annotate dataset.py @ 360:0e3af3c53ac7

common.misc.runcmd can now take input
author Joseph Turian <turian@iro.umontreal.ca>
date Wed, 02 Jul 2008 16:10:00 -0400
parents 18702ceb2096
children 835830e52b42
rev   line source
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2 from lookup_list import LookupList as Example
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3 from common.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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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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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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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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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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106 - dataset[i] returns an Example.
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108 - dataset[[i1,i2,...in]] returns a. Example with examples i1,i2,...in.
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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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114 - dataset.subset[i1:i2:s] returns a DataSet with the examples i1,i1+s,...i2-s.
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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
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311 [self.dataset.valuesVStack(name,[first_part[name],second_part[name]])
101
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diff changeset
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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diff changeset
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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diff changeset
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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parents: 73
diff changeset
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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diff changeset
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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diff changeset
334 offset = 0):
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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
36
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354 The minibatches iterator is expected to return upon each call to next()
290
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diff changeset
355 a DataSetFields object, which is a Example (indexed by the field names) whose
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
356 elements are iterable and indexable over the minibatch examples, and which keeps a pointer to
36
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diff changeset
357 a sub-dataset that can be used to iterate over the individual examples
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diff changeset
358 in the minibatch. Hence a minibatch can be converted back to a regular
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diff changeset
359 dataset or its fields can be looked at individually (and possibly iterated over).
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diff changeset
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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diff changeset
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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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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parents: 330
diff changeset
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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diff changeset
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
353
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Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 351
diff changeset
384 batches only, raise StopIteration.
47538a45b878 Cached dataset seems debug, using n_batches... is n_batches around to stay?
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parents: 351
diff changeset
385 @ATTENTION: minibatches returns a LookupList, we can't iterate over examples on it.
331
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parents: 330
diff changeset
386
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diff changeset
387 """
331
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parents: 330
diff changeset
388 #return DataSet.MinibatchWrapAroundIterator(self,fieldnames,minibatch_size,n_batches,offset)\
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parents: 330
diff changeset
389 assert offset >= 0
52aa031e1fe3 IMPORTANT: minibatches now returns minibatch_nowrap with a minimum of assert before. Should implement the good behavior, e.g. returning only complete batches and let the user figure out what he wants.
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 330
diff changeset
390 assert offset < len(self)
334
a0f150a33b0f debug in an assert of minibatches
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 332
diff changeset
391 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
392 if fieldnames == None :
5e38ed2b3a75 debugging when fieldnames = None, now -> fieldnames = fieldNames()
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 335
diff changeset
393 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
394 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
395
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
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parents: 36
diff changeset
396 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
397 """
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
398 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
399 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
400 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
401 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
402 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
403 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
404 That next() method can assert that its next row will always be within [0,len(dataset)).
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
405 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
406 a next_index() method either, as this will be provided by MinibatchWrapAroundIterator.
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
407 """
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
408 raise AbstractFunction()
22
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
bengioy@esprit.iro.umontreal.ca
parents: 20
diff changeset
409
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
410 def is_unbounded(self):
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
411 """
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
412 Tests whether a dataset is unbounded (e.g. a stream).
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
413 """
123
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 110
diff changeset
414 return len(self)==maxint
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
415
26
672fe4b23032 Fixed dataset errors so that _test_dataset.py works again.
bengioy@grenat.iro.umontreal.ca
parents: 23
diff changeset
416 def hasFields(self,*fieldnames):
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
417 """
22
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
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parents: 20
diff changeset
418 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
419 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
420 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
421
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
422 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
423 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
424 """
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
425 return len(unique_elements_list_intersection(fieldnames,self.fieldNames()))>0
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
426
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
427 def fieldNames(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
428 """
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
429 Return the list of field names that are supported by the iterators,
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
430 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
431 """
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
432 raise AbstractFunction()
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
433
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
434 def __call__(self,*fieldnames):
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
435 """
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
436 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
437 """
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
438 assert self.hasFields(*fieldnames)
354
d580b3a369a4 dataset__call__() returns a FieldsSubsetDataSet, so still a subset of fields, but not cached any more. I added the function dataset.cached_fields_subset(self,*fieldnames) that returns the old version, cached, in case someone needs it. Current behaviour passes the tests.
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 353
diff changeset
439 #return self.fields(*fieldnames).examples()
d580b3a369a4 dataset__call__() returns a FieldsSubsetDataSet, so still a subset of fields, but not cached any more. I added the function dataset.cached_fields_subset(self,*fieldnames) that returns the old version, cached, in case someone needs it. Current behaviour passes the tests.
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 353
diff changeset
440 fieldnames_list = list(fieldnames)
d580b3a369a4 dataset__call__() returns a FieldsSubsetDataSet, so still a subset of fields, but not cached any more. I added the function dataset.cached_fields_subset(self,*fieldnames) that returns the old version, cached, in case someone needs it. Current behaviour passes the tests.
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 353
diff changeset
441 return FieldsSubsetDataSet(self,fieldnames_list)
d580b3a369a4 dataset__call__() returns a FieldsSubsetDataSet, so still a subset of fields, but not cached any more. I added the function dataset.cached_fields_subset(self,*fieldnames) that returns the old version, cached, in case someone needs it. Current behaviour passes the tests.
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 353
diff changeset
442
d580b3a369a4 dataset__call__() returns a FieldsSubsetDataSet, so still a subset of fields, but not cached any more. I added the function dataset.cached_fields_subset(self,*fieldnames) that returns the old version, cached, in case someone needs it. Current behaviour passes the tests.
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 353
diff changeset
443 def cached_fields_subset(self,*fieldnames) :
d580b3a369a4 dataset__call__() returns a FieldsSubsetDataSet, so still a subset of fields, but not cached any more. I added the function dataset.cached_fields_subset(self,*fieldnames) that returns the old version, cached, in case someone needs it. Current behaviour passes the tests.
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 353
diff changeset
444 """
d580b3a369a4 dataset__call__() returns a FieldsSubsetDataSet, so still a subset of fields, but not cached any more. I added the function dataset.cached_fields_subset(self,*fieldnames) that returns the old version, cached, in case someone needs it. Current behaviour passes the tests.
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 353
diff changeset
445 Behaviour is supposed to be the same as __call__(*fieldnames), but the dataset returned is cached.
d580b3a369a4 dataset__call__() returns a FieldsSubsetDataSet, so still a subset of fields, but not cached any more. I added the function dataset.cached_fields_subset(self,*fieldnames) that returns the old version, cached, in case someone needs it. Current behaviour passes the tests.
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 353
diff changeset
446 @see : dataset.__call__
d580b3a369a4 dataset__call__() returns a FieldsSubsetDataSet, so still a subset of fields, but not cached any more. I added the function dataset.cached_fields_subset(self,*fieldnames) that returns the old version, cached, in case someone needs it. Current behaviour passes the tests.
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 353
diff changeset
447 """
d580b3a369a4 dataset__call__() returns a FieldsSubsetDataSet, so still a subset of fields, but not cached any more. I added the function dataset.cached_fields_subset(self,*fieldnames) that returns the old version, cached, in case someone needs it. Current behaviour passes the tests.
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 353
diff changeset
448 assert self.hasFields(*fieldnames)
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
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parents: 41
diff changeset
449 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
450
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
451 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
452 """
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
453 Return a DataSetFields object associated with this dataset.
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
454 """
74
b4159cbdc06b Fixed errors raised by test_dataset
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 73
diff changeset
455 return DataSetFields(self,fieldnames)
11
be128b9127c8 Debugged (to the extent of my tests) the new version of dataset
bengioy@esprit.iro.umontreal.ca
parents: 9
diff changeset
456
269
fdce496c3b56 deprecating __getitem__[fieldname] syntax
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parents: 268
diff changeset
457 def getitem_key(self, fieldname):
fdce496c3b56 deprecating __getitem__[fieldname] syntax
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parents: 268
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458 """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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459 getitem.
fdce496c3b56 deprecating __getitem__[fieldname] syntax
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parents: 268
diff changeset
460 """
fdce496c3b56 deprecating __getitem__[fieldname] syntax
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parents: 268
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461 #removing as per discussion June 4. --JSB
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parents: 268
diff changeset
462
fdce496c3b56 deprecating __getitem__[fieldname] syntax
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parents: 268
diff changeset
463 i = fieldname
fdce496c3b56 deprecating __getitem__[fieldname] syntax
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parents: 268
diff changeset
464 # else check for a fieldname
fdce496c3b56 deprecating __getitem__[fieldname] syntax
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parents: 268
diff changeset
465 if self.hasFields(i):
fdce496c3b56 deprecating __getitem__[fieldname] syntax
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parents: 268
diff changeset
466 return self.minibatches(fieldnames=[i],minibatch_size=len(self),n_batches=1,offset=0).next()[0]
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parents: 268
diff changeset
467 # else we are trying to access a property of the dataset
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parents: 268
diff changeset
468 assert i in self.__dict__ # else it means we are trying to access a non-existing property
fdce496c3b56 deprecating __getitem__[fieldname] syntax
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 268
diff changeset
469 return self.__dict__[i]
fdce496c3b56 deprecating __getitem__[fieldname] syntax
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parents: 268
diff changeset
470
2
3fddb1c8f955 Rewrote DataSet interface and created FiniteDataSet interface.
bengioy@bengiomac.local
parents: 1
diff changeset
471 def __getitem__(self,i):
28
541a273bc89f Removed __array__ method from dataset, whose
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parents: 26
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472 """
290
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
473 @rtype: Example
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
474 @returns: single or multiple examples
1
2cd82666b9a7 Added statscollector and started writing dataset and learner.
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parents: 0
diff changeset
475
290
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parents: 274
diff changeset
476 @type i: integer or slice or <iterable> of integers
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
477 @param i:
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
478 dataset[i] returns the (i+1)-th example of the dataset.
309
923de30457f0 get item now returns LookupLists
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 296
diff changeset
479 dataset[i:j] returns a LookupList with examples i,i+1,...,j-1.
923de30457f0 get item now returns LookupLists
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 296
diff changeset
480 dataset[i:j:s] returns a LookupList with examples i,i+2,i+4...,j-2.
923de30457f0 get item now returns LookupLists
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 296
diff changeset
481 dataset[[i1,i2,..,in]] returns a LookupList with examples i1,i2,...,in.
290
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diff changeset
482
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parents: 274
diff changeset
483 @note:
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parents: 274
diff changeset
484 Some stream datasets may be unable to implement random access, i.e.
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parents: 274
diff changeset
485 arbitrary slicing/indexing because they can only iterate through
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diff changeset
486 examples one or a minibatch at a time and do not actually store or keep
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parents: 274
diff changeset
487 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
488
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
489 The default implementation of getitem uses the minibatches iterator
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
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parents: 39
diff changeset
490 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
491 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
492 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
493 """
290
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parents: 274
diff changeset
494
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
495 if type(i) is int:
309
923de30457f0 get item now returns LookupLists
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 296
diff changeset
496 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
497 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
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498 raise IndexError
290
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diff changeset
499 i_batch = self.minibatches_nowrap(self.fieldNames(),
293
4bfdda107a17 still merging
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parents: 292
diff changeset
500 minibatch_size=1, n_batches=1, offset=i)
290
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parents: 274
diff changeset
501 return DataSet.MinibatchToSingleExampleIterator(i_batch).next()
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parents: 274
diff changeset
502
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parents: 274
diff changeset
503 #if i is a contiguous slice
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parents: 274
diff changeset
504 if type(i) is slice and (i.step in (None, 1)):
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parents: 274
diff changeset
505 offset = 0 if i.start is None else i.start
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parents: 274
diff changeset
506 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
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 310
diff changeset
507 upper_bound = min(len(self) , upper_bound)
309
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508 #return MinibatchDataSet(self.minibatches_nowrap(self.fieldNames(),
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diff changeset
509 # minibatch_size=upper_bound - offset,
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diff changeset
510 # n_batches=1,
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diff changeset
511 # offset=offset).next())
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512 # now returns a LookupList
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513 return self.minibatches_nowrap(self.fieldNames(),
290
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514 minibatch_size=upper_bound - offset,
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515 n_batches=1,
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516 offset=offset).next()
290
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517
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diff changeset
518 # if slice has a step param, convert it to list and handle it with the
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519 # list code
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520 if type(i) is slice:
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521 offset = 0 if i.start is None else i.start
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522 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
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523 upper_bound = min(len(self) , upper_bound)
290
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diff changeset
524 i = list(range(offset, upper_bound, i.step))
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525
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526 # handle tuples, arrays, lists
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527 if hasattr(i, '__getitem__'):
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528 for idx in i:
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diff changeset
529 #dis-allow nested slices
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530 if not isinstance(idx, int):
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531 raise TypeError(idx)
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532 if idx >= len(self) :
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533 raise IndexError
290
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534 # call back into self.__getitem__
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535 examples = [self.minibatches_nowrap(self.fieldNames(),
293
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536 minibatch_size=1, n_batches=1, offset=ii).next()
290
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537 for ii in i]
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538 # re-index the fields in each example by field instead of by example
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539 field_values = [[] for blah in self.fieldNames()]
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540 for e in examples:
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541 for f,v in zip(field_values, e):
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diff changeset
542 f.append(v)
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543 #build them into a LookupList (a.ka. Example)
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544 zz = zip(self.fieldNames(),field_values)
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diff changeset
545 vst = [self.valuesVStack(fieldname,field_values) for fieldname,field_values in zz]
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546 example = Example(self.fieldNames(), vst)
309
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547 #return MinibatchDataSet(example, self.valuesVStack, self.valuesHStack)
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548 # now returns a LookupList
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Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
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549 return example
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Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 296
diff changeset
550
923de30457f0 get item now returns LookupLists
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
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diff changeset
551 # what in the world is i?
269
fdce496c3b56 deprecating __getitem__[fieldname] syntax
James Bergstra <bergstrj@iro.umontreal.ca>
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diff changeset
552 raise TypeError(i, type(i))
22
b6b36f65664f Created virtual sub-classes of DataSet: {Finite{Length,Width},Sliceable}DataSet,
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diff changeset
553
310
ebccfd05ccd5 dataset.subset implemented
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554
ebccfd05ccd5 dataset.subset implemented
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555 """
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parents: 309
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556 Enables the call dataset.subset[a:b:c] that will return a DataSet
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
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diff changeset
557 around the examples returned by __getitem__(slice(a,b,c))
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diff changeset
558
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
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diff changeset
559 @SEE DataSet.__getsubset(self)
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diff changeset
560 """
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Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
561 subset = property(lambda s : s.__getsubset(),doc="returns a subset as a DataSet")
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parents: 309
diff changeset
562
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
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diff changeset
563
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
564 def __getsubset(self) :
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parents: 309
diff changeset
565 """
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parents: 309
diff changeset
566 Enables the call data.subset[a:b:c], returns a DataSet.
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Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
567 Default implementation is a simple wrap around __getitem__() using MinibatchDataSet.
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Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
568
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Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
569 @RETURN DataSet
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Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
570 @SEE DataSet.subset = property(lambda s : s.__getsubset())
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Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
571 """
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
572 _self = self
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Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
573 class GetSliceReturnsDataSet(object) :
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
574 def __getitem__(self,slice) :
ebccfd05ccd5 dataset.subset implemented
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parents: 309
diff changeset
575 return MinibatchDataSet(_self.__getitem__(slice))
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Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
576 return GetSliceReturnsDataSet()
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Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
577
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
578
ebccfd05ccd5 dataset.subset implemented
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 309
diff changeset
579
36
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diff changeset
580 def valuesHStack(self,fieldnames,fieldvalues):
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bengioy@zircon.iro.umontreal.ca
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diff changeset
581 """
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parents: 29
diff changeset
582 Return a value that corresponds to concatenating (horizontally) several field values.
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bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
583 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
584 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
585 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
586 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
587 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
588 then the result should be a Lx(N1+N2+..) matrix equal to numpy.hstack(values).
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parents: 29
diff changeset
589 The default is to use numpy.hstack for numpy.ndarray values, and a list
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bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
590 pointing to the original values for other data types.
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bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
591 """
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bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
592 all_numpy=True
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bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
593 for value in fieldvalues:
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bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
594 if not type(value) is numpy.ndarray:
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bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
595 all_numpy=False
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parents: 29
diff changeset
596 if all_numpy:
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parents: 29
diff changeset
597 return numpy.hstack(fieldvalues)
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parents: 29
diff changeset
598 # the default implementation of horizontal stacking is to put values in a list
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bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
599 return fieldvalues
26
672fe4b23032 Fixed dataset errors so that _test_dataset.py works again.
bengioy@grenat.iro.umontreal.ca
parents: 23
diff changeset
600
36
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
601 def valuesVStack(self,fieldname,values):
438440ba0627 Rewriting dataset.py completely
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parents: 29
diff changeset
602 """
290
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
603 @param fieldname: the name of the field from which the values were taken
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
604 @type fieldname: any type
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parents: 274
diff changeset
605
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
606 @param values: bits near the beginning or end of the dataset
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
607 @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
608
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
609 @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
610 @rtype: something suitable as a minibatch field
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
611 """
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
612 rval = []
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James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
613 for v in values:
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
614 rval.extend(v)
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James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
615 return rval
17
759d17112b23 more comments, looping ArrayDataSet iterator, bugfixes to lookup_list, more tests
bergstrj@iro.umontreal.ca
parents: 16 12
diff changeset
616
36
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parents: 29
diff changeset
617 def __or__(self,other):
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parents: 29
diff changeset
618 """
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parents: 29
diff changeset
619 dataset1 | dataset2 returns a dataset whose list of fields is the concatenation of the list of
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parents: 29
diff changeset
620 fields of the argument datasets. This only works if they all have the same length.
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parents: 29
diff changeset
621 """
135
0d8e721cc63c Fixed bugs in dataset to make test_mlp.py work
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parents: 134
diff changeset
622 return HStackedDataSet([self,other])
3
378b68d5c4ad Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents: 2
diff changeset
623
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
624 def __and__(self,other):
36
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parents: 29
diff changeset
625 """
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
626 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
627 (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
628 works if they all have the same fields.
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parents: 29
diff changeset
629 """
135
0d8e721cc63c Fixed bugs in dataset to make test_mlp.py work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 134
diff changeset
630 return VStackedDataSet([self,other])
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
631
36
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parents: 29
diff changeset
632 def hstack(datasets):
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parents: 29
diff changeset
633 """
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diff changeset
634 hstack(dataset1,dataset2,...) returns dataset1 | datataset2 | ...
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parents: 29
diff changeset
635 which is a dataset whose fields list is the concatenation of the fields
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parents: 29
diff changeset
636 of the individual datasets.
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
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
639 if len(datasets)==1:
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bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
640 return datasets[0]
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parents: 29
diff changeset
641 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
642
36
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diff changeset
643 def vstack(datasets):
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parents: 29
diff changeset
644 """
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
645 vstack(dataset1,dataset2,...) returns dataset1 & datataset2 & ...
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
646 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
647 over those of dataset2, etc.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
648 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
649 assert len(datasets)>0
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
650 if len(datasets)==1:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
651 return datasets[0]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
652 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
653
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
654 class FieldsSubsetDataSet(DataSet):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
655 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
656 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
657 """
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
658 def __init__(self,src,fieldnames):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
659 self.src=src
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
660 self.fieldnames=fieldnames
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
661 assert src.hasFields(*fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
662 self.valuesHStack = src.valuesHStack
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
663 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
664
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
665 def __len__(self): return len(self.src)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
666
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
667 def fieldNames(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
668 return self.fieldnames
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
669
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
670 def __iter__(self):
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
671 class FieldsSubsetIterator(object):
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
672 def __init__(self,ds):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
673 self.ds=ds
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
674 self.src_iter=ds.src.__iter__()
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
675 self.example=None
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
676 def __iter__(self): return self
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
677 def next(self):
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
678 complete_example = self.src_iter.next()
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
679 if self.example:
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
680 self.example._values=[complete_example[field]
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
681 for field in self.ds.fieldnames]
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
682 else:
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
683 self.example=Example(self.ds.fieldnames,
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
684 [complete_example[field] for field in self.ds.fieldnames])
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
685 return self.example
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
686 return FieldsSubsetIterator(self)
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
687
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
688 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
689 assert self.hasFields(*fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
690 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
691 def dontuse__getitem__(self,i):
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
692 return FieldsSubsetDataSet(self.src[i],self.fieldnames)
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
693
328
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
694 class RenamedFieldsDataSet(DataSet):
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 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
697 """
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
698 def __init__(self,src,src_fieldnames,new_fieldnames):
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
699 self.src=src
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
700 self.src_fieldnames=src_fieldnames
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
701 self.new_fieldnames=new_fieldnames
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
702 assert src.hasFields(*src_fieldnames)
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
703 assert len(src_fieldnames)==len(new_fieldnames)
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
704 self.valuesHStack = src.valuesHStack
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
705 self.valuesVStack = src.valuesVStack
351
7545207466d4 debugged RenamedFieldsDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 344
diff changeset
706 self.lookup_fields = Example(new_fieldnames,src_fieldnames)
328
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
707
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
708 def __len__(self): return len(self.src)
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
709
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
710 def fieldNames(self):
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
711 return self.new_fieldnames
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
712
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
713 def __iter__(self):
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
714 class FieldsSubsetIterator(object):
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
715 def __init__(self,ds):
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
716 self.ds=ds
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
717 self.src_iter=ds.src.__iter__()
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
718 self.example=None
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
719 def __iter__(self): return self
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
720 def next(self):
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
721 complete_example = self.src_iter.next()
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
722 if self.example:
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
723 self.example._values=[complete_example[field]
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
724 for field in self.ds.src_fieldnames]
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
725 else:
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
726 self.example=Example(self.ds.new_fieldnames,
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
727 [complete_example[field]
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
728 for field in self.ds.src_fieldnames])
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
729 return self.example
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
730 return FieldsSubsetIterator(self)
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
731
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
732 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
733 assert self.hasFields(*fieldnames)
351
7545207466d4 debugged RenamedFieldsDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 344
diff changeset
734 cursor = Example(fieldnames,[0]*len(fieldnames))
7545207466d4 debugged RenamedFieldsDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 344
diff changeset
735 for batch in self.src.minibatches_nowrap([self.lookup_fields[f] for f in fieldnames],minibatch_size,n_batches,offset):
7545207466d4 debugged RenamedFieldsDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 344
diff changeset
736 cursor._values=batch._values
7545207466d4 debugged RenamedFieldsDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 344
diff changeset
737 yield cursor
7545207466d4 debugged RenamedFieldsDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 344
diff changeset
738
328
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
739 def __getitem__(self,i):
333
7d2f7b8fe213 bugfix in RenamedDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 332
diff changeset
740 # return FieldsSubsetDataSet(self.src[i],self.new_fieldnames)
7d2f7b8fe213 bugfix in RenamedDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 332
diff changeset
741 complete_example = self.src[i]
7d2f7b8fe213 bugfix in RenamedDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 332
diff changeset
742 return Example(self.new_fieldnames,
7d2f7b8fe213 bugfix in RenamedDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 332
diff changeset
743 [complete_example[field]
7d2f7b8fe213 bugfix in RenamedDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 332
diff changeset
744 for field in self.src_fieldnames])
7d2f7b8fe213 bugfix in RenamedDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 332
diff changeset
745
328
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
746
09140ba68e17 Added untested RenamedFieldsDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 322
diff changeset
747
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
748 class DataSetFields(Example):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
749 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
750 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
751 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
752 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
753
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
754 To iterate over fields, one can do
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
755 * for fields in dataset.fields()
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
756 * 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
757 * 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
758 and each of these fields is iterable over the examples:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
759 * for field_examples in dataset.fields():
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
760 for example_value in field_examples:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
761 ...
241
ddb88a8e9fd2 If I understand properly, the length of an unbounded stream is sys.maxint
delallea@opale.iro.umontreal.ca
parents: 231
diff changeset
762 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
763 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
764 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
765 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
766 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
767 be turned back into a DataSet with its examples() method:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
768 dataset2 = dataset1.fields().examples()
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
769 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
770
88fd1cce08b9 replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
bengioy@esprit.iro.umontreal.ca
parents: 39
diff changeset
771 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
772 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
773 the examples.
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
774 """
74
b4159cbdc06b Fixed errors raised by test_dataset
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 73
diff changeset
775 def __init__(self,dataset,fieldnames):
65
d48eba49a2f4 fixed the infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 64
diff changeset
776 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
777 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
778 fieldnames=dataset.fieldNames()
274
ed70580f2324 bugfix in FieldSubsetDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 273
diff changeset
779 elif not list(fieldnames)==list(dataset.fieldNames()):
ed70580f2324 bugfix in FieldSubsetDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 273
diff changeset
780 #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
781 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
782 assert dataset.hasFields(*fieldnames)
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
783 self.dataset=dataset
66
dde1fb1b63ba fixed test and removed print
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 65
diff changeset
784
64
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
785 if isinstance(dataset,MinibatchDataSet):
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
786 Example.__init__(self,fieldnames,list(dataset._fields))
65
d48eba49a2f4 fixed the infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 64
diff changeset
787 elif isinstance(original_dataset,MinibatchDataSet):
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
788 Example.__init__(self,fieldnames,
65
d48eba49a2f4 fixed the infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 64
diff changeset
789 [original_dataset._fields[field]
d48eba49a2f4 fixed the infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 64
diff changeset
790 for field in fieldnames])
64
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
791 else:
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
792 minibatch_iterator = dataset.minibatches(fieldnames,
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
793 minibatch_size=len(dataset),
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
794 n_batches=1)
863da25a60f1 trying to fix infinite loop
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 62
diff changeset
795 minibatch=minibatch_iterator.next()
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
796 Example.__init__(self,fieldnames,minibatch)
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
797
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
798 def examples(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
799 return self.dataset
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
800
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
801 def __or__(self,other):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
802 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
803 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
804 of the list of examples of DataSetFields fields1 and fields2.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
805 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
806 return (self.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
807
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
808 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
809 """
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
810 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
811 of the fields of DataSetFields fields1 and fields2.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
812 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
813 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
814
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
815
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
816 class MinibatchDataSet(DataSet):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
817 """
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
818 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
819 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
820 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
821 def __init__(self,fields_lookuplist,values_vstack=DataSet().valuesVStack,
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
822 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
823 """
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
824 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
825 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
826 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
827 """
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
828
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
829 self._fields=fields_lookuplist
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
830 assert len(fields_lookuplist)>0
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
831 self.length=len(fields_lookuplist[0])
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
832 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
833 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
834 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
835 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
836 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
837 print 'field=',field
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
838 print 'fields_lookuplist=', fields_lookuplist
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
839 assert self.length==len(field)
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
840 self.valuesVStack=values_vstack
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
841 self.valuesHStack=values_hstack
3
378b68d5c4ad Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents: 2
diff changeset
842
378b68d5c4ad Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents: 2
diff changeset
843 def __len__(self):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
844 return self.length
28
541a273bc89f Removed __array__ method from dataset, whose
bengioy@grenat.iro.umontreal.ca
parents: 26
diff changeset
845
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
846 def dontuse__getitem__(self,i):
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
847 if type(i) in (slice,list):
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
848 return DataSetFields(MinibatchDataSet(
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
849 Example(self._fields.keys(),[field[i] for field in self._fields])),self.fieldNames())
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
850 if type(i) is int:
85
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 83
diff changeset
851 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
852 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
853 return self._fields[i]
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
854 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
855 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
856
29
46c5c90019c2 Changed apply_function so that it propagates methods of the source.
bengioy@grenat.iro.umontreal.ca
parents: 28
diff changeset
857 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
858 return self._fields.keys()
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
859
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
860 def hasFields(self,*fieldnames):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
861 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
862 if fieldname not in self._fields.keys():
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
863 return False
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
864 return True
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
865
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
866 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
867 #@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
868 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
869 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
870 # 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
871 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
872 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
873
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
874 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
875 self.next_example=offset
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
876 assert minibatch_size >= 0
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
877 if offset+minibatch_size > ds.length:
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
878 raise NotImplementedError()
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
879 def __iter__(self):
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
880 return self
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
881 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
882 upper = self.next_example+minibatch_size
353
47538a45b878 Cached dataset seems debug, using n_batches... is n_batches around to stay?
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 351
diff changeset
883 if upper > len(self.ds) :
47538a45b878 Cached dataset seems debug, using n_batches... is n_batches around to stay?
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 351
diff changeset
884 raise StopIteration()
47538a45b878 Cached dataset seems debug, using n_batches... is n_batches around to stay?
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 351
diff changeset
885 assert upper<=len(self.ds) # instead of 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
886 #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
887 # [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
888 # 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
889 # 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
890 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
891 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
892 #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
893 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
894 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
895 #print minibatch
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
896 self.next_example+=minibatch_size
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
897 return minibatch
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
898
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
899 # 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
900 return Iterator(self,fieldnames)
20
266c68cb6136 Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents: 19
diff changeset
901
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
902 class HStackedDataSet(DataSet):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
903 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
904 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
905 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
906
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
907 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
908 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
909 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
910
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
911 @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
912 """
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
913 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
914 DataSet.__init__(self,description,field_types)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
915 self.datasets=datasets
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
916 self.accept_nonunique_names=accept_nonunique_names
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
917 self.fieldname2dataset={}
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
918
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
919 def rename_field(fieldname,dataset,i):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
920 if hasattr(dataset,"__name__"):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
921 return dataset.__name__ + "." + fieldname
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
922 return fieldname+"."+str(i)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
923
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
924 # 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
925 self.length=None
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
926 names_to_change=[]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
927 for i in xrange(len(datasets)):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
928 dataset = datasets[i]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
929 length=len(dataset)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
930 if self.length:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
931 assert self.length==length
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
932 else:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
933 self.length=length
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
934 for fieldname in dataset.fieldNames():
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
935 if fieldname in self.fieldname2dataset: # name conflict!
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
936 if accept_nonunique_names:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
937 fieldname=rename_field(fieldname,dataset,i)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
938 names2change.append((fieldname,i))
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
939 else:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
940 raise ValueError("Incompatible datasets: non-unique field name = "+fieldname)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
941 self.fieldname2dataset[fieldname]=i
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
942 for fieldname,i in names_to_change:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
943 del self.fieldname2dataset[fieldname]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
944 self.fieldname2dataset[rename_field(fieldname,self.datasets[i],i)]=i
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
945
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
946 def hasFields(self,*fieldnames):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
947 for fieldname in fieldnames:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
948 if not fieldname in self.fieldname2dataset:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
949 return False
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
950 return True
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
951
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
952 def fieldNames(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
953 return self.fieldname2dataset.keys()
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
954
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
955 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
956
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
957 class HStackedIterator(object):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
958 def __init__(self,hsds,iterators):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
959 self.hsds=hsds
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
960 self.iterators=iterators
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
961 def __iter__(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
962 return self
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
963 def next(self):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
964 # 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
965 l=Example()
140
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 136
diff changeset
966 for iter in self.iterators:
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 136
diff changeset
967 l.append_lookuplist(iter.next())
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 136
diff changeset
968 return l
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
969
125
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 123
diff changeset
970 assert self.hasFields(*fieldnames)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
971 # 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
972 # and construct corresponding minibatch iterators
140
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 136
diff changeset
973 if fieldnames and fieldnames!=self.fieldNames():
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
974 datasets=set([])
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
975 fields_in_dataset=dict([(dataset,[]) for dataset in datasets])
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
976 for fieldname in fieldnames:
136
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 125
diff changeset
977 dataset=self.datasets[self.fieldname2dataset[fieldname]]
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
978 datasets.add(dataset)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
979 fields_in_dataset[dataset].append(fieldname)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
980 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
981 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
982 for dataset in datasets]
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
983 else:
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
984 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
985 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
986 return HStackedIterator(self,iterators)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
987
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
988
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
989 def untested_valuesVStack(self,fieldname,fieldvalues):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
990 return self.datasets[self.fieldname2dataset[fieldname]].valuesVStack(fieldname,fieldvalues)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
991
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
992 def untested_valuesHStack(self,fieldnames,fieldvalues):
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
993 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
994 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
995 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
996 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
997 all the fieldnames are of the same sub-dataset.
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
998 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
999 return self.datasets[self.fieldname2dataset[fieldnames[0]]].valuesHStack(fieldnames,fieldvalues)
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
1000
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
1001 class VStackedDataSet(DataSet):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
1002 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1003 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
1004 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
1005 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
1006
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1007 @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
1008 """
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
1009 def __init__(self,datasets):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
1010 self.datasets=datasets
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
1011 self.length=0
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
1012 self.index2dataset={}
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1013 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
1014 fieldnames = datasets[-1].fieldNames()
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1015 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
1016 # 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
1017 # 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
1018 for dataset,k in enumerate(datasets[0:-1]):
48
b6730f9a336d Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents: 46
diff changeset
1019 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
1020 L=len(dataset)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
1021 for i in xrange(L):
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
1022 self.index2dataset[self.length+i]=k
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1023 self.datasets_start_row.append(self.length)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
1024 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
1025 assert dataset.fieldNames()==fieldnames
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1026 self.datasets_start_row.append(self.length)
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
1027 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
1028 # 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
1029 # 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
1030 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
1031 # 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
1032 # TODO
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1033 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
1034
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1035 def __len__(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1036 return self.length
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1037
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1038 def fieldNames(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1039 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
1040
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1041 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
1042 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
1043
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1044 def locate_row(self,row):
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1045 """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
1046 dataset_index = self.index2dataset[row]
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1047 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
1048 return dataset_index, row_within_dataset
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1049
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1050 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
1051
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
1052 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
1053 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
1054 self.vsds=vsds
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1055 self.next_row=offset
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1056 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
1057 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
1058 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
1059
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1060 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
1061 L=len(dataset)
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1062 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
1063 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
1064 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
1065 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
1066 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
1067 n_left_in_mb=minibatch_size-L
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1068 ds_nbatches=1
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1069 else:
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1070 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
1071 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
1072 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
1073
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1074 def move_to_next_dataset(self):
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1075 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
1076 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
1077 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
1078 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
1079 else:
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1080 self.next_dataset_index +=1
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1081 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
1082 self.next_dataset_index = 0
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1083 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
1084 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
1085
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1086 def __iter__(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1087 return self
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1088
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1089 def next(self):
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1090 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
1091 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
1092 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
1093 extra_mb = []
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1094 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
1095 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
1096 extra_mb.append(self.next_iterator.next())
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1097 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
1098 [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
1099 [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
1100 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
1101
37
73c4212ba5b3 Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents: 36
diff changeset
1102 self.next_row+=minibatch_size
38
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1103 self.next_dataset_row+=minibatch_size
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1104 if self.next_row+minibatch_size>len(dataset):
d637ad8f7352 Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents: 37
diff changeset
1105 self.move_to_next_dataset()
44
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
1106 return examples
5a85fda9b19b Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents: 43
diff changeset
1107 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
1108
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1109 class ArrayFieldsDataSet(DataSet):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1110 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1111 Virtual super-class of datasets whose field values are numpy array,
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1112 thus defining valuesHStack and valuesVStack for sub-classes.
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1113 """
268
3f1cd8897fda reverting dataset
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 266
diff changeset
1114 def __init__(self,description=None,field_types=None):
3f1cd8897fda reverting dataset
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 266
diff changeset
1115 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
1116 def untested_valuesHStack(self,fieldnames,fieldvalues):
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1117 """Concatenate field values horizontally, e.g. two vectors
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1118 become a longer vector, two matrices become a wider matrix, etc."""
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1119 return numpy.hstack(fieldvalues)
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1120 def untested_valuesVStack(self,fieldname,values):
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1121 """Concatenate field values vertically, e.g. two vectors
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1122 become a two-row matrix, two matrices become a longer matrix, etc."""
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1123 return numpy.vstack(values)
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1124
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
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
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
1127 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
1128 """
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
1129 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
1130 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
1131 """
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
1132 #@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
1133 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
1134 """
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
1135 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
1136 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
1137 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
1138 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
1139
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
1140 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
1141 """
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
1142 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
1143 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
1144 assert len(fieldnames) > 0
322
ad8be93b3c55 small bugs fixed with NArrayDataSet
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 321
diff changeset
1145 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
1146 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
1147 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
1148 self._fieldnames = fieldnames
322
ad8be93b3c55 small bugs fixed with NArrayDataSet
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 321
diff changeset
1149 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
1150 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
1151 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
1152 # 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
1153 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
1154 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
1155 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
1156
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
1157
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
1158 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
1159 """
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1160 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
1161 """
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
1162 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
1163
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
1164 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
1165 """
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1166 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
1167 """
5fe6d0c93109 getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 314
diff changeset
1168 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
1169
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
1170 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
1171 """
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
1172 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
1173 """
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
1174 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
1175
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
1176 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
1177 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
1178 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
1179 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
1180 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
1181 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
1182 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
1183 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
1184 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
1185 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
1186 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
1187 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
1188
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
1189 #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
1190
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
1191
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
1192
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
1193
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1194 class ArrayDataSet(ArrayFieldsDataSet):
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1195 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1196 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
1197 whose first axis iterates over examples, second axis determines fields.
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1198 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
1199 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
1200 """
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1201
188
f01ac276c6fb added __contains__ to Dataset, added parent constructor call to ArrayDataSet
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 171
diff changeset
1202 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
1203 """
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1204 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
1205 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
1206 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
1207 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
1208 """
188
f01ac276c6fb added __contains__ to Dataset, added parent constructor call to ArrayDataSet
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 171
diff changeset
1209 ArrayFieldsDataSet.__init__(self, **kwargs)
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1210 self.data=data_array
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1211 self.fields_columns=fields_columns
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1212
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1213 # check consistency and complete slices definitions
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1214 for fieldname, fieldcolumns in self.fields_columns.items():
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1215 if type(fieldcolumns) is int:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1216 assert fieldcolumns>=0 and fieldcolumns<data_array.shape[1]
268
3f1cd8897fda reverting dataset
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 266
diff changeset
1217 if 1:
227
17c5d080964b reinstating changeset 216 clobbered accidentally by 218
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 223
diff changeset
1218 #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
1219 # 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
1220 # 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
1221 # - James 22/05/2008
17c5d080964b reinstating changeset 216 clobbered accidentally by 218
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 223
diff changeset
1222 self.fields_columns[fieldname]=[fieldcolumns]
17c5d080964b reinstating changeset 216 clobbered accidentally by 218
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 223
diff changeset
1223 else:
17c5d080964b reinstating changeset 216 clobbered accidentally by 218
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 223
diff changeset
1224 self.fields_columns[fieldname]=fieldcolumns
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1225 elif type(fieldcolumns) is slice:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1226 start,step=None,None
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1227 if not fieldcolumns.start:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1228 start=0
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1229 if not fieldcolumns.step:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1230 step=1
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1231 if start or step:
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1232 self.fields_columns[fieldname]=slice(start,fieldcolumns.stop,step)
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1233 elif hasattr(fieldcolumns,"__iter__"): # something like a list
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1234 for i in fieldcolumns:
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1235 assert i>=0 and i<data_array.shape[1]
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1236
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1237 def fieldNames(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1238 return self.fields_columns.keys()
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1239
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1240 def __len__(self):
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1241 return len(self.data)
41
283e95c15b47 Added ArrayDataSet
bengioy@grenat.iro.umontreal.ca
parents: 40
diff changeset
1242
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
1243 def __getitem__(self,key):
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1244 """More efficient implementation than the default __getitem__"""
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1245 fieldnames=self.fields_columns.keys()
243
c8f19a9eb10f Optimisation in ArrayDataSet::__getitem__
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 242
diff changeset
1246 values=self.fields_columns.values()
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1247 if type(key) is int:
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1248 return Example(fieldnames,
243
c8f19a9eb10f Optimisation in ArrayDataSet::__getitem__
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 242
diff changeset
1249 [self.data[key,col] for col in values])
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1250 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
1251 return Example(fieldnames,[self.data[key,col] for col in values])
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1252 if type(key) is list:
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1253 for i in range(len(key)):
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1254 if self.hasFields(key[i]):
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1255 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
1256 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
1257 #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
1258 # 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
1259 # 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
1260 [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
1261 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
1262 self.data[key,col] for col in values])
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1263
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1264 # else check for a fieldname
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1265 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
1266 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
1267 # else we are trying to access a property of the dataset
80
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 66
diff changeset
1268 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
1269 return self.__dict__[key]
55
66619ce44497 Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 48
diff changeset
1270
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1271 def dontuse__iter__(self):
270
1cafd495098c code cleanup and small optimisation
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 254
diff changeset
1272 class ArrayDataSetIteratorIter(object):
1cafd495098c code cleanup and small optimisation
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 254
diff changeset
1273 def __init__(self,dataset,fieldnames):
228
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1274 if fieldnames is None: fieldnames = dataset.fieldNames()
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1275 # 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
1276 self.minibatch = Example(fieldnames,[0]*len(fieldnames))
228
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1277 self.dataset=dataset
270
1cafd495098c code cleanup and small optimisation
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 254
diff changeset
1278 self.current=0
238
ae1d85aca858 optimization in ArrayDataSet::__iter__
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 235
diff changeset
1279 self.columns = [self.dataset.fields_columns[f]
ae1d85aca858 optimization in ArrayDataSet::__iter__
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 235
diff changeset
1280 for f in self.minibatch._names]
270
1cafd495098c code cleanup and small optimisation
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 254
diff changeset
1281 self.l = self.dataset.data.shape[0]
228
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1282 def __iter__(self):
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1283 return self
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1284 def next(self):
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1285 #@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
1286 # Otherwise, MinibatchWrapAroundIterator do it.
270
1cafd495098c code cleanup and small optimisation
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 254
diff changeset
1287 if self.current>=self.l:
228
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1288 raise StopIteration
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1289 sub_data = self.dataset.data[self.current]
238
ae1d85aca858 optimization in ArrayDataSet::__iter__
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 235
diff changeset
1290 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
1291
270
1cafd495098c code cleanup and small optimisation
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 254
diff changeset
1292 self.current+=1
228
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1293 return self.minibatch
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1294
270
1cafd495098c code cleanup and small optimisation
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 254
diff changeset
1295 return ArrayDataSetIteratorIter(self,self.fieldNames())
228
6f55e301c687 optimisation of ArrayDataSet
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 203
diff changeset
1296
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1297 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
1298 cursor = Example(fieldnames,[0]*len(fieldnames))
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1299 fieldnames = self.fieldNames() if fieldnames is None else fieldnames
339
aa8aff6abbf7 n_minibatches in ArrayDataSet automatically computed
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 337
diff changeset
1300 if n_batches == None:
aa8aff6abbf7 n_minibatches in ArrayDataSet automatically computed
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 337
diff changeset
1301 n_batches = (len(self) - offset) / minibatch_size
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1302 for n in xrange(n_batches):
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1303 if offset == len(self):
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1304 break
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1305 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
1306 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
1307 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
1308 yield cursor
42
9b68774fcc6b Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents: 41
diff changeset
1309
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1310 #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
1311
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1312
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1313 class CachedDataSet(DataSet):
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1314 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1315 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
1316 (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
1317 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
1318 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
1319
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1320 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
1321 (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
1322 first access.
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1323
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1324 @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
1325 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
1326
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1327 @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
1328 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
1329 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
1330 """
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1331 def __init__(self,source_dataset,cache_all_upon_construction=False):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1332 self.source_dataset=source_dataset
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1333 self.cache_all_upon_construction=cache_all_upon_construction
152
3f627e844cba Fixes in CacheDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 151
diff changeset
1334 self.cached_examples = []
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1335 if cache_all_upon_construction:
77
1e2bb5bad636 toying with different ways to implement learners
bengioy@bengiomac.local
parents: 74
diff changeset
1336 # this potentially brings all the source examples
1e2bb5bad636 toying with different ways to implement learners
bengioy@bengiomac.local
parents: 74
diff changeset
1337 # into memory at once, which may be too much
1e2bb5bad636 toying with different ways to implement learners
bengioy@bengiomac.local
parents: 74
diff changeset
1338 # the work could possibly be done by minibatches
1e2bb5bad636 toying with different ways to implement learners
bengioy@bengiomac.local
parents: 74
diff changeset
1339 # that are as large as possible but no more than what memory allows.
353
47538a45b878 Cached dataset seems debug, using n_batches... is n_batches around to stay?
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 351
diff changeset
1340 #
47538a45b878 Cached dataset seems debug, using n_batches... is n_batches around to stay?
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 351
diff changeset
1341 # field_values is supposed to be an DataSetFields, that inherits from LookupList
47538a45b878 Cached dataset seems debug, using n_batches... is n_batches around to stay?
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 351
diff changeset
1342 #fields_values = source_dataset.minibatches(minibatch_size=len(source_dataset)).__iter__().next()
47538a45b878 Cached dataset seems debug, using n_batches... is n_batches around to stay?
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 351
diff changeset
1343 fields_values = DataSetFields(source_dataset,None)
152
3f627e844cba Fixes in CacheDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 151
diff changeset
1344 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
1345 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
1346 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
1347
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1348 self.fieldNames = source_dataset.fieldNames
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1349 self.hasFields = source_dataset.hasFields
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1350 self.valuesHStack = source_dataset.valuesHStack
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1351 self.valuesVStack = source_dataset.valuesVStack
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1352
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1353 def __len__(self):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1354 return len(self.source_dataset)
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1355
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1356 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1357 class CacheIterator(object):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1358 def __init__(self,dataset):
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1359 self.dataset=dataset
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1360 self.current=offset
254
8ec867d12428 optimication in CachedDataSet.minibatches_nowrap
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 253
diff changeset
1361 self.all_fields = self.dataset.fieldNames()==fieldnames
353
47538a45b878 Cached dataset seems debug, using n_batches... is n_batches around to stay?
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 351
diff changeset
1362 self.n_batches = n_batches
47538a45b878 Cached dataset seems debug, using n_batches... is n_batches around to stay?
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 351
diff changeset
1363 self.batch_counter = 0
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1364 def __iter__(self): return self
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1365 def next(self):
353
47538a45b878 Cached dataset seems debug, using n_batches... is n_batches around to stay?
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 351
diff changeset
1366 self.batch_counter += 1
47538a45b878 Cached dataset seems debug, using n_batches... is n_batches around to stay?
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 351
diff changeset
1367 if self.n_batches and self.batch_counter > self.n_batches :
47538a45b878 Cached dataset seems debug, using n_batches... is n_batches around to stay?
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 351
diff changeset
1368 raise StopIteration()
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1369 upper = self.current+minibatch_size
353
47538a45b878 Cached dataset seems debug, using n_batches... is n_batches around to stay?
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 351
diff changeset
1370 if upper > len(self.dataset.source_dataset):
47538a45b878 Cached dataset seems debug, using n_batches... is n_batches around to stay?
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 351
diff changeset
1371 raise StopIteration()
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1372 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
1373 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
1374 # cache everything from current length to upper
353
47538a45b878 Cached dataset seems debug, using n_batches... is n_batches around to stay?
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 351
diff changeset
1375 #for example in self.dataset.source_dataset[cache_len:upper]:
47538a45b878 Cached dataset seems debug, using n_batches... is n_batches around to stay?
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 351
diff changeset
1376 for example in self.dataset.source_dataset.subset[cache_len:upper]:
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1377 self.dataset.cached_examples.append(example)
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1378 all_fields_minibatch = Example(self.dataset.fieldNames(),
152
3f627e844cba Fixes in CacheDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 151
diff changeset
1379 zip(*self.dataset.cached_examples[self.current:self.current+minibatch_size]))
353
47538a45b878 Cached dataset seems debug, using n_batches... is n_batches around to stay?
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents: 351
diff changeset
1380
163
d7d67651d67c bugfix, we should advence by the minibatch size.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 159
diff changeset
1381 self.current+=minibatch_size
254
8ec867d12428 optimication in CachedDataSet.minibatches_nowrap
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 253
diff changeset
1382 if self.all_fields:
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1383 return all_fields_minibatch
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1384 return Example(fieldnames,[all_fields_minibatch[name] for name in fieldnames])
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1385 return CacheIterator(self)
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1386
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1387 def dontuse__getitem__(self,i):
153
71107b0ac860 optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 151
diff changeset
1388 if type(i)==int and len(self.cached_examples)>i:
71107b0ac860 optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 151
diff changeset
1389 return self.cached_examples[i]
71107b0ac860 optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 151
diff changeset
1390 else:
251
7e6edee187e3 optimization of CachedDataSet__getitem__
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 243
diff changeset
1391 return self.source_dataset[i]
252
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1392
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1393 def __iter__(self):
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1394 class CacheIteratorIter(object):
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1395 def __init__(self,dataset):
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1396 self.dataset=dataset
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1397 self.l = len(dataset)
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1398 self.current = 0
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1399 self.fieldnames = self.dataset.fieldNames()
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1400 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
1401 def __iter__(self): return self
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1402 def next(self):
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1403 if self.current>=self.l:
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1404 raise StopIteration
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1405 cache_len = len(self.dataset.cached_examples)
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1406 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
1407 # cache everything from current length to upper
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1408 self.dataset.cached_examples.append(
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1409 self.dataset.source_dataset[self.current])
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1410 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
1411 self.current+=1
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1412 return self.example
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1413
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1414 return CacheIteratorIter(self)
856d14dc4468 implemented CachedDataSet.__iter__ as an optimization
Frederic Bastien <bastienf@iro.umontreal.ca>
parents: 251
diff changeset
1415
57
1aabd2e2bb5f Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents: 56
diff changeset
1416 class ApplyFunctionDataSet(DataSet):
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1417 """
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1418 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
1419 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
1420 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
1421 (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
1422
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1423 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
1424
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1425 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
1426 (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
1427 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
1428 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
1429 (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
1430 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
1431 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
1432
290
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1433 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
1434 To avoid re-doing computation, wrap this dataset inside a CachedDataSet.
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1435
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1436 If the values_{h,v}stack functions are not provided, then
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1437 the input_dataset.values{H,V}Stack functions are used by default.
296
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1438
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1439 """
296
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1440
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1441 def __init__(self,input_dataset,function,output_names,minibatch_mode=True,
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1442 values_hstack=None,values_vstack=None,
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1443 description=None,fieldtypes=None):
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1444 """
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1445 Constructor takes an input dataset that has as many fields as the function
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1446 expects as inputs. The resulting dataset has as many fields as the function
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1447 produces as outputs, and that should correspond to the number of output names
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1448 (provided in a list).
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1449
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1450 Note that the expected semantics of the function differs in minibatch mode
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1451 (it takes minibatches of inputs and produces minibatches of outputs, as
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1452 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
1453
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1454 TBM: are filedtypes the old field types (from input_dataset) or the new ones
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1455 (for the new dataset created)?
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1456 """
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1457 self.input_dataset=input_dataset
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1458 self.function=function
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1459 self.output_names=output_names
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1460 self.minibatch_mode=minibatch_mode
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1461 DataSet.__init__(self,description,fieldtypes)
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1462 self.valuesHStack = values_hstack if values_hstack else input_dataset.valuesHStack
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1463 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
1464
290
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1465 def __len__(self):
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1466 return len(self.input_dataset)
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1467
290
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1468 def fieldNames(self):
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1469 return self.output_names
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1470
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1471 def minibatches_nowrap(self, fieldnames, *args, **kwargs):
296
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1472 all_input_fieldNames = self.input_dataset.fieldNames()
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1473 mbnw = self.input_dataset.minibatches_nowrap
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1474
296
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1475 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
1476 if self.minibatch_mode:
296
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1477 all_output_fields = self.function(*input_fields)
290
9b533cc7874a trying to get default implemenations to work
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parents: 274
diff changeset
1478 else:
296
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1479 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
1480 output_examples = [self.function(*input_example)
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1481 for input_example in input_examples]
296
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1482 all_output_fields = zip(*output_examples)
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1483
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1484 all_outputs = Example(self.output_names, all_output_fields)
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1485 #print 'input_fields', input_fields
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1486 #print 'all_outputs', all_outputs
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1487 if fieldnames==self.output_names:
293
4bfdda107a17 still merging
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 292
diff changeset
1488 rval = all_outputs
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1489 else:
293
4bfdda107a17 still merging
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 292
diff changeset
1490 rval = Example(fieldnames,[all_outputs[name] for name in fieldnames])
296
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1491 #print 'rval', rval
f5d33f9c0b9c ApplyFunctionDataSet passing
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 293
diff changeset
1492 #print '--------'
293
4bfdda107a17 still merging
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 292
diff changeset
1493 yield rval
73
69f97aad3faf Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents: 72
diff changeset
1494
290
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1495 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
1496 class ApplyFunctionSingleExampleIterator(object):
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1497 def __init__(self,output_dataset):
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1498 self.current=0
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1499 self.output_dataset=output_dataset
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1500 self.input_iterator=output_dataset.input_dataset.__iter__()
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1501 def __iter__(self): return self
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1502 def next(self):
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1503 if self.output_dataset.minibatch_mode:
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1504 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
1505 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
1506 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
1507 function_outputs = [output[0] for output in outputs]
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1508 else:
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1509 function_inputs = self.input_iterator.next()
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1510 function_outputs = self.output_dataset.function(*function_inputs)
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1511 return Example(self.output_dataset.output_names,function_outputs)
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1512 return ApplyFunctionSingleExampleIterator(self)
9b533cc7874a trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents: 274
diff changeset
1513
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1514 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
1515 """
167
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1516 Wraps an arbitrary L{DataSet} into one for supervised learning tasks
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1517 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
1518 and a set of fields as the 'target' field. Optionally, a single
4803cb76e26b Updated documentation
Joseph Turian <turian@gmail.com>
parents: 166
diff changeset
1519 weight_field can also be defined.
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1520 """
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1521 args = ((input_fields,'input'),(output_fields,'target'))
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1522 if weight_field: args+=(([weight_field],'weight'))
36
438440ba0627 Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents: 29
diff changeset
1523 return src_dataset.merge_fields(*args)
23
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1524
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1525
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1526
526e192b0699 Working on ApplyFunctionDataSet, added constraint that
bengioy@esprit.iro.umontreal.ca
parents: 22
diff changeset
1527