Mercurial > pylearn
annotate dataset.py @ 91:eee739fefdff
corrected test from discution about the syntax with Yoshua
| author | Frederic Bastien <bastienf@iro.umontreal.ca> |
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| date | Mon, 05 May 2008 17:13:53 -0400 |
| parents | a289b8bed64c |
| children | 6fe972a7393c |
| rev | line source |
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2 from lookup_list import LookupList |
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3 Example = LookupList |
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4 from misc import unique_elements_list_intersection |
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5 from string import join |
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6 from sys import maxint |
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7 import numpy |
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9 class AbstractFunction (Exception): """Derived class must override this function""" |
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10 class NotImplementedYet (NotImplementedError): """Work in progress, this should eventually be implemented""" |
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12 class DataSet(object): |
| 16 | 13 """A virtual base class for datasets. |
| 14 | |
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15 A DataSet can be seen as a generalization of a matrix, meant to be used in conjunction |
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16 with learning algorithms (for training and testing them): rows/records are called examples, and |
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17 columns/attributes are called fields. The field value for a particular example can be an arbitrary |
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18 python object, which depends on the particular dataset. |
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19 |
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20 We call a DataSet a 'stream' when its length is unbounded (otherwise its __len__ method |
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21 should return sys.maxint). |
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| 16 | 23 A DataSet is a generator of iterators; these iterators can run through the |
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24 examples or the fields in a variety of ways. A DataSet need not necessarily have a finite |
| 16 | 25 or known length, so this class can be used to interface to a 'stream' which |
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26 feeds on-line learning (however, as noted below, some operations are not |
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27 feasible or not recommanded on streams). |
| 16 | 28 |
| 29 To iterate over examples, there are several possibilities: | |
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30 - for example in dataset: |
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31 - for val1,val2,... in dataset: |
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32 - for example in dataset(field1, field2,field3, ...): |
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33 - for val1,val2,val3 in dataset(field1, field2,field3): |
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34 - for minibatch in dataset.minibatches([field1, field2, ...],minibatch_size=N): |
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35 - for mini1,mini2,mini3 in dataset.minibatches([field1, field2, field3], minibatch_size=N): |
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36 - for example in dataset:: |
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37 print example['x'] |
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38 - for x,y,z in dataset: |
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39 Each of these is documented below. All of these iterators are expected |
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40 to provide, in addition to the usual 'next()' method, a 'next_index()' method |
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41 which returns a non-negative integer pointing to the position of the next |
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42 example that will be returned by 'next()' (or of the first example in the |
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43 next minibatch returned). This is important because these iterators |
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44 can wrap around the dataset in order to do multiple passes through it, |
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45 in possibly unregular ways if the minibatch size is not a divisor of the |
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46 dataset length. |
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47 |
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48 To iterate over fields, one can do |
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49 - for field in dataset.fields(): |
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50 for field_value in field: # iterate over the values associated to that field for all the dataset examples |
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51 - for field in dataset(field1,field2,...).fields() to select a subset of fields |
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52 - for field in dataset.fields(field1,field2,...) to select a subset of fields |
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53 and each of these fields is iterable over the examples: |
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54 - for field_examples in dataset.fields(): |
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55 for example_value in field_examples: |
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56 ... |
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57 but when the dataset is a stream (unbounded length), it is not recommanded to do |
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58 such things because the underlying dataset may refuse to access the different fields in |
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59 an unsynchronized ways. Hence the fields() method is illegal for streams, by default. |
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60 The result of fields() is a DataSetFields object, which iterates over fields, |
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61 and whose elements are iterable over examples. A DataSetFields object can |
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62 be turned back into a DataSet with its examples() method:: |
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63 dataset2 = dataset1.fields().examples() |
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64 and dataset2 should behave exactly like dataset1 (in fact by default dataset2==dataset1). |
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65 |
| 16 | 66 Note: Fields are not mutually exclusive, i.e. two fields can overlap in their actual content. |
| 67 | |
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68 Note: The content of a field can be of any type. Field values can also be 'missing' |
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69 (e.g. to handle semi-supervised learning), and in the case of numeric (numpy array) |
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70 fields (i.e. an ArrayFieldsDataSet), NaN plays the role of a missing value. |
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71 What about non-numeric values? None. |
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72 |
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73 Dataset elements can be indexed and sub-datasets (with a subset |
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74 of examples) can be extracted. These operations are not supported |
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75 by default in the case of streams. |
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76 |
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77 - dataset[:n] returns a dataset with the n first examples. |
| 16 | 78 |
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79 - dataset[i1:i2:s] returns a dataset with the examples i1,i1+s,...i2-s. |
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80 |
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81 - dataset[i] returns an Example. |
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82 |
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83 - dataset[[i1,i2,...in]] returns a dataset with examples i1,i2,...in. |
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84 |
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85 - dataset[fieldname] an iterable over the values of the field fieldname across |
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86 the dataset (the iterable is obtained by default by calling valuesVStack |
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87 over the values for individual examples). |
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88 |
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89 - dataset.<property> returns the value of a property associated with |
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90 the name <property>. The following properties should be supported: |
| 41 | 91 - 'description': a textual description or name for the dataset |
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92 - 'fieldtypes': a list of types (one per field) |
| 78 | 93 A DataSet may have other attributes that it makes visible to other objects. These are |
| 94 used to store information that is not example-wise but global to the dataset. | |
| 95 The list of names of these attributes is given by the attribute_names() method. | |
| 41 | 96 |
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97 Datasets can be concatenated either vertically (increasing the length) or |
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98 horizontally (augmenting the set of fields), if they are compatible, using |
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99 the following operations (with the same basic semantics as numpy.hstack |
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100 and numpy.vstack): |
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101 |
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102 - dataset1 | dataset2 | dataset3 == dataset.hstack([dataset1,dataset2,dataset3]) |
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103 |
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104 creates a new dataset whose list of fields is the concatenation of the list of |
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105 fields of the argument datasets. This only works if they all have the same length. |
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106 |
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107 - dataset1 & dataset2 & dataset3 == dataset.vstack([dataset1,dataset2,dataset3]) |
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108 |
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109 creates a new dataset that concatenates the examples from the argument datasets |
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110 (and whose length is the sum of the length of the argument datasets). This only |
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111 works if they all have the same fields. |
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112 |
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113 According to the same logic, and viewing a DataSetFields object associated to |
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114 a DataSet as a kind of transpose of it, fields1 & fields2 concatenates fields of |
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115 a DataSetFields fields1 and fields2, and fields1 | fields2 concatenates their |
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116 examples. |
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117 |
| 41 | 118 A dataset can hold arbitrary key-value pairs that may be used to access meta-data |
| 119 or other properties of the dataset or associated with the dataset or the result | |
| 120 of a computation stored in a dataset. These can be accessed through the [key] syntax | |
| 121 when key is a string (or more specifically, neither an integer, a slice, nor a list). | |
| 78 | 122 |
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123 A DataSet sub-class should always redefine the following methods: |
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124 - __len__ if it is not a stream |
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125 - fieldNames |
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126 - minibatches_nowrap (called by DataSet.minibatches()) |
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127 - valuesHStack |
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128 - valuesVStack |
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129 For efficiency of implementation, a sub-class might also want to redefine |
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130 - hasFields |
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131 - __getitem__ may not be feasible with some streams |
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132 - __iter__ |
| 78 | 133 A sub-class should also append attributes to self._attribute_names |
| 134 (the default value returned by attributeNames()). | |
| 135 By convention, attributes not in attributeNames() should have a name | |
| 136 starting with an underscore. | |
| 137 @todo enforce/test that convention! | |
|
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138 """ |
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139 |
| 83 | 140 numpy_vstack = lambda fieldname,values: numpy.vstack(values) |
| 141 numpy_hstack = lambda fieldnames,values: numpy.hstack(values) | |
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142 |
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143 def __init__(self,description=None,fieldtypes=None): |
| 41 | 144 if description is None: |
| 145 # by default return "<DataSetType>(<SuperClass1>,<SuperClass2>,...)" | |
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146 description = type(self).__name__ + " ( " + join([x.__name__ for x in type(self).__bases__]) + " )" |
| 41 | 147 self.description=description |
| 60 | 148 self.fieldtypes=fieldtypes |
| 78 | 149 self._attribute_names = ["description"] |
| 150 if fieldtypes: | |
| 151 self._attribute_names.append("fieldtypes") | |
| 152 | |
| 153 def attributeNames(self): return self._attribute_names | |
| 154 | |
| 155 def setAttributes(self,attribute_names,attribute_values): | |
| 156 for name,value in zip(attribute_names,attribute_values): | |
| 157 self.__setattr__(name,value) | |
|
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158 |
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159 class MinibatchToSingleExampleIterator(object): |
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160 """ |
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161 Converts the result of minibatch iterator with minibatch_size==1 into |
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162 single-example values in the result. Therefore the result of |
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163 iterating on the dataset itself gives a sequence of single examples |
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164 (whereas the result of iterating over minibatches gives in each |
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165 Example field an iterable object over the individual examples in |
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166 the minibatch). |
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167 """ |
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168 def __init__(self, minibatch_iterator): |
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169 self.minibatch_iterator = minibatch_iterator |
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170 self.minibatch = None |
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171 def __iter__(self): #makes for loop work |
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172 return self |
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173 def next(self): |
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174 size1_minibatch = self.minibatch_iterator.next() |
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175 if not self.minibatch: |
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176 self.minibatch = Example(size1_minibatch.keys(),[value[0] for value in size1_minibatch.values()]) |
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177 else: |
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178 self.minibatch._values = [value[0] for value in size1_minibatch.values()] |
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179 return self.minibatch |
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180 |
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181 def next_index(self): |
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182 return self.minibatch_iterator.next_index() |
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183 |
|
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184 def __iter__(self): |
| 16 | 185 """Supports the syntax "for i in dataset: ..." |
|
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186 |
| 16 | 187 Using this syntax, "i" will be an Example instance (or equivalent) with |
| 188 all the fields of DataSet self. Every field of "i" will give access to | |
|
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189 a field of a single example. Fields should be accessible via |
|
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190 i["fielname"] or i[3] (in the order defined by the elements of the |
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191 Example returned by this iterator), but the derived class is free |
|
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192 to accept any type of identifier, and add extra functionality to the iterator. |
| 16 | 193 |
|
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194 The default implementation calls the minibatches iterator and extracts the first example of each field. |
|
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195 """ |
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196 return DataSet.MinibatchToSingleExampleIterator(self.minibatches(None, minibatch_size = 1)) |
|
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197 |
|
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198 |
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199 class MinibatchWrapAroundIterator(object): |
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200 """ |
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201 An iterator for minibatches that handles the case where we need to wrap around the |
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202 dataset because n_batches*minibatch_size > len(dataset). It is constructed from |
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203 a dataset that provides a minibatch iterator that does not need to handle that problem. |
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204 This class is a utility for dataset subclass writers, so that they do not have to handle |
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205 this issue multiple times, nor check that fieldnames are valid, nor handle the |
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206 empty fieldnames (meaning 'use all the fields'). |
|
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207 """ |
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208 def __init__(self,dataset,fieldnames,minibatch_size,n_batches,offset): |
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209 self.dataset=dataset |
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210 self.fieldnames=fieldnames |
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211 self.minibatch_size=minibatch_size |
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212 self.n_batches=n_batches |
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213 self.n_batches_done=0 |
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214 self.next_row=offset |
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215 self.L=len(dataset) |
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216 assert offset+minibatch_size<=self.L |
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217 ds_nbatches = (self.L-offset)/minibatch_size |
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218 if n_batches is not None: |
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219 ds_nbatches = max(n_batches,ds_nbatches) |
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220 if fieldnames: |
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221 assert dataset.hasFields(*fieldnames) |
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222 else: |
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223 fieldnames=dataset.fieldNames() |
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224 self.iterator = dataset.minibatches_nowrap(fieldnames,minibatch_size,ds_nbatches,offset) |
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225 |
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226 def __iter__(self): |
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227 return self |
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228 |
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229 def next_index(self): |
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230 return self.next_row |
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231 |
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232 def next(self): |
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233 if self.n_batches and self.n_batches_done==self.n_batches: |
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234 raise StopIteration |
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235 upper = self.next_row+self.minibatch_size |
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236 if upper <=self.L: |
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237 minibatch = self.iterator.next() |
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238 else: |
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239 if not self.n_batches: |
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240 raise StopIteration |
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241 # we must concatenate (vstack) the bottom and top parts of our minibatch |
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242 # first get the beginning of our minibatch (top of dataset) |
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243 first_part = self.dataset.minibatches_nowrap(fieldnames,self.L-self.next_row,1,self.next_row).next() |
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244 second_part = self.dataset.minibatches_nowrap(fieldnames,upper-self.L,1,0).next() |
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245 minibatch = Example(self.fieldnames, |
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246 [self.dataset.valuesVStack(name,[first_part[name],second_part[name]]) |
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247 for name in self.fieldnames]) |
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248 self.next_row=upper |
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249 self.n_batches_done+=1 |
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250 if upper >= self.L and self.n_batches: |
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251 self.next_row -= self.L |
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252 return DataSetFields(MinibatchDataSet(minibatch,self.dataset.valuesVStack, |
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253 self.dataset.valuesHStack), |
|
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254 minibatch.keys()) |
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255 |
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256 |
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257 minibatches_fieldnames = None |
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258 minibatches_minibatch_size = 1 |
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259 minibatches_n_batches = None |
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260 def minibatches(self, |
|
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261 fieldnames = minibatches_fieldnames, |
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262 minibatch_size = minibatches_minibatch_size, |
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263 n_batches = minibatches_n_batches, |
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264 offset = 0): |
|
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265 """ |
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266 Return an iterator that supports three forms of syntax: |
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267 |
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268 for i in dataset.minibatches(None,**kwargs): ... |
| 16 | 269 |
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270 for i in dataset.minibatches([f1, f2, f3],**kwargs): ... |
| 16 | 271 |
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272 for i1, i2, i3 in dataset.minibatches([f1, f2, f3],**kwargs): ... |
| 16 | 273 |
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274 Using the first two syntaxes, "i" will be an indexable object, such as a list, |
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275 tuple, or Example instance. In both cases, i[k] is a list-like container |
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276 of a batch of current examples. In the second case, i[0] is |
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277 list-like container of the f1 field of a batch current examples, i[1] is |
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278 a list-like container of the f2 field, etc. |
|
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279 |
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280 Using the first syntax, all the fields will be returned in "i". |
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281 Using the third syntax, i1, i2, i3 will be list-like containers of the |
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282 f1, f2, and f3 fields of a batch of examples on each loop iteration. |
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283 |
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284 The minibatches iterator is expected to return upon each call to next() |
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285 a DataSetFields object, which is a LookupList (indexed by the field names) whose |
| 80 | 286 elements are iterable and indexable over the minibatch examples, and which keeps a pointer to |
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287 a sub-dataset that can be used to iterate over the individual examples |
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288 in the minibatch. Hence a minibatch can be converted back to a regular |
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289 dataset or its fields can be looked at individually (and possibly iterated over). |
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290 |
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291 PARAMETERS |
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292 - fieldnames (list of any type, default None): |
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293 The loop variables i1, i2, i3 (in the example above) should contain the |
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294 f1, f2, and f3 fields of the current batch of examples. If None, the |
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295 derived class can choose a default, e.g. all fields. |
| 16 | 296 |
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297 - minibatch_size (integer, default 1) |
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298 On every iteration, the variables i1, i2, i3 will have |
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299 exactly minibatch_size elements. e.g. len(i1) == minibatch_size |
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300 |
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301 - n_batches (integer, default None) |
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302 The iterator will loop exactly this many times, and then stop. If None, |
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303 the derived class can choose a default. If (-1), then the returned |
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304 iterator should support looping indefinitely. |
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305 |
|
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306 - offset (integer, default 0) |
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307 The iterator will start at example 'offset' in the dataset, rather than the default. |
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308 |
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309 Note: A list-like container is something like a tuple, list, numpy.ndarray or |
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310 any other object that supports integer indexing and slicing. |
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311 |
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312 """ |
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313 return DataSet.MinibatchWrapAroundIterator(self,fieldnames,minibatch_size,n_batches,offset) |
|
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314 |
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315 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
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316 """ |
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317 This is the minibatches iterator generator that sub-classes must define. |
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318 It does not need to worry about wrapping around multiple times across the dataset, |
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319 as this is handled by MinibatchWrapAroundIterator when DataSet.minibatches() is called. |
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320 The next() method of the returned iterator does not even need to worry about |
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321 the termination condition (as StopIteration will be raised by DataSet.minibatches |
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322 before an improper call to minibatches_nowrap's next() is made). |
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323 That next() method can assert that its next row will always be within [0,len(dataset)). |
|
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324 The iterator returned by minibatches_nowrap does not need to implement |
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325 a next_index() method either, as this will be provided by MinibatchWrapAroundIterator. |
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326 """ |
|
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327 raise AbstractFunction() |
|
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328 |
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329 def __len__(self): |
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330 """ |
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331 len(dataset) returns the number of examples in the dataset. |
|
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332 By default, a DataSet is a 'stream', i.e. it has an unbounded length (sys.maxint). |
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333 Sub-classes which implement finite-length datasets should redefine this method. |
|
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334 Some methods only make sense for finite-length datasets. |
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335 """ |
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336 return sys.maxint |
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337 |
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338 def is_unbounded(self): |
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339 """ |
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340 Tests whether a dataset is unbounded (e.g. a stream). |
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341 """ |
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342 return len(self)==sys.maxint |
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343 |
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344 def hasFields(self,*fieldnames): |
|
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345 """ |
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346 Return true if the given field name (or field names, if multiple arguments are |
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347 given) is recognized by the DataSet (i.e. can be used as a field name in one |
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348 of the iterators). |
|
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349 |
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350 The default implementation may be inefficient (O(# fields in dataset)), as it calls the fieldNames() |
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351 method. Many datasets may store their field names in a dictionary, which would allow more efficiency. |
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352 """ |
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353 return len(unique_elements_list_intersection(fieldnames,self.fieldNames()))>0 |
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354 |
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355 def fieldNames(self): |
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356 """ |
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357 Return the list of field names that are supported by the iterators, |
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358 and for which hasFields(fieldname) would return True. |
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359 """ |
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360 raise AbstractFunction() |
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361 |
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362 def __call__(self,*fieldnames): |
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363 """ |
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364 Return a dataset that sees only the fields whose name are specified. |
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365 """ |
|
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366 assert self.hasFields(*fieldnames) |
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367 return self.fields(*fieldnames).examples() |
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368 |
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369 def fields(self,*fieldnames): |
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370 """ |
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371 Return a DataSetFields object associated with this dataset. |
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372 """ |
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373 return DataSetFields(self,fieldnames) |
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374 |
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375 def __getitem__(self,i): |
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376 """ |
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377 dataset[i] returns the (i+1)-th example of the dataset. |
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378 dataset[i:j] returns the subdataset with examples i,i+1,...,j-1. |
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379 dataset[i:j:s] returns the subdataset with examples i,i+2,i+4...,j-2. |
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380 dataset[[i1,i2,..,in]] returns the subdataset with examples i1,i2,...,in. |
| 41 | 381 dataset['key'] returns a property associated with the given 'key' string. |
| 382 If 'key' is a fieldname, then the VStacked field values (iterable over | |
| 383 field values) for that field is returned. Other keys may be supported | |
| 384 by different dataset subclasses. The following key names are encouraged: | |
| 385 - 'description': a textual description or name for the dataset | |
| 386 - '<fieldname>.type': a type name or value for a given <fieldname> | |
|
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387 |
| 39 | 388 Note that some stream datasets may be unable to implement random access, i.e. |
| 389 arbitrary slicing/indexing | |
|
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390 because they can only iterate through examples one or a minibatch at a time |
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391 and do not actually store or keep past (or future) examples. |
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392 |
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393 The default implementation of getitem uses the minibatches iterator |
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394 to obtain one example, one slice, or a list of examples. It may not |
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395 always be the most efficient way to obtain the result, especially if |
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396 the data are actually stored in a memory array. |
|
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397 """ |
| 41 | 398 # check for an index |
|
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399 if type(i) is int: |
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400 return DataSet.MinibatchToSingleExampleIterator( |
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401 self.minibatches(minibatch_size=1,n_batches=1,offset=i)).next() |
| 41 | 402 rows=None |
| 403 # or a slice | |
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404 if type(i) is slice: |
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405 if not i.start: i.start=0 |
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406 if not i.step: i.step=1 |
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407 if i.step is 1: |
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408 return self.minibatches(minibatch_size=i.stop-i.start,n_batches=1,offset=i.start).next().examples() |
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409 rows = range(i.start,i.stop,i.step) |
| 41 | 410 # or a list of indices |
| 411 elif type(i) is list: | |
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412 rows = i |
| 41 | 413 if rows is not None: |
|
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414 examples = [self[row] for row in rows] |
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415 fields_values = zip(*examples) |
|
45
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416 return MinibatchDataSet( |
| 41 | 417 Example(self.fieldNames(),[ self.valuesVStack(fieldname,field_values) |
| 418 for fieldname,field_values | |
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419 in zip(self.fieldNames(),fields_values)]), |
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420 self.valuesVStack,self.valuesHStack) |
| 41 | 421 # else check for a fieldname |
| 422 if self.hasFields(i): | |
| 423 return self.minibatches(fieldnames=[i],minibatch_size=len(self),n_batches=1,offset=0).next()[0] | |
| 424 # else we are trying to access a property of the dataset | |
| 425 assert i in self.__dict__ # else it means we are trying to access a non-existing property | |
| 426 return self.__dict__[i] | |
|
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427 |
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428 def valuesHStack(self,fieldnames,fieldvalues): |
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429 """ |
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430 Return a value that corresponds to concatenating (horizontally) several field values. |
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431 This can be useful to merge some fields. The implementation of this operation is likely |
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432 to involve a copy of the original values. When the values are numpy arrays, the |
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433 result should be numpy.hstack(values). If it makes sense, this operation should |
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434 work as well when each value corresponds to multiple examples in a minibatch |
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435 e.g. if each value is a Ni-vector and a minibatch of length L is a LxNi matrix, |
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436 then the result should be a Lx(N1+N2+..) matrix equal to numpy.hstack(values). |
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437 The default is to use numpy.hstack for numpy.ndarray values, and a list |
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438 pointing to the original values for other data types. |
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439 """ |
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440 all_numpy=True |
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441 for value in fieldvalues: |
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442 if not type(value) is numpy.ndarray: |
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443 all_numpy=False |
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444 if all_numpy: |
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445 return numpy.hstack(fieldvalues) |
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446 # the default implementation of horizontal stacking is to put values in a list |
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447 return fieldvalues |
|
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448 |
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449 |
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450 def valuesVStack(self,fieldname,values): |
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451 """ |
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452 Return a value that corresponds to concatenating (vertically) several values of the |
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453 same field. This can be important to build a minibatch out of individual examples. This |
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454 is likely to involve a copy of the original values. When the values are numpy arrays, the |
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455 result should be numpy.vstack(values). |
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456 The default is to use numpy.vstack for numpy.ndarray values, and a list |
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457 pointing to the original values for other data types. |
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458 """ |
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459 all_numpy=True |
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460 for value in values: |
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461 if not type(value) is numpy.ndarray: |
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462 all_numpy=False |
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463 if all_numpy: |
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464 return numpy.vstack(values) |
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465 # the default implementation of vertical stacking is to put values in a list |
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466 return values |
|
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467 |
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468 def __or__(self,other): |
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469 """ |
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470 dataset1 | dataset2 returns a dataset whose list of fields is the concatenation of the list of |
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471 fields of the argument datasets. This only works if they all have the same length. |
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472 """ |
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473 return HStackedDataSet(self,other) |
|
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474 |
|
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475 def __and__(self,other): |
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476 """ |
|
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477 dataset1 & dataset2 is a dataset that concatenates the examples from the argument datasets |
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478 (and whose length is the sum of the length of the argument datasets). This only |
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479 works if they all have the same fields. |
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480 """ |
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481 return VStackedDataSet(self,other) |
|
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482 |
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483 def hstack(datasets): |
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484 """ |
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485 hstack(dataset1,dataset2,...) returns dataset1 | datataset2 | ... |
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486 which is a dataset whose fields list is the concatenation of the fields |
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487 of the individual datasets. |
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488 """ |
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489 assert len(datasets)>0 |
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490 if len(datasets)==1: |
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491 return datasets[0] |
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492 return HStackedDataSet(datasets) |
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493 |
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494 def vstack(datasets): |
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495 """ |
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496 vstack(dataset1,dataset2,...) returns dataset1 & datataset2 & ... |
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497 which is a dataset which iterates first over the examples of dataset1, then |
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498 over those of dataset2, etc. |
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499 """ |
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500 assert len(datasets)>0 |
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501 if len(datasets)==1: |
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502 return datasets[0] |
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503 return VStackedDataSet(datasets) |
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504 |
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505 class FieldsSubsetDataSet(DataSet): |
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506 """ |
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507 A sub-class of DataSet that selects a subset of the fields. |
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508 """ |
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509 def __init__(self,src,fieldnames): |
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510 self.src=src |
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511 self.fieldnames=fieldnames |
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512 assert src.hasFields(*fieldnames) |
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513 self.valuesHStack = src.valuesHStack |
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514 self.valuesVStack = src.valuesVStack |
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515 |
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516 def __len__(self): return len(self.src) |
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517 |
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518 def fieldNames(self): |
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519 return self.fieldnames |
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520 |
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521 def __iter__(self): |
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522 class FieldsSubsetIterator(object): |
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523 def __init__(self,ds): |
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524 self.ds=ds |
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525 self.src_iter=ds.src.__iter__() |
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526 self.example=None |
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527 def __iter__(self): return self |
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528 def next(self): |
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529 complete_example = self.src_iter.next() |
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530 if self.example: |
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531 self.example._values=[complete_example[field] |
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532 for field in self.ds.fieldnames] |
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533 else: |
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534 self.example=Example(self.ds.fieldnames, |
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535 [complete_example[field] for field in self.ds.fieldnames]) |
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536 return self.example |
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537 return FieldsSubsetIterator(self) |
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538 |
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539 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
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540 assert self.hasFields(*fieldnames) |
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541 return self.src.minibatches_nowrap(fieldnames,minibatch_size,n_batches,offset) |
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542 def __getitem__(self,i): |
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543 return FieldsSubsetDataSet(self.src[i],self.fieldnames) |
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544 |
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545 |
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546 class DataSetFields(LookupList): |
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547 """ |
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548 Although a DataSet iterates over examples (like rows of a matrix), an associated |
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549 DataSetFields iterates over fields (like columns of a matrix), and can be understood |
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550 as a transpose of the associated dataset. |
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551 |
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552 To iterate over fields, one can do |
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553 * for fields in dataset.fields() |
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554 * for fields in dataset(field1,field2,...).fields() to select a subset of fields |
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555 * for fields in dataset.fields(field1,field2,...) to select a subset of fields |
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556 and each of these fields is iterable over the examples: |
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557 * for field_examples in dataset.fields(): |
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558 for example_value in field_examples: |
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559 ... |
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560 but when the dataset is a stream (unbounded length), it is not recommanded to do |
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561 such things because the underlying dataset may refuse to access the different fields in |
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562 an unsynchronized ways. Hence the fields() method is illegal for streams, by default. |
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563 The result of fields() is a DataSetFields object, which iterates over fields, |
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564 and whose elements are iterable over examples. A DataSetFields object can |
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565 be turned back into a DataSet with its examples() method: |
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566 dataset2 = dataset1.fields().examples() |
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567 and dataset2 should behave exactly like dataset1 (in fact by default dataset2==dataset1). |
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568 |
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569 DataSetFields can be concatenated vertically or horizontally. To be consistent with |
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570 the syntax used for DataSets, the | concatenates the fields and the & concatenates |
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571 the examples. |
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572 """ |
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573 def __init__(self,dataset,fieldnames): |
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574 original_dataset=dataset |
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575 if not fieldnames: |
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576 fieldnames=dataset.fieldNames() |
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577 elif not fieldnames==dataset.fieldNames(): |
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578 dataset = FieldsSubsetDataSet(dataset,fieldnames) |
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579 assert dataset.hasFields(*fieldnames) |
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580 self.dataset=dataset |
|
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581 |
|
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582 if isinstance(dataset,MinibatchDataSet): |
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583 LookupList.__init__(self,fieldnames,list(dataset._fields)) |
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584 elif isinstance(original_dataset,MinibatchDataSet): |
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585 LookupList.__init__(self,fieldnames, |
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|
586 [original_dataset._fields[field] |
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587 for field in fieldnames]) |
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588 else: |
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589 minibatch_iterator = dataset.minibatches(fieldnames, |
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590 minibatch_size=len(dataset), |
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591 n_batches=1) |
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592 minibatch=minibatch_iterator.next() |
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593 LookupList.__init__(self,fieldnames,minibatch) |
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594 |
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595 def examples(self): |
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596 return self.dataset |
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597 |
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598 def __or__(self,other): |
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599 """ |
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600 fields1 | fields2 is a DataSetFields that whose list of examples is the concatenation |
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601 of the list of examples of DataSetFields fields1 and fields2. |
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602 """ |
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603 return (self.examples() + other.examples()).fields() |
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604 |
|
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605 def __and__(self,other): |
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|
606 """ |
|
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607 fields1 + fields2 is a DataSetFields that whose list of fields is the concatenation |
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608 of the fields of DataSetFields fields1 and fields2. |
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609 """ |
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610 return (self.examples() | other.examples()).fields() |
|
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611 |
|
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612 |
|
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613 class MinibatchDataSet(DataSet): |
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614 """ |
| 85 | 615 Turn a LookupList of same-length (iterable) fields into an example-iterable dataset. |
|
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616 Each element of the lookup-list should be an iterable and sliceable, all of the same length. |
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617 """ |
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618 def __init__(self,fields_lookuplist,values_vstack=DataSet().valuesVStack, |
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619 values_hstack=DataSet().valuesHStack): |
|
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620 """ |
|
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621 The user can (and generally should) also provide values_vstack(fieldname,fieldvalues) |
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622 and a values_hstack(fieldnames,fieldvalues) functions behaving with the same |
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623 semantics as the DataSet methods of the same name (but without the self argument). |
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624 """ |
|
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625 self._fields=fields_lookuplist |
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626 assert len(fields_lookuplist)>0 |
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627 self.length=len(fields_lookuplist[0]) |
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628 for field in fields_lookuplist[1:]: |
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629 assert self.length==len(field) |
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630 self.values_vstack=values_vstack |
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631 self.values_hstack=values_hstack |
|
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632 |
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633 def __len__(self): |
|
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634 return self.length |
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635 |
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636 def __getitem__(self,i): |
| 80 | 637 if type(i) in (slice,list): |
|
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638 return DataSetFields(MinibatchDataSet( |
| 80 | 639 Example(self._fields.keys(),[field[i] for field in self._fields])),self.fieldNames()) |
| 640 if type(i) is int: | |
| 85 | 641 return Example(self._fields.keys(),[field[i] for field in self._fields]) |
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642 if self.hasFields(i): |
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643 return self._fields[i] |
|
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644 assert i in self.__dict__ # else it means we are trying to access a non-existing property |
|
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645 return self.__dict__[i] |
|
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646 |
|
29
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647 def fieldNames(self): |
|
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648 return self._fields.keys() |
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649 |
|
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650 def hasFields(self,*fieldnames): |
|
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651 for fieldname in fieldnames: |
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652 if fieldname not in self._fields.keys(): |
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653 return False |
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654 return True |
|
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655 |
|
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656 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
|
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657 class Iterator(object): |
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658 def __init__(self,ds): |
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659 self.ds=ds |
|
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660 self.next_example=offset |
|
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661 assert minibatch_size > 0 |
| 41 | 662 if offset+minibatch_size > ds.length: |
|
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663 raise NotImplementedError() |
|
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664 def __iter__(self): |
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665 return self |
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666 def next(self): |
|
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667 upper = self.next_example+minibatch_size |
|
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668 assert upper<=self.ds.length |
|
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669 minibatch = Example(self.ds._fields.keys(), |
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670 [field[self.next_example:upper] |
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671 for field in self.ds._fields]) |
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672 self.next_example+=minibatch_size |
|
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673 return minibatch |
|
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|
674 |
|
40
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675 return Iterator(self) |
|
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676 |
|
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677 def valuesVStack(self,fieldname,fieldvalues): |
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678 return self.values_vstack(fieldname,fieldvalues) |
|
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|
679 |
|
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680 def valuesHStack(self,fieldnames,fieldvalues): |
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681 return self.values_hstack(fieldnames,fieldvalues) |
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682 |
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683 class HStackedDataSet(DataSet): |
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684 """ |
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685 A DataSet that wraps several datasets and shows a view that includes all their fields, |
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686 i.e. whose list of fields is the concatenation of their lists of fields. |
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687 |
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688 If a field name is found in more than one of the datasets, then either an error is |
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689 raised or the fields are renamed (either by prefixing the __name__ attribute |
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690 of the dataset + ".", if it exists, or by suffixing the dataset index in the argument list). |
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691 |
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692 TODO: automatically detect a chain of stacked datasets due to A | B | C | D ... |
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693 """ |
| 41 | 694 def __init__(self,datasets,accept_nonunique_names=False,description=None,field_types=None): |
| 695 DataSet.__init__(self,description,field_types) | |
|
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696 self.datasets=datasets |
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697 self.accept_nonunique_names=accept_nonunique_names |
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698 self.fieldname2dataset={} |
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|
699 |
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700 def rename_field(fieldname,dataset,i): |
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701 if hasattr(dataset,"__name__"): |
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702 return dataset.__name__ + "." + fieldname |
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703 return fieldname+"."+str(i) |
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704 |
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705 # make sure all datasets have the same length and unique field names |
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706 self.length=None |
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707 names_to_change=[] |
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708 for i in xrange(len(datasets)): |
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709 dataset = datasets[i] |
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710 length=len(dataset) |
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711 if self.length: |
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712 assert self.length==length |
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713 else: |
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714 self.length=length |
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715 for fieldname in dataset.fieldNames(): |
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716 if fieldname in self.fieldname2dataset: # name conflict! |
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717 if accept_nonunique_names: |
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718 fieldname=rename_field(fieldname,dataset,i) |
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719 names2change.append((fieldname,i)) |
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720 else: |
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721 raise ValueError("Incompatible datasets: non-unique field name = "+fieldname) |
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722 self.fieldname2dataset[fieldname]=i |
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723 for fieldname,i in names_to_change: |
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724 del self.fieldname2dataset[fieldname] |
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725 self.fieldname2dataset[rename_field(fieldname,self.datasets[i],i)]=i |
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726 |
|
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727 def hasFields(self,*fieldnames): |
|
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|
728 for fieldname in fieldnames: |
|
438440ba0627
Rewriting dataset.py completely
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parents:
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diff
changeset
|
729 if not fieldname in self.fieldname2dataset: |
|
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Rewriting dataset.py completely
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parents:
29
diff
changeset
|
730 return False |
|
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Rewriting dataset.py completely
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parents:
29
diff
changeset
|
731 return True |
|
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parents:
29
diff
changeset
|
732 |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
733 def fieldNames(self): |
|
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Rewriting dataset.py completely
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parents:
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diff
changeset
|
734 return self.fieldname2dataset.keys() |
|
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Rewriting dataset.py completely
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diff
changeset
|
735 |
| 41 | 736 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
|
36
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parents:
29
diff
changeset
|
737 |
|
44
5a85fda9b19b
Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents:
43
diff
changeset
|
738 class HStackedIterator(object): |
|
36
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
739 def __init__(self,hsds,iterators): |
|
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diff
changeset
|
740 self.hsds=hsds |
|
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Rewriting dataset.py completely
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parents:
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diff
changeset
|
741 self.iterators=iterators |
|
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Rewriting dataset.py completely
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parents:
29
diff
changeset
|
742 def __iter__(self): |
|
438440ba0627
Rewriting dataset.py completely
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parents:
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diff
changeset
|
743 return self |
|
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parents:
29
diff
changeset
|
744 def next(self): |
|
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parents:
29
diff
changeset
|
745 # concatenate all the fields of the minibatches |
|
73
69f97aad3faf
Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents:
72
diff
changeset
|
746 return reduce(LookupList.__add__,[iterator.next() for iterator in self.iterators]) |
|
36
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Rewriting dataset.py completely
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diff
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|
747 |
|
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Rewriting dataset.py completely
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parents:
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diff
changeset
|
748 assert self.hasfields(fieldnames) |
|
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Rewriting dataset.py completely
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parents:
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diff
changeset
|
749 # find out which underlying datasets are necessary to service the required fields |
|
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Rewriting dataset.py completely
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parents:
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diff
changeset
|
750 # and construct corresponding minibatch iterators |
|
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parents:
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diff
changeset
|
751 if fieldnames: |
|
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parents:
29
diff
changeset
|
752 datasets=set([]) |
|
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Rewriting dataset.py completely
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parents:
29
diff
changeset
|
753 fields_in_dataset=dict([(dataset,[]) for dataset in datasets]) |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
754 for fieldname in fieldnames: |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
755 dataset=self.datasets[self.fieldnames2dataset[fieldname]] |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
756 datasets.add(dataset) |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
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diff
changeset
|
757 fields_in_dataset[dataset].append(fieldname) |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
758 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
|
759 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
|
760 for dataset in datasets] |
|
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Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
761 else: |
|
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Rewriting dataset.py completely
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parents:
29
diff
changeset
|
762 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
|
763 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
|
764 return HStackedIterator(self,iterators) |
|
36
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
765 |
|
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Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
766 |
|
438440ba0627
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bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
767 def valuesVStack(self,fieldname,fieldvalues): |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
768 return self.datasets[self.fieldname2dataset[fieldname]].valuesVStack(fieldname,fieldvalues) |
|
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Rewriting dataset.py completely
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parents:
29
diff
changeset
|
769 |
|
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parents:
29
diff
changeset
|
770 def valuesHStack(self,fieldnames,fieldvalues): |
|
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parents:
29
diff
changeset
|
771 """ |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
772 We will use the sub-dataset associated with the first fieldname in the fieldnames list |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
773 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
|
774 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
|
775 all the fieldnames are of the same sub-dataset. |
|
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Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
776 """ |
|
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parents:
29
diff
changeset
|
777 return self.datasets[self.fieldname2dataset[fieldnames[0]]].valuesHStack(fieldnames,fieldvalues) |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
778 |
|
438440ba0627
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parents:
29
diff
changeset
|
779 class VStackedDataSet(DataSet): |
|
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Rewriting dataset.py completely
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parents:
29
diff
changeset
|
780 """ |
|
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parents:
29
diff
changeset
|
781 A DataSet that wraps several datasets and shows a view that includes all their examples, |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
782 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
|
783 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
|
784 |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
785 TODO: automatically detect a chain of stacked datasets due to A + B + C + D ... |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
786 """ |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
787 def __init__(self,datasets): |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
788 self.datasets=datasets |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
789 self.length=0 |
|
438440ba0627
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bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
790 self.index2dataset={} |
|
37
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
791 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
|
792 fieldnames = datasets[-1].fieldNames() |
|
38
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
793 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
|
794 # 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
|
795 # 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
|
796 for dataset,k in enumerate(datasets[0:-1]): |
|
48
b6730f9a336d
Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents:
46
diff
changeset
|
797 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
|
798 L=len(dataset) |
|
36
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
799 for i in xrange(L): |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
800 self.index2dataset[self.length+i]=k |
|
38
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
801 self.datasets_start_row.append(self.length) |
|
36
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
802 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
|
803 assert dataset.fieldNames()==fieldnames |
|
38
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
804 self.datasets_start_row.append(self.length) |
|
36
438440ba0627
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parents:
29
diff
changeset
|
805 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
|
806 # 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
|
807 # 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
|
808 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
|
809 # 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
|
810 # TODO |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
811 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
|
812 |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
813 def __len__(self): |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
814 return self.length |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
815 |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
816 def fieldNames(self): |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
817 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
|
818 |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
819 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
|
820 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
|
821 |
|
38
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
822 def locate_row(self,row): |
|
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
823 """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
|
824 dataset_index = self.index2dataset[row] |
|
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
825 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
|
826 return dataset_index, row_within_dataset |
|
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
827 |
| 41 | 828 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
|
829 |
|
5a85fda9b19b
Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents:
43
diff
changeset
|
830 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
|
831 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
|
832 self.vsds=vsds |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
833 self.next_row=offset |
|
38
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
834 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
|
835 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
|
836 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
|
837 |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
838 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
|
839 L=len(dataset) |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
840 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
|
841 if batches_left is not None: |
|
73c4212ba5b3
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bengioy@esprit.iro.umontreal.ca
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diff
changeset
|
842 ds_nbatches = max(batches_left,ds_nbatches) |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
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diff
changeset
|
843 if minibatch_size>L: |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
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diff
changeset
|
844 ds_minibatch_size=L |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
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parents:
36
diff
changeset
|
845 n_left_in_mb=minibatch_size-L |
|
38
d637ad8f7352
Finished first untested version of VStackedDataset
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37
diff
changeset
|
846 ds_nbatches=1 |
|
d637ad8f7352
Finished first untested version of VStackedDataset
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parents:
37
diff
changeset
|
847 else: |
|
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
848 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
|
849 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
|
850 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
|
851 |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
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parents:
36
diff
changeset
|
852 def move_to_next_dataset(self): |
|
38
d637ad8f7352
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bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
853 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
|
854 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
|
855 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
|
856 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
|
857 else: |
|
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
858 self.next_dataset_index +=1 |
|
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
859 if self.next_dataset_index==len(self.vsds.datasets): |
|
d637ad8f7352
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bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
860 self.next_dataset_index = 0 |
|
d637ad8f7352
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bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
861 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
|
862 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
|
863 |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
864 def __iter__(self): |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
865 return self |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
866 |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
867 def next(self): |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
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diff
changeset
|
868 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
|
869 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
|
870 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
|
871 extra_mb = [] |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
872 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
|
873 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
|
874 extra_mb.append(self.next_iterator.next()) |
|
73
69f97aad3faf
Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents:
72
diff
changeset
|
875 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
|
876 [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
|
877 [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
|
878 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
|
879 |
|
37
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
880 self.next_row+=minibatch_size |
|
38
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
881 self.next_dataset_row+=minibatch_size |
|
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
882 if self.next_row+minibatch_size>len(dataset): |
|
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
883 self.move_to_next_dataset() |
|
44
5a85fda9b19b
Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents:
43
diff
changeset
|
884 return examples |
|
5a85fda9b19b
Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents:
43
diff
changeset
|
885 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
|
886 |
| 41 | 887 class ArrayFieldsDataSet(DataSet): |
| 888 """ | |
| 889 Virtual super-class of datasets whose field values are numpy array, | |
| 890 thus defining valuesHStack and valuesVStack for sub-classes. | |
| 891 """ | |
| 892 def __init__(self,description=None,field_types=None): | |
| 893 DataSet.__init__(self,description,field_types) | |
| 894 def valuesHStack(self,fieldnames,fieldvalues): | |
| 895 """Concatenate field values horizontally, e.g. two vectors | |
| 896 become a longer vector, two matrices become a wider matrix, etc.""" | |
| 897 return numpy.hstack(fieldvalues) | |
| 898 def valuesVStack(self,fieldname,values): | |
| 899 """Concatenate field values vertically, e.g. two vectors | |
| 900 become a two-row matrix, two matrices become a longer matrix, etc.""" | |
| 901 return numpy.vstack(values) | |
| 902 | |
| 903 class ArrayDataSet(ArrayFieldsDataSet): | |
| 904 """ | |
| 905 An ArrayDataSet stores the fields as groups of columns in a numpy tensor, | |
| 906 whose first axis iterates over examples, second axis determines fields. | |
| 907 If the underlying array is N-dimensional (has N axes), then the field | |
| 908 values are (N-2)-dimensional objects (i.e. ordinary numbers if N=2). | |
| 909 """ | |
| 910 | |
|
42
9b68774fcc6b
Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents:
41
diff
changeset
|
911 def __init__(self, data_array, fields_columns): |
|
55
66619ce44497
Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
48
diff
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|
912 """ |
|
66619ce44497
Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
48
diff
changeset
|
913 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
|
914 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
|
915 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
|
916 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
|
917 """ |
| 41 | 918 self.data=data_array |
|
42
9b68774fcc6b
Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents:
41
diff
changeset
|
919 self.fields_columns=fields_columns |
| 41 | 920 |
| 921 # check consistency and complete slices definitions | |
|
42
9b68774fcc6b
Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents:
41
diff
changeset
|
922 for fieldname, fieldcolumns in self.fields_columns.items(): |
| 41 | 923 if type(fieldcolumns) is int: |
| 924 assert fieldcolumns>=0 and fieldcolumns<data_array.shape[1] | |
| 925 elif type(fieldcolumns) is slice: | |
| 926 start,step=None,None | |
| 927 if not fieldcolumns.start: | |
| 928 start=0 | |
| 929 if not fieldcolumns.step: | |
| 930 step=1 | |
| 931 if start or step: | |
|
42
9b68774fcc6b
Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents:
41
diff
changeset
|
932 self.fields_columns[fieldname]=slice(start,fieldcolumns.stop,step) |
| 41 | 933 elif hasattr(fieldcolumns,"__iter__"): # something like a list |
| 934 for i in fieldcolumns: | |
| 935 assert i>=0 and i<data_array.shape[1] | |
| 936 | |
|
42
9b68774fcc6b
Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents:
41
diff
changeset
|
937 def fieldNames(self): |
|
9b68774fcc6b
Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents:
41
diff
changeset
|
938 return self.fields_columns.keys() |
| 41 | 939 |
|
42
9b68774fcc6b
Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents:
41
diff
changeset
|
940 def __len__(self): |
|
9b68774fcc6b
Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents:
41
diff
changeset
|
941 return len(self.data) |
| 41 | 942 |
| 80 | 943 def __getitem__(self,key): |
|
55
66619ce44497
Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
48
diff
changeset
|
944 """More efficient implementation than the default __getitem__""" |
|
66619ce44497
Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
48
diff
changeset
|
945 fieldnames=self.fields_columns.keys() |
| 80 | 946 if type(key) is int: |
|
55
66619ce44497
Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
48
diff
changeset
|
947 return Example(fieldnames, |
| 80 | 948 [self.data[key,self.fields_columns[f]] for f in fieldnames]) |
| 949 if type(key) is slice: | |
|
55
66619ce44497
Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
48
diff
changeset
|
950 return MinibatchDataSet(Example(fieldnames, |
| 80 | 951 [self.data[key,self.fields_columns[f]] for f in fieldnames])) |
| 952 if type(key) is list: | |
| 953 for i in range(len(key)): | |
| 954 if self.hasFields(key[i]): | |
| 955 key[i]=self.fields_columns[key[i]] | |
| 956 return MinibatchDataSet(Example(fieldnames, | |
|
88
6749d18e11c8
bugfix as numpy numpy don't support self.data[[i1,...],[i2,...]] when their is more then two i1 and i2
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
85
diff
changeset
|
957 #we must separate differently for list as numpy |
|
6749d18e11c8
bugfix as numpy numpy don't support self.data[[i1,...],[i2,...]] when their is more then two i1 and i2
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
85
diff
changeset
|
958 # don't support self.data[[i1,...],[i2,...]] |
|
6749d18e11c8
bugfix as numpy numpy don't support self.data[[i1,...],[i2,...]] when their is more then two i1 and i2
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
85
diff
changeset
|
959 # when their is more then two i1 and i2 |
|
6749d18e11c8
bugfix as numpy numpy don't support self.data[[i1,...],[i2,...]] when their is more then two i1 and i2
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
85
diff
changeset
|
960 [self.data[key,:][:,self.fields_columns[f]] |
|
6749d18e11c8
bugfix as numpy numpy don't support self.data[[i1,...],[i2,...]] when their is more then two i1 and i2
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
85
diff
changeset
|
961 if isinstance(self.fields_columns[f],list) else |
|
6749d18e11c8
bugfix as numpy numpy don't support self.data[[i1,...],[i2,...]] when their is more then two i1 and i2
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
85
diff
changeset
|
962 self.data[key,self.fields_columns[f]] |
|
6749d18e11c8
bugfix as numpy numpy don't support self.data[[i1,...],[i2,...]] when their is more then two i1 and i2
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
85
diff
changeset
|
963 for f in fieldnames]), |
|
73
69f97aad3faf
Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents:
72
diff
changeset
|
964 self.valuesVStack,self.valuesHStack) |
| 80 | 965 |
|
55
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Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
48
diff
changeset
|
966 # else check for a fieldname |
| 80 | 967 if self.hasFields(key): |
| 968 return self.data[self.fields_columns[key],:] | |
|
55
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Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
48
diff
changeset
|
969 # else we are trying to access a property of the dataset |
| 80 | 970 assert key in self.__dict__ # else it means we are trying to access a non-existing property |
| 971 return self.__dict__[key] | |
|
55
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Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
48
diff
changeset
|
972 |
| 41 | 973 |
|
42
9b68774fcc6b
Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents:
41
diff
changeset
|
974 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
|
975 class ArrayDataSetIterator(object): |
|
42
9b68774fcc6b
Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents:
41
diff
changeset
|
976 def __init__(self,dataset,fieldnames,minibatch_size,n_batches,offset): |
|
9b68774fcc6b
Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents:
41
diff
changeset
|
977 if fieldnames is None: fieldnames = dataset.fieldNames() |
|
44
5a85fda9b19b
Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents:
43
diff
changeset
|
978 # store the resulting minibatch in a lookup-list of values |
|
5a85fda9b19b
Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents:
43
diff
changeset
|
979 self.minibatch = LookupList(fieldnames,[0]*len(fieldnames)) |
|
42
9b68774fcc6b
Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents:
41
diff
changeset
|
980 self.dataset=dataset |
|
9b68774fcc6b
Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents:
41
diff
changeset
|
981 self.minibatch_size=minibatch_size |
|
9b68774fcc6b
Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents:
41
diff
changeset
|
982 assert offset>=0 and offset<len(dataset.data) |
|
9b68774fcc6b
Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents:
41
diff
changeset
|
983 assert offset+minibatch_size<=len(dataset.data) |
|
9b68774fcc6b
Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents:
41
diff
changeset
|
984 self.current=offset |
|
9b68774fcc6b
Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents:
41
diff
changeset
|
985 def __iter__(self): |
|
9b68774fcc6b
Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents:
41
diff
changeset
|
986 return self |
|
9b68774fcc6b
Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents:
41
diff
changeset
|
987 def next(self): |
|
9b68774fcc6b
Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents:
41
diff
changeset
|
988 sub_data = self.dataset.data[self.current:self.current+self.minibatch_size] |
|
44
5a85fda9b19b
Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents:
43
diff
changeset
|
989 self.minibatch._values = [sub_data[:,self.dataset.fields_columns[f]] for f in self.minibatch._names] |
|
43
e92244f30116
Corrected iterator logic errors
bengioy@grenat.iro.umontreal.ca
parents:
42
diff
changeset
|
990 self.current+=self.minibatch_size |
|
44
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991 return self.minibatch |
|
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992 |
|
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993 return ArrayDataSetIterator(self,fieldnames,minibatch_size,n_batches,offset) |
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|
994 |
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|
995 |
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996 class CachedDataSet(DataSet): |
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997 """ |
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998 Wrap a dataset whose values are computationally expensive to obtain |
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999 (e.g. because they involve some computation, or disk access), |
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1000 so that repeated accesses to the same example are done cheaply, |
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1001 by caching every example value that has been accessed at least once. |
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1002 |
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1003 Optionally, for finite-length dataset, all the values can be computed |
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1004 (and cached) upon construction of the CachedDataSet, rather at the |
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1005 first access. |
|
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1006 |
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1007 @todo when cache_all_upon_construction create mini-batches that are as |
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1008 large as possible but not so large as to fill up memory. |
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1009 |
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1010 @todo add disk-buffering capability, so that when the cache becomes too |
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1011 big for memory, we cache things on disk, trying to keep in memory only |
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1012 the record most likely to be accessed next. |
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1013 """ |
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1014 def __init__(self,source_dataset,cache_all_upon_construction=False): |
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1015 self.source_dataset=source_dataset |
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1016 self.cache_all_upon_construction=cache_all_upon_construction |
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1017 if cache_all_upon_construction: |
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1018 # this potentially brings all the source examples |
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1019 # into memory at once, which may be too much |
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1020 # the work could possibly be done by minibatches |
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1021 # that are as large as possible but no more than what memory allows. |
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1022 self.cached_examples = zip(*source_dataset.minibatches(minibatch_size=len(source_dataset)).__iter__().next()) |
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1023 else: |
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1024 self.cached_examples = [] |
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1025 |
|
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1026 self.fieldNames = source_dataset.fieldNames |
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1027 self.hasFields = source_dataset.hasFields |
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1028 self.valuesHStack = source_dataset.valuesHStack |
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1029 self.valuesVStack = source_dataset.valuesVStack |
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1030 |
|
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1031 def __len__(self): |
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1032 return len(self.source_dataset) |
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1033 |
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1034 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
|
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1035 class CacheIterator(object): |
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1036 def __init__(self,dataset): |
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1037 self.dataset=dataset |
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1038 self.current=offset |
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1039 def __iter__(self): return self |
|
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1040 def next(self): |
|
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1041 upper = self.current+minibatch_size |
|
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1042 cache_len = len(self.dataset.cached_examples) |
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1043 if upper>=cache_len: # whole minibatch is not already in cache |
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1044 # cache everything from current length to upper |
|
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|
1045 for example in self.dataset.source_dataset[cache_len:upper]: |
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1046 self.dataset.cached_examples.append(example) |
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1047 all_fields_minibatch = Example(self.dataset.fieldNames(), |
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1048 self.dataset.cached_examples[self.current:self.current+minibatch_size]) |
|
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1049 if self.dataset.fieldNames()==fieldnames: |
|
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1050 return all_fields_minibatch |
|
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1051 return Example(fieldnames,[all_fields_minibatch[name] for name in fieldnames]) |
|
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1052 return CacheIterator(self) |
|
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|
1053 |
|
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|
1054 |
|
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|
1055 class ApplyFunctionDataSet(DataSet): |
|
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|
1056 """ |
|
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|
1057 A dataset that contains as fields the results of applying a given function |
|
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|
1058 example-wise or minibatch-wise to all the fields of an input dataset. |
|
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|
1059 The output of the function should be an iterable (e.g. a list or a LookupList) |
|
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|
1060 over the resulting values. |
|
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|
1061 |
|
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|
1062 In minibatch mode, the function is expected to work on minibatches (takes |
|
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|
1063 a minibatch in input and returns a minibatch in output). More precisely, |
|
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|
1064 it means that each element of the input or output list should be iterable |
|
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|
1065 and indexable over the individual example values (typically these |
|
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|
1066 elements will be numpy arrays). All of the elements in the input and |
|
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|
1067 output lists should have the same length, which is the length of the |
|
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|
1068 minibatch. |
|
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diff
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|
1069 |
|
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|
1070 The function is applied each time an example or a minibatch is accessed. |
|
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|
1071 To avoid re-doing computation, wrap this dataset inside a CachedDataSet. |
|
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|
1072 |
|
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|
1073 If the values_{h,v}stack functions are not provided, then |
|
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1074 the input_dataset.values{H,V}Stack functions are used by default. |
|
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|
1075 """ |
|
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|
1076 def __init__(self,input_dataset,function,output_names,minibatch_mode=True, |
|
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1077 values_hstack=None,values_vstack=None, |
|
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1078 description=None,fieldtypes=None): |
|
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|
1079 """ |
|
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|
1080 Constructor takes an input dataset that has as many fields as the function |
|
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|
1081 expects as inputs. The resulting dataset has as many fields as the function |
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1082 produces as outputs, and that should correspond to the number of output names |
|
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|
1083 (provided in a list). |
|
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|
1084 |
|
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|
1085 Note that the expected semantics of the function differs in minibatch mode |
|
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1086 (it takes minibatches of inputs and produces minibatches of outputs, as |
|
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|
1087 documented in the class comment). |
|
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|
1088 """ |
|
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|
1089 self.input_dataset=input_dataset |
|
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|
1090 self.function=function |
|
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|
1091 self.output_names=output_names |
|
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1092 self.minibatch_mode=minibatch_mode |
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1093 DataSet.__init__(description,fieldtypes) |
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1094 self.valuesHStack = values_hstack if values_hstack else input_dataset.valuesHStack |
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1095 self.valuesVStack = values_vstack if values_vstack else input_dataset.valuesVStack |
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|
1096 |
|
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|
1097 def __len__(self): |
|
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1098 return len(self.input_dataset) |
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|
1099 |
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1100 def fieldnames(self): |
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1101 return self.output_names |
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1102 |
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1103 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
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1104 class ApplyFunctionIterator(object): |
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1105 def __init__(self,output_dataset): |
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1106 self.input_dataset=output_dataset.input_dataset |
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1107 self.output_dataset=output_dataset |
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1108 self.input_iterator=input_dataset.minibatches(minibatch_size=minibatch_size, |
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1109 n_batches=n_batches,offset=offset).__iter__() |
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1110 |
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1111 def __iter__(self): return self |
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1112 |
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1113 def next(self): |
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1114 function_inputs = self.input_iterator.next() |
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1115 all_output_names = self.output_dataset.output_names |
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1116 if self.output_dataset.minibatch_mode: |
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1117 function_outputs = self.output_dataset.function(function_inputs) |
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1118 else: |
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1119 input_examples = zip(*function_inputs) |
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1120 output_examples = [self.output_dataset.function(input_example) |
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1121 for input_example in input_examples] |
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1122 function_outputs = [self.output_dataset.valuesVStack(name,values) |
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1123 for name,values in zip(all_output_names, |
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1124 zip(*output_examples))] |
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1125 all_outputs = Example(all_output_names,function_outputs) |
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1126 if fieldnames==all_output_names: |
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1127 return all_outputs |
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1128 return Example(fieldnames,[all_outputs[name] for name in fieldnames]) |
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1129 |
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1130 return ApplyFunctionIterator(self.input_dataset,self) |
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1131 |
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1132 def __iter__(self): # only implemented for increased efficiency |
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1133 class ApplyFunctionSingleExampleIterator(object): |
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1134 def __init__(self,output_dataset): |
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1135 self.current=0 |
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1136 self.output_dataset=output_dataset |
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1137 self.input_iterator=output_dataset.input_dataset.__iter__() |
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1138 def __iter__(self): return self |
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1139 def next(self): |
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1140 function_inputs = self.input_iterator.next() |
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1141 if self.output_dataset.minibatch_mode: |
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1142 function_outputs = [output[0] for output in self.output_dataset.function(function_inputs)] |
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1143 else: |
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1144 function_outputs = self.output_dataset.function(function_inputs) |
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1145 return Example(self.output_dataset.output_names,function_outputs) |
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1146 return ApplyFunctionSingleExampleIterator(self) |
|
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1147 |
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1148 |
|
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1149 def supervised_learning_dataset(src_dataset,input_fields,target_fields,weight_field=None): |
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1150 """ |
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1151 Wraps an arbitrary DataSet into one for supervised learning tasks by forcing the |
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1152 user to define a set of fields as the 'input' field and a set of fields |
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1153 as the 'target' field. Optionally, a single weight_field can also be defined. |
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1154 """ |
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1155 args = ((input_fields,'input'),(output_fields,'target')) |
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1156 if weight_field: args+=(([weight_field],'weight')) |
|
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1157 return src_dataset.merge_fields(*args) |
|
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1158 |
|
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1159 |
|
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1160 |
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1161 |