Example} of same-length (iterable) fields into an example-iterable dataset.
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
803 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
804 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
805 def __init__(self,fields_lookuplist,values_vstack=DataSet().valuesVStack,
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
806 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
807 """
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
808 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
809 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
810 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
811 """
211
bd728c83faff in __get__, problem if the i.stop was None, i being the slice, added one line replacing None by the len(self)
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 203
diff changeset
812
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
813 self._fields=fields_lookuplist
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
814 assert len(fields_lookuplist)>0
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
815 self.length=len(fields_lookuplist[0])
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
816 for field in fields_lookuplist[1:]:
223
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
817 if self.length != len(field) :
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
818 print 'self.length = ',self.length
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
819 print 'len(field) = ', len(field)
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
820 print 'self._fields.keys() = ', self._fields.keys()
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
821 print 'field=',field
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
822 print 'fields_lookuplist=', fields_lookuplist
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
823 assert self.length==len(field)
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
824 self.valuesVStack=values_vstack
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
825 self.valuesHStack=values_hstack
3
378b68d5c4ad Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents: 2
diff changeset
826
378b68d5c4ad Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents: 2
diff changeset
827 def __len__(self):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
828 return self.length
28
541a273bc89f Removed __array__ method from dataset, whose
bengioy@grenat.iro.umontreal.ca
parents: 26
diff changeset
829
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
830 def dontuse__getitem__(self,i):
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
831 if type(i) in (slice,list):
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
832 return DataSetFields(MinibatchDataSet(
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
833 Example(self._fields.keys(),[field[i] for field in self._fields])),self.fieldNames())
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
834 if type(i) is int:
85
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 83
diff changeset
835 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
836 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
837 return self._fields[i]
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
838 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
839 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
840
29
46c5c90019c2 Changed apply_function so that it propagates methods of the source.
bengioy@grenat.iro.umontreal.ca
parents: 28
diff changeset
841 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
842 return self._fields.keys()
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
843
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
844 def hasFields(self,*fieldnames):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
845 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
846 if fieldname not in self._fields.keys():
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
847 return False
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
848 return True
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
849
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
850 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
223
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
851 #@TODO bug somewhere here, fieldnames doesnt seem to be well handled
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
852 class Iterator(object):
223
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
853 def __init__(self,ds,fieldnames):
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
854 # tbm: added two next lines to handle fieldnames
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
855 if fieldnames is None: fieldnames = ds._fields.keys()
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
856 self.fieldnames = fieldnames
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
857
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
858 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
859 self.next_example=offset
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
860 assert minibatch_size >= 0
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
861 if offset+minibatch_size > ds.length:
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
862 raise NotImplementedError()
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
863 def __iter__(self):
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
864 return self
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
865 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
866 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
867 assert upper<=self.ds.length
223
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
868 #minibatch = Example(self.ds._fields.keys(),
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
869 # [field[self.next_example:upper]
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
870 # for field in self.ds._fields])
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
871 # tbm: modif to use fieldnames
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
872 values = []
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
873 for f in self.fieldnames :
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
874 #print 'we have field',f,'in fieldnames'
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
875 values.append( self.ds._fields[f][self.next_example:upper] )
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
876 minibatch = Example(self.fieldnames,values)
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
877 #print minibatch
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
878 self.next_example+=minibatch_size
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
879 return minibatch
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
880
223
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
881 # tbm: added fieldnames to handle subset of fieldnames
517364d48ae0 should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 218
diff changeset
882 return Iterator(self,fieldnames)
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
883
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
884 class HStackedDataSet(DataSet):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
885 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
886 A L{DataSet} that wraps several datasets and shows a view that includes all their fields,
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
887 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
888
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
889 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
890 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
891 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
892
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
893 @todo: automatically detect a chain of stacked datasets due to A | B | C | D ...
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
894 """
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
895 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
896 DataSet.__init__(self,description,field_types)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
897 self.datasets=datasets
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
898 self.accept_nonunique_names=accept_nonunique_names
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
899 self.fieldname2dataset={}
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
900
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
901 def rename_field(fieldname,dataset,i):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
902 if hasattr(dataset,"__name__"):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
903 return dataset.__name__ + "." + fieldname
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
904 return fieldname+"."+str(i)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
905
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
906 # 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
907 self.length=None
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
908 names_to_change=[]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
909 for i in xrange(len(datasets)):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
910 dataset = datasets[i]
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bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
911 length=len(dataset)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
912 if self.length:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
913 assert self.length==length
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
914 else:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
915 self.length=length
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
916 for fieldname in dataset.fieldNames():
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
917 if fieldname in self.fieldname2dataset: # name conflict!
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
918 if accept_nonunique_names:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
919 fieldname=rename_field(fieldname,dataset,i)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
920 names2change.append((fieldname,i))
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
921 else:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
922 raise ValueError("Incompatible datasets: non-unique field name = "+fieldname)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
923 self.fieldname2dataset[fieldname]=i
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
924 for fieldname,i in names_to_change:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
925 del self.fieldname2dataset[fieldname]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
926 self.fieldname2dataset[rename_field(fieldname,self.datasets[i],i)]=i
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
927
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
928 def hasFields(self,*fieldnames):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
929 for fieldname in fieldnames:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
930 if not fieldname in self.fieldname2dataset:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
931 return False
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
932 return True
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
933
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
934 def fieldNames(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
935 return self.fieldname2dataset.keys()
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
936
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
937 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
938
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
939 class HStackedIterator(object):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
940 def __init__(self,hsds,iterators):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
941 self.hsds=hsds
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
942 self.iterators=iterators
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
943 def __iter__(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
944 return self
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
945 def next(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
946 # concatenate all the fields of the minibatches
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
947 l=Example()
140
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 136
diff changeset
948 for iter in self.iterators:
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 136
diff changeset
949 l.append_lookuplist(iter.next())
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 136
diff changeset
950 return l
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
951
125
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 123
diff changeset
952 assert self.hasFields(*fieldnames)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
953 # 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
954 # and construct corresponding minibatch iterators
140
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 136
diff changeset
955 if fieldnames and fieldnames!=self.fieldNames():
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
956 datasets=set([])
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
957 fields_in_dataset=dict([(dataset,[]) for dataset in datasets])
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
958 for fieldname in fieldnames:
136
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 125
diff changeset
959 dataset=self.datasets[self.fieldname2dataset[fieldname]]
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
960 datasets.add(dataset)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
961 fields_in_dataset[dataset].append(fieldname)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
962 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
963 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
964 for dataset in datasets]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
965 else:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
966 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
967 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
968 return HStackedIterator(self,iterators)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
969
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
970
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
971 def untested_valuesVStack(self,fieldname,fieldvalues):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
972 return self.datasets[self.fieldname2dataset[fieldname]].valuesVStack(fieldname,fieldvalues)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
973
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
974 def untested_valuesHStack(self,fieldnames,fieldvalues):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
975 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
976 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
977 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
978 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
979 all the fieldnames are of the same sub-dataset.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
980 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
981 return self.datasets[self.fieldname2dataset[fieldnames[0]]].valuesHStack(fieldnames,fieldvalues)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
982
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
983 class VStackedDataSet(DataSet):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
984 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
985 A L{DataSet} that wraps several datasets and shows a view that includes all their examples,
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
986 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
987 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
988
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
989 @todo: automatically detect a chain of stacked datasets due to A + B + C + D ...
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
990 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
991 def __init__(self,datasets):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
992 self.datasets=datasets
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
993 self.length=0
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
994 self.index2dataset={}
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
995 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
996 fieldnames = datasets[-1].fieldNames()
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
997 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
998 # 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
999 # 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
1000 for dataset,k in enumerate(datasets[0:-1]):
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
1001 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
1002 L=len(dataset)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
1003 for i in xrange(L):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
1004 self.index2dataset[self.length+i]=k
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1005 self.datasets_start_row.append(self.length)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
1006 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
1007 assert dataset.fieldNames()==fieldnames
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1008 self.datasets_start_row.append(self.length)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
1009 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
1010 # 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
1011 # 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
1012 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
1013 # 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
1014 # TODO
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1015 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
1016
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1017 def __len__(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1018 return self.length
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1019
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1020 def fieldNames(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1021 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
1022
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1023 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
1024 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
1025
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1026 def locate_row(self,row):
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1027 """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
1028 dataset_index = self.index2dataset[row]
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1029 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
1030 return dataset_index, row_within_dataset
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1031
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1032 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
1033
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
1034 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
1035 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
1036 self.vsds=vsds
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1037 self.next_row=offset
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1038 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
1039 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
1040 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
1041
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1042 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
1043 L=len(dataset)
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1044 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
1045 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
1046 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
1047 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
1048 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
1049 n_left_in_mb=minibatch_size-L
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1050 ds_nbatches=1
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1051 else:
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1052 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
1053 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
1054 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
1055
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1056 def move_to_next_dataset(self):
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1057 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
1058 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
1059 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
1060 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
1061 else:
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1062 self.next_dataset_index +=1
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1063 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
1064 self.next_dataset_index = 0
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1065 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
1066 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
1067
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1068 def __iter__(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1069 return self
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1070
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1071 def next(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1072 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
1073 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
1074 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
1075 extra_mb = []
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1076 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
1077 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
1078 extra_mb.append(self.next_iterator.next())
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1079 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
1080 [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
1081 [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
1082 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
1083
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1084 self.next_row+=minibatch_size
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1085 self.next_dataset_row+=minibatch_size
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1086 if self.next_row+minibatch_size>len(dataset):
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1087 self.move_to_next_dataset()
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
1088 return examples
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
1089 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
1090
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1091 class ArrayFieldsDataSet(DataSet):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1092 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1093 Virtual super-class of datasets whose field values are numpy array,
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1094 thus defining valuesHStack and valuesVStack for sub-classes.
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1095 """
268
3f1cd8897fda reverting dataset
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 266
diff changeset
1096 def __init__(self,description=None,field_types=None):
3f1cd8897fda reverting dataset
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 266
diff changeset
1097 DataSet.__init__(self,description,field_types)
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1098 def untested_valuesHStack(self,fieldnames,fieldvalues):
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1099 """Concatenate field values horizontally, e.g. two vectors
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1100 become a longer vector, two matrices become a wider matrix, etc."""
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1101 return numpy.hstack(fieldvalues)
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1102 def untested_valuesVStack(self,fieldname,values):
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1103 """Concatenate field values vertically, e.g. two vectors
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1104 become a two-row matrix, two matrices become a longer matrix, etc."""
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1105 return numpy.vstack(values)
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1106
316
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1107
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1108
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1109 class NArraysDataSet(ArrayFieldsDataSet) :
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1110 """
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1111 An NArraysDataSet stores fields that are numpy tensor, whose first axis
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1112 iterates over examples. It's a generalization of ArrayDataSet.
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1113 """
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1114 #@TODO not completely implemented yet
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1115 def __init__(self, data_arrays, fieldnames, **kwargs) :
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1116 """
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1117 Construct an NArraysDataSet from a list of numpy tensor (data_arrays) and a list
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1118 of fieldnames. The number of arrays must be the same as the number of
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1119 fieldnames. Each set of numpy tensor must have the same first dimension (first
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1120 axis) corresponding to the number of examples.
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1121
321
f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 320
diff changeset
1122 Every tensor is treated as a numpy array (using numpy.asarray)
316
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1123 """
318
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1124 ArrayFieldsDataSet.__init__(self,**kwargs)
316
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1125 assert len(data_arrays) == len(fieldnames)
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1126 assert len(fieldnames) > 0
322
ad8be93b3c55 small bugs fixed with NArrayDataSet
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 321
diff changeset
1127 ndarrays = [numpy.asarray(a) for a in data_arrays]
321
f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 320
diff changeset
1128 lens = [a.shape[0] for a in ndarrays]
f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 320
diff changeset
1129 num_examples = lens[0] #they must all be equal anyway
316
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1130 self._fieldnames = fieldnames
322
ad8be93b3c55 small bugs fixed with NArrayDataSet
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 321
diff changeset
1131 for k in ndarrays :
321
f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 320
diff changeset
1132 assert k.shape[0] == num_examples
f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 320
diff changeset
1133 self._datas = ndarrays
f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 320
diff changeset
1134 # create dict
f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 320
diff changeset
1135 self.map_field_idx = dict()
f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 320
diff changeset
1136 for k in range(len(fieldnames)):
f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 320
diff changeset
1137 self.map_field_idx[fieldnames[k]] = k
316
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1138
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1139
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1140 def __len__(self) :
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1141 """
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1142 Length of the dataset is based on the first array = data_arrays[0], using its shape
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1143 """
318
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1144 return self._datas[0].shape[0]
316
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1145
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1146 def fieldNames(self) :
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1147 """
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1148 Returns the fieldnames as set in self.__init__
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1149 """
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1150 return self._fieldnames
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1151
321
f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 320
diff changeset
1152 def field_pos(self,fieldname) :
f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 320
diff changeset
1153 """
f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 320
diff changeset
1154 Returns the index of a given fieldname. Fieldname must exists! see fieldNames().
f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 320
diff changeset
1155 """
f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 320
diff changeset
1156 return self.map_field_idx[fieldname]
f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 320
diff changeset
1157
318
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1158 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1159 cursor = Example(fieldnames,[0]*len(fieldnames))
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1160 fieldnames = self.fieldNames() if fieldnames is None else fieldnames
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1161 for n in xrange(n_batches):
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1162 if offset == len(self):
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1163 break
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1164 for f in range(len(cursor._names)) :
321
f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 320
diff changeset
1165 idx = self.field_pos(cursor._names[f])
f03ae06fadc8 NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 320
diff changeset
1166 sub_data = self._datas[idx][offset : offset+minibatch_size]
318
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1167 cursor._values[f] = sub_data
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1168 offset += len(sub_data) #can be less than minibatch_size at end
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1169 yield cursor
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1170
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1171 #return ArrayDataSetIterator(self,fieldnames,minibatch_size,n_batches,offset)
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1172
e2eab74b6a28 NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 317
diff changeset
1173
316
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1174
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1175
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1176 class ArrayDataSet(ArrayFieldsDataSet):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1177 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1178 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
1179 whose first axis iterates over examples, second axis determines fields.
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1180 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
1181 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
1182 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1183
188
f01ac276c6fb added __contains__ to Dataset, added parent constructor call to ArrayDataSet
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 171
diff changeset
1184 def __init__(self, data_array, fields_columns, **kwargs):
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1185 """
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1186 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
1187 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
1188 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
1189 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
1190 """
188
f01ac276c6fb added __contains__ to Dataset, added parent constructor call to ArrayDataSet
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 171
diff changeset
1191 ArrayFieldsDataSet.__init__(self, **kwargs)
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1192 self.data=data_array
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1193 self.fields_columns=fields_columns
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1194
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1195 # check consistency and complete slices definitions
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1196 for fieldname, fieldcolumns in self.fields_columns.items():
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1197 if type(fieldcolumns) is int:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1198 assert fieldcolumns>=0 and fieldcolumns<data_array.shape[1]
268
3f1cd8897fda reverting dataset
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 266
diff changeset
1199 if 1:
227
17c5d080964b reinstating changeset 216 clobbered accidentally by 218
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 223
diff changeset
1200 #I changed this because it didn't make sense to me,
17c5d080964b reinstating changeset 216 clobbered accidentally by 218
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 223
diff changeset
1201 # and it made it more difficult to write my learner.
17c5d080964b reinstating changeset 216 clobbered accidentally by 218
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 223
diff changeset
1202 # If it breaks stuff, let's talk about it.
17c5d080964b reinstating changeset 216 clobbered accidentally by 218
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 223
diff changeset
1203 # - James 22/05/2008
17c5d080964b reinstating changeset 216 clobbered accidentally by 218
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 223
diff changeset
1204 self.fields_columns[fieldname]=[fieldcolumns]
17c5d080964b reinstating changeset 216 clobbered accidentally by 218
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 223
diff changeset
1205 else:
17c5d080964b reinstating changeset 216 clobbered accidentally by 218
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 223
diff changeset
1206 self.fields_columns[fieldname]=fieldcolumns
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1207 elif type(fieldcolumns) is slice:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1208 start,step=None,None
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1209 if not fieldcolumns.start:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1210 start=0
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1211 if not fieldcolumns.step:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1212 step=1
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1213 if start or step:
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1214 self.fields_columns[fieldname]=slice(start,fieldcolumns.stop,step)
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1215 elif hasattr(fieldcolumns,"__iter__"): # something like a list
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1216 for i in fieldcolumns:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1217 assert i>=0 and i<data_array.shape[1]
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1218
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1219 def fieldNames(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1220 return self.fields_columns.keys()
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1221
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1222 def __len__(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1223 return len(self.data)
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1224
316
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1225 def __getitem__(self,key):
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1226 """More efficient implementation than the default __getitem__"""
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1227 fieldnames=self.fields_columns.keys()
243
c8f19a9eb10f Optimisation in ArrayDataSet::__getitem__
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 242
diff changeset
1228 values=self.fields_columns.values()
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1229 if type(key) is int:
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1230 return Example(fieldnames,
243
c8f19a9eb10f Optimisation in ArrayDataSet::__getitem__
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 242
diff changeset
1231 [self.data[key,col] for col in values])
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1232 if type(key) is slice:
316
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1233 return Example(fieldnames,[self.data[key,col] for col in values])
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1234 if type(key) is list:
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1235 for i in range(len(key)):
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1236 if self.hasFields(key[i]):
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1237 key[i]=self.fields_columns[key[i]]
316
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1238 return Example(fieldnames,
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1239 #we must separate differently for list as numpy
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1240 # doesn't support self.data[[i1,...],[i2,...]]
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1241 # when their is more then two i1 and i2
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1242 [self.data[key,:][:,col]
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1243 if isinstance(col,list) else
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1244 self.data[key,col] for col in values])
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1245
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1246 # else check for a fieldname
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1247 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
1248 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
1249 # else we are trying to access a property of the dataset
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1250 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
1251 return self.__dict__[key]
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1252
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1253 def dontuse__iter__(self):
270
1cafd495098c code cleanup and small optimisation
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 254
diff changeset
1254 class ArrayDataSetIteratorIter(object):
1cafd495098c code cleanup and small optimisation
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 254
diff changeset
1255 def __init__(self,dataset,fieldnames):
228
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1256 if fieldnames is None: fieldnames = dataset.fieldNames()
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1257 # store the resulting minibatch in a lookup-list of values
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1258 self.minibatch = Example(fieldnames,[0]*len(fieldnames))
228
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1259 self.dataset=dataset
270
1cafd495098c code cleanup and small optimisation
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 254
diff changeset
1260 self.current=0
238
ae1d85aca858 optimization in ArrayDataSet::__iter__
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 235
diff changeset
1261 self.columns = [self.dataset.fields_columns[f]
ae1d85aca858 optimization in ArrayDataSet::__iter__
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 235
diff changeset
1262 for f in self.minibatch._names]
270
1cafd495098c code cleanup and small optimisation
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 254
diff changeset
1263 self.l = self.dataset.data.shape[0]
228
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1264 def __iter__(self):
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1265 return self
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1266 def next(self):
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1267 #@todo: we suppose that we need to stop only when minibatch_size == 1.
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1268 # Otherwise, MinibatchWrapAroundIterator do it.
270
1cafd495098c code cleanup and small optimisation
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 254
diff changeset
1269 if self.current>=self.l:
228
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1270 raise StopIteration
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1271 sub_data = self.dataset.data[self.current]
238
ae1d85aca858 optimization in ArrayDataSet::__iter__
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 235
diff changeset
1272 self.minibatch._values = [sub_data[c] for c in self.columns]
ae1d85aca858 optimization in ArrayDataSet::__iter__
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 235
diff changeset
1273
270
1cafd495098c code cleanup and small optimisation
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 254
diff changeset
1274 self.current+=1
228
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1275 return self.minibatch
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1276
270
1cafd495098c code cleanup and small optimisation
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 254
diff changeset
1277 return ArrayDataSetIteratorIter(self,self.fieldNames())
228
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1278
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1279 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1280 cursor = Example(fieldnames,[0]*len(fieldnames))
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1281 fieldnames = self.fieldNames() if fieldnames is None else fieldnames
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1282 for n in xrange(n_batches):
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1283 if offset == len(self):
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1284 break
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1285 sub_data = self.data[offset : offset+minibatch_size]
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1286 offset += len(sub_data) #can be less than minibatch_size at end
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1287 cursor._values = [sub_data[:,self.fields_columns[f]] for f in cursor._names]
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1288 yield cursor
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1289
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1290 #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
1291
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1292
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1293 class CachedDataSet(DataSet):
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1294 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1295 Wrap a L{DataSet} whose values are computationally expensive to obtain
57
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1296 (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
1297 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
1298 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
1299
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1300 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
1301 (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
1302 first access.
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1303
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1304 @todo: when cache_all_upon_construction create mini-batches that are as
77
1e2bb5bad636 toying with different ways to implement learners
bengioy@bengiomac.local
parents: 74
diff changeset
1305 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
1306
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1307 @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
1308 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
1309 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
1310 """
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1311 def __init__(self,source_dataset,cache_all_upon_construction=False):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1312 self.source_dataset=source_dataset
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1313 self.cache_all_upon_construction=cache_all_upon_construction
152
3f627e844cba Fixes in CacheDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 151
diff changeset
1314 self.cached_examples = []
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1315 if cache_all_upon_construction:
77
1e2bb5bad636 toying with different ways to implement learners
bengioy@bengiomac.local
parents: 74
diff changeset
1316 # this potentially brings all the source examples
1e2bb5bad636 toying with different ways to implement learners
bengioy@bengiomac.local
parents: 74
diff changeset
1317 # into memory at once, which may be too much
1e2bb5bad636 toying with different ways to implement learners
bengioy@bengiomac.local
parents: 74
diff changeset
1318 # the work could possibly be done by minibatches
1e2bb5bad636 toying with different ways to implement learners
bengioy@bengiomac.local
parents: 74
diff changeset
1319 # 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
1320 fields_values = source_dataset.minibatches(minibatch_size=len(source_dataset)).__iter__().next()
152
3f627e844cba Fixes in CacheDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 151
diff changeset
1321 assert all([len(self)==len(field_values) for field_values in fields_values])
3f627e844cba Fixes in CacheDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 151
diff changeset
1322 for example in fields_values.examples():
171
895b4b60f5e8 bugfix. Otherwise the example was writed over and not a new one was returned
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 167
diff changeset
1323 self.cached_examples.append(copy.copy(example))
57
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1324
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1325 self.fieldNames = source_dataset.fieldNames
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1326 self.hasFields = source_dataset.hasFields
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1327 self.valuesHStack = source_dataset.valuesHStack
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1328 self.valuesVStack = source_dataset.valuesVStack
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1329
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1330 def __len__(self):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1331 return len(self.source_dataset)
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1332
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1333 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1334 class CacheIterator(object):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1335 def __init__(self,dataset):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1336 self.dataset=dataset
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1337 self.current=offset
254
8ec867d12428 optimication in CachedDataSet.minibatches_nowrap
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 253
diff changeset
1338 self.all_fields = self.dataset.fieldNames()==fieldnames
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1339 def __iter__(self): return self
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1340 def next(self):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1341 upper = self.current+minibatch_size
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1342 cache_len = len(self.dataset.cached_examples)
135
0d8e721cc63c Fixed bugs in dataset to make test_mlp.py work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 134
diff changeset
1343 if upper>cache_len: # whole minibatch is not already in cache
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1344 # cache everything from current length to upper
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1345 for example in self.dataset.source_dataset[cache_len:upper]:
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1346 self.dataset.cached_examples.append(example)
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1347 all_fields_minibatch = Example(self.dataset.fieldNames(),
152
3f627e844cba Fixes in CacheDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 151
diff changeset
1348 zip(*self.dataset.cached_examples[self.current:self.current+minibatch_size]))
163
d7d67651d67c bugfix, we should advence by the minibatch size.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 159
diff changeset
1349 self.current+=minibatch_size
254
8ec867d12428 optimication in CachedDataSet.minibatches_nowrap
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 253
diff changeset
1350 if self.all_fields:
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1351 return all_fields_minibatch
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1352 return Example(fieldnames,[all_fields_minibatch[name] for name in fieldnames])
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1353 return CacheIterator(self)
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1354
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1355 def dontuse__getitem__(self,i):
153
71107b0ac860 optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 151
diff changeset
1356 if type(i)==int and len(self.cached_examples)>i:
71107b0ac860 optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 151
diff changeset
1357 return self.cached_examples[i]
71107b0ac860 optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 151
diff changeset
1358 else:
251
7e6edee187e3 optimization of CachedDataSet__getitem__
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 243
diff changeset
1359 return self.source_dataset[i]
252
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1360
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1361 def __iter__(self):
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1362 class CacheIteratorIter(object):
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1363 def __init__(self,dataset):
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1364 self.dataset=dataset
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1365 self.l = len(dataset)
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1366 self.current = 0
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1367 self.fieldnames = self.dataset.fieldNames()
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1368 self.example = Example(self.fieldnames,[0]*len(self.fieldnames))
252
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1369 def __iter__(self): return self
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1370 def next(self):
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1371 if self.current>=self.l:
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1372 raise StopIteration
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1373 cache_len = len(self.dataset.cached_examples)
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1374 if self.current>=cache_len: # whole minibatch is not already in cache
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1375 # cache everything from current length to upper
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1376 self.dataset.cached_examples.append(
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1377 self.dataset.source_dataset[self.current])
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1378 self.example._values = self.dataset.cached_examples[self.current]
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1379 self.current+=1
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1380 return self.example
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1381
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1382 return CacheIteratorIter(self)
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1383
57
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1384 class ApplyFunctionDataSet(DataSet):
290
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1385 """
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parents: 274
diff changeset
1386 A L{DataSet} that contains as fields the results of applying a
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1387 given function example-wise or minibatch-wise to all the fields of
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1388 an input dataset. The output of the function should be an iterable
296
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1389 (e.g. a list or a LookupList) over the resulting values.
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1390
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1391 The function take as input the fields of the dataset, not the examples.
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1392
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1393 In minibatch mode, the function is expected to work on minibatches
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1394 (takes a minibatch in input and returns a minibatch in output). More
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1395 precisely, it means that each element of the input or output list
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1396 should be iterable and indexable over the individual example values
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1397 (typically these elements will be numpy arrays). All of the elements
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1398 in the input and output lists should have the same length, which is
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1399 the length of the minibatch.
57
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1400
290
9b533cc7874a trying to get default implemenations to work
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diff changeset
1401 The function is applied each time an example or a minibatch is accessed.
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1402 To avoid re-doing computation, wrap this dataset inside a CachedDataSet.
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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diff changeset
1403
290
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parents: 274
diff changeset
1404 If the values_{h,v}stack functions are not provided, then
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1405 the input_dataset.values{H,V}Stack functions are used by default.
296
f5d33f9c0b9c ApplyFunctionDataSet passing
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parents: 293
diff changeset
1406
290
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diff changeset
1407 """
296
f5d33f9c0b9c ApplyFunctionDataSet passing
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parents: 293
diff changeset
1408
290
9b533cc7874a trying to get default implemenations to work
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diff changeset
1409 def __init__(self,input_dataset,function,output_names,minibatch_mode=True,
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1410 values_hstack=None,values_vstack=None,
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parents: 274
diff changeset
1411 description=None,fieldtypes=None):
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parents: 274
diff changeset
1412 """
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parents: 274
diff changeset
1413 Constructor takes an input dataset that has as many fields as the function
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1414 expects as inputs. The resulting dataset has as many fields as the function
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1415 produces as outputs, and that should correspond to the number of output names
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1416 (provided in a list).
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
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parents: 72
diff changeset
1417
290
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parents: 274
diff changeset
1418 Note that the expected semantics of the function differs in minibatch mode
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1419 (it takes minibatches of inputs and produces minibatches of outputs, as
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1420 documented in the class comment).
211
bd728c83faff in __get__, problem if the i.stop was None, i being the slice, added one line replacing None by the len(self)
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 203
diff changeset
1421
290
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1422 TBM: are filedtypes the old field types (from input_dataset) or the new ones
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parents: 274
diff changeset
1423 (for the new dataset created)?
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1424 """
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1425 self.input_dataset=input_dataset
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parents: 274
diff changeset
1426 self.function=function
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
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diff changeset
1427 self.output_names=output_names
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James Bergstra <bergstrj@iro.umontreal.ca>
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diff changeset
1428 self.minibatch_mode=minibatch_mode
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diff changeset
1429 DataSet.__init__(self,description,fieldtypes)
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diff changeset
1430 self.valuesHStack = values_hstack if values_hstack else input_dataset.valuesHStack
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1431 self.valuesVStack = values_vstack if values_vstack else input_dataset.valuesVStack
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1432
290
9b533cc7874a trying to get default implemenations to work
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diff changeset
1433 def __len__(self):
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parents: 274
diff changeset
1434 return len(self.input_dataset)
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1435
290
9b533cc7874a trying to get default implemenations to work
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diff changeset
1436 def fieldNames(self):
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1437 return self.output_names
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1438
290
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1439 def minibatches_nowrap(self, fieldnames, *args, **kwargs):
296
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1440 all_input_fieldNames = self.input_dataset.fieldNames()
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1441 mbnw = self.input_dataset.minibatches_nowrap
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1442
296
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1443 for input_fields in mbnw(all_input_fieldNames, *args, **kwargs):
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1444 if self.minibatch_mode:
296
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1445 all_output_fields = self.function(*input_fields)
290
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1446 else:
296
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1447 input_examples = zip(*input_fields) #makes so that [i] means example i
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1448 output_examples = [self.function(*input_example)
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1449 for input_example in input_examples]
296
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1450 all_output_fields = zip(*output_examples)
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1451
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1452 all_outputs = Example(self.output_names, all_output_fields)
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1453 #print 'input_fields', input_fields
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1454 #print 'all_outputs', all_outputs
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1455 if fieldnames==self.output_names:
293
4bfdda107a17 still merging
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 292
diff changeset
1456 rval = all_outputs
290
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1457 else:
293
4bfdda107a17 still merging
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 292
diff changeset
1458 rval = Example(fieldnames,[all_outputs[name] for name in fieldnames])
296
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1459 #print 'rval', rval
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1460 #print '--------'
293
4bfdda107a17 still merging
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parents: 292
diff changeset
1461 yield rval
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1462
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1463 def untested__iter__(self): # only implemented for increased efficiency
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1464 class ApplyFunctionSingleExampleIterator(object):
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1465 def __init__(self,output_dataset):
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1466 self.current=0
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1467 self.output_dataset=output_dataset
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1468 self.input_iterator=output_dataset.input_dataset.__iter__()
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parents: 274
diff changeset
1469 def __iter__(self): return self
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1470 def next(self):
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1471 if self.output_dataset.minibatch_mode:
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1472 function_inputs = [[input] for input in self.input_iterator.next()]
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1473 outputs = self.output_dataset.function(*function_inputs)
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1474 assert all([hasattr(output,'__iter__') for output in outputs])
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1475 function_outputs = [output[0] for output in outputs]
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1476 else:
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parents: 274
diff changeset
1477 function_inputs = self.input_iterator.next()
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1478 function_outputs = self.output_dataset.function(*function_inputs)
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1479 return Example(self.output_dataset.output_names,function_outputs)
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1480 return ApplyFunctionSingleExampleIterator(self)
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1481
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1482 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
1483 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1484 Wraps an arbitrary L{DataSet} into one for supervised learning tasks
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1485 by forcing the user to define a set of fields as the 'input' field
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1486 and a set of fields as the 'target' field. Optionally, a single
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1487 weight_field can also be defined.
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1488 """
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1489 args = ((input_fields,'input'),(output_fields,'target'))
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1490 if weight_field: args+=(([weight_field],'weight'))
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
1491 return src_dataset.merge_fields(*args)
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1492
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1493
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1494
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1495