Mercurial > pylearn
annotate dataset.py @ 105:8c0a1b11b007
bugfix, we keep all the line, but only a some columns
| author | Frederic Bastien <bastienf@iro.umontreal.ca> |
|---|---|
| date | Tue, 06 May 2008 16:34:48 -0400 |
| parents | a1740a99b81f |
| children | 8fa1ef2411a0 |
| 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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22 |
| 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 Each of these is documented below. All of these iterators are expected |
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37 to provide, in addition to the usual 'next()' method, a 'next_index()' method |
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38 which returns a non-negative integer pointing to the position of the next |
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39 example that will be returned by 'next()' (or of the first example in the |
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40 next minibatch returned). This is important because these iterators |
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41 can wrap around the dataset in order to do multiple passes through it, |
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42 in possibly unregular ways if the minibatch size is not a divisor of the |
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43 dataset length. |
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44 |
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45 To iterate over fields, one can do |
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46 - for field in dataset.fields(): |
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47 for field_value in field: # iterate over the values associated to that field for all the dataset examples |
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48 - for field in dataset(field1,field2,...).fields() to select a subset of fields |
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49 - for field in dataset.fields(field1,field2,...) to select a subset of fields |
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50 and each of these fields is iterable over the examples: |
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51 - for field_examples in dataset.fields(): |
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52 for example_value in field_examples: |
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53 ... |
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54 but when the dataset is a stream (unbounded length), it is not recommanded to do |
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55 such things because the underlying dataset may refuse to access the different fields in |
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56 an unsynchronized ways. Hence the fields() method is illegal for streams, by default. |
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57 The result of fields() is a DataSetFields object, which iterates over fields, |
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58 and whose elements are iterable over examples. A DataSetFields object can |
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59 be turned back into a DataSet with its examples() method:: |
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60 dataset2 = dataset1.fields().examples() |
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61 and dataset2 should behave exactly like dataset1 (in fact by default dataset2==dataset1). |
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62 |
| 16 | 63 Note: Fields are not mutually exclusive, i.e. two fields can overlap in their actual content. |
| 64 | |
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65 Note: The content of a field can be of any type. Field values can also be 'missing' |
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66 (e.g. to handle semi-supervised learning), and in the case of numeric (numpy array) |
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67 fields (i.e. an ArrayFieldsDataSet), NaN plays the role of a missing value. |
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68 What about non-numeric values? None. |
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69 |
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70 Dataset elements can be indexed and sub-datasets (with a subset |
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71 of examples) can be extracted. These operations are not supported |
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72 by default in the case of streams. |
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73 |
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74 - dataset[:n] returns a dataset with the n first examples. |
| 16 | 75 |
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76 - dataset[i1:i2:s] returns a dataset with the examples i1,i1+s,...i2-s. |
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77 |
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78 - dataset[i] returns an Example. |
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79 |
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80 - dataset[[i1,i2,...in]] returns a dataset with examples i1,i2,...in. |
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81 |
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82 - dataset[fieldname] an iterable over the values of the field fieldname across |
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83 the dataset (the iterable is obtained by default by calling valuesVStack |
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84 over the values for individual examples). |
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85 |
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86 - dataset.<property> returns the value of a property associated with |
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87 the name <property>. The following properties should be supported: |
| 41 | 88 - 'description': a textual description or name for the dataset |
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89 - 'fieldtypes': a list of types (one per field) |
| 78 | 90 A DataSet may have other attributes that it makes visible to other objects. These are |
| 91 used to store information that is not example-wise but global to the dataset. | |
| 92 The list of names of these attributes is given by the attribute_names() method. | |
| 41 | 93 |
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94 Datasets can be concatenated either vertically (increasing the length) or |
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95 horizontally (augmenting the set of fields), if they are compatible, using |
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96 the following operations (with the same basic semantics as numpy.hstack |
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97 and numpy.vstack): |
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98 |
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99 - dataset1 | dataset2 | dataset3 == dataset.hstack([dataset1,dataset2,dataset3]) |
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100 |
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101 creates a new dataset whose list of fields is the concatenation of the list of |
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102 fields of the argument datasets. This only works if they all have the same length. |
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103 |
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104 - dataset1 & dataset2 & dataset3 == dataset.vstack([dataset1,dataset2,dataset3]) |
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105 |
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106 creates a new dataset that concatenates the examples from the argument datasets |
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107 (and whose length is the sum of the length of the argument datasets). This only |
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108 works if they all have the same fields. |
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109 |
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110 According to the same logic, and viewing a DataSetFields object associated to |
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111 a DataSet as a kind of transpose of it, fields1 & fields2 concatenates fields of |
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112 a DataSetFields fields1 and fields2, and fields1 | fields2 concatenates their |
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113 examples. |
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114 |
| 41 | 115 A dataset can hold arbitrary key-value pairs that may be used to access meta-data |
| 116 or other properties of the dataset or associated with the dataset or the result | |
| 117 of a computation stored in a dataset. These can be accessed through the [key] syntax | |
| 118 when key is a string (or more specifically, neither an integer, a slice, nor a list). | |
| 78 | 119 |
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120 A DataSet sub-class should always redefine the following methods: |
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121 - __len__ if it is not a stream |
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122 - fieldNames |
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123 - minibatches_nowrap (called by DataSet.minibatches()) |
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124 - valuesHStack |
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125 - valuesVStack |
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126 For efficiency of implementation, a sub-class might also want to redefine |
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127 - hasFields |
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128 - __getitem__ may not be feasible with some streams |
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129 - __iter__ |
| 78 | 130 A sub-class should also append attributes to self._attribute_names |
| 131 (the default value returned by attributeNames()). | |
| 132 By convention, attributes not in attributeNames() should have a name | |
| 133 starting with an underscore. | |
| 134 @todo enforce/test that convention! | |
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135 """ |
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136 |
| 83 | 137 numpy_vstack = lambda fieldname,values: numpy.vstack(values) |
| 138 numpy_hstack = lambda fieldnames,values: numpy.hstack(values) | |
|
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139 |
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140 def __init__(self,description=None,fieldtypes=None): |
| 41 | 141 if description is None: |
| 142 # by default return "<DataSetType>(<SuperClass1>,<SuperClass2>,...)" | |
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143 description = type(self).__name__ + " ( " + join([x.__name__ for x in type(self).__bases__]) + " )" |
| 41 | 144 self.description=description |
| 60 | 145 self.fieldtypes=fieldtypes |
| 78 | 146 self._attribute_names = ["description"] |
| 147 if fieldtypes: | |
| 148 self._attribute_names.append("fieldtypes") | |
| 149 | |
| 150 def attributeNames(self): return self._attribute_names | |
| 151 | |
| 152 def setAttributes(self,attribute_names,attribute_values): | |
| 153 for name,value in zip(attribute_names,attribute_values): | |
| 154 self.__setattr__(name,value) | |
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155 |
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156 class MinibatchToSingleExampleIterator(object): |
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157 """ |
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158 Converts the result of minibatch iterator with minibatch_size==1 into |
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159 single-example values in the result. Therefore the result of |
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160 iterating on the dataset itself gives a sequence of single examples |
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161 (whereas the result of iterating over minibatches gives in each |
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162 Example field an iterable object over the individual examples in |
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163 the minibatch). |
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164 """ |
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165 def __init__(self, minibatch_iterator): |
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166 self.minibatch_iterator = minibatch_iterator |
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167 self.minibatch = None |
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168 def __iter__(self): #makes for loop work |
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169 return self |
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170 def next(self): |
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171 size1_minibatch = self.minibatch_iterator.next() |
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172 if not self.minibatch: |
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173 self.minibatch = Example(size1_minibatch.keys(),[value[0] for value in size1_minibatch.values()]) |
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174 else: |
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175 self.minibatch._values = [value[0] for value in size1_minibatch.values()] |
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176 return self.minibatch |
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177 |
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178 def next_index(self): |
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179 return self.minibatch_iterator.next_index() |
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180 |
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181 def __iter__(self): |
| 16 | 182 """Supports the syntax "for i in dataset: ..." |
|
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183 |
| 16 | 184 Using this syntax, "i" will be an Example instance (or equivalent) with |
| 185 all the fields of DataSet self. Every field of "i" will give access to | |
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186 a field of a single example. Fields should be accessible via |
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187 i["fielname"] or i[3] (in the order defined by the elements of the |
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188 Example returned by this iterator), but the derived class is free |
|
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189 to accept any type of identifier, and add extra functionality to the iterator. |
| 16 | 190 |
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191 The default implementation calls the minibatches iterator and extracts the first example of each field. |
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192 """ |
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193 return DataSet.MinibatchToSingleExampleIterator(self.minibatches(None, minibatch_size = 1)) |
|
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194 |
|
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195 |
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196 class MinibatchWrapAroundIterator(object): |
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197 """ |
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198 An iterator for minibatches that handles the case where we need to wrap around the |
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199 dataset because n_batches*minibatch_size > len(dataset). It is constructed from |
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200 a dataset that provides a minibatch iterator that does not need to handle that problem. |
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201 This class is a utility for dataset subclass writers, so that they do not have to handle |
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202 this issue multiple times, nor check that fieldnames are valid, nor handle the |
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203 empty fieldnames (meaning 'use all the fields'). |
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204 """ |
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205 def __init__(self,dataset,fieldnames,minibatch_size,n_batches,offset): |
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206 self.dataset=dataset |
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207 self.fieldnames=fieldnames |
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208 self.minibatch_size=minibatch_size |
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209 self.n_batches=n_batches |
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210 self.n_batches_done=0 |
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211 self.next_row=offset |
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212 self.offset=offset |
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213 self.L=len(dataset) |
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214 assert offset+minibatch_size<=self.L |
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215 ds_nbatches = (self.L-self.next_row)/self.minibatch_size |
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216 if n_batches is not None: |
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217 ds_nbatches = min(n_batches,ds_nbatches) |
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218 if fieldnames: |
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219 assert dataset.hasFields(*fieldnames) |
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220 else: |
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221 self.fieldnames=dataset.fieldNames() |
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222 self.iterator = self.dataset.minibatches_nowrap(self.fieldnames,self.minibatch_size, |
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223 ds_nbatches,self.next_row) |
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224 |
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225 def __iter__(self): |
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226 return self |
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227 |
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228 def next_index(self): |
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229 return self.next_row |
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230 |
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231 def next(self): |
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232 if self.n_batches and self.n_batches_done==self.n_batches: |
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233 raise StopIteration |
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234 elif not self.n_batches and self.next_row ==self.L: |
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235 raise StopIteration |
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236 upper = self.next_row+self.minibatch_size |
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237 if upper <=self.L: |
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238 minibatch = self.iterator.next() |
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239 else: |
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240 if not self.n_batches: |
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241 upper=min(upper, self.L) |
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242 # if their is not a fixed number of batch, we continue to the end of the dataset. |
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243 # this can create a minibatch that is smaller then the minibatch_size |
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244 assert (self.L-self.next_row)<=self.minibatch_size |
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245 minibatch = self.dataset.minibatches_nowrap(self.fieldnames,self.L-self.next_row,1,self.next_row).next() |
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246 else: |
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247 # we must concatenate (vstack) the bottom and top parts of our minibatch |
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248 # first get the beginning of our minibatch (top of dataset) |
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249 first_part = self.dataset.minibatches_nowrap(self.fieldnames,self.L-self.next_row,1,self.next_row).next() |
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250 second_part = self.dataset.minibatches_nowrap(self.fieldnames,upper-self.L,1,0).next() |
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251 minibatch = Example(self.fieldnames, |
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252 [self.dataset.valuesVStack(name,[first_part[name],second_part[name]]) |
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253 for name in self.fieldnames]) |
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254 self.next_row=upper |
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255 self.n_batches_done+=1 |
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256 if upper >= self.L and self.n_batches: |
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257 self.next_row -= self.L |
|
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258 ds_nbatches = (self.L-self.next_row)/self.minibatch_size |
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259 if self.n_batches is not None: |
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260 ds_nbatches = min(self.n_batches,ds_nbatches) |
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261 self.iterator = self.dataset.minibatches_nowrap(self.fieldnames,self.minibatch_size, |
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262 ds_nbatches,self.next_row) |
|
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263 return DataSetFields(MinibatchDataSet(minibatch,self.dataset.valuesVStack, |
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264 self.dataset.valuesHStack), |
|
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265 minibatch.keys()) |
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266 |
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267 |
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268 minibatches_fieldnames = None |
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269 minibatches_minibatch_size = 1 |
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270 minibatches_n_batches = None |
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271 def minibatches(self, |
|
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272 fieldnames = minibatches_fieldnames, |
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273 minibatch_size = minibatches_minibatch_size, |
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274 n_batches = minibatches_n_batches, |
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275 offset = 0): |
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276 """ |
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277 Return an iterator that supports three forms of syntax: |
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278 |
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279 for i in dataset.minibatches(None,**kwargs): ... |
| 16 | 280 |
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281 for i in dataset.minibatches([f1, f2, f3],**kwargs): ... |
| 16 | 282 |
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283 for i1, i2, i3 in dataset.minibatches([f1, f2, f3],**kwargs): ... |
| 16 | 284 |
|
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285 Using the first two syntaxes, "i" will be an indexable object, such as a list, |
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286 tuple, or Example instance. In both cases, i[k] is a list-like container |
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287 of a batch of current examples. In the second case, i[0] is |
|
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288 list-like container of the f1 field of a batch current examples, i[1] is |
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289 a list-like container of the f2 field, etc. |
|
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290 |
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291 Using the first syntax, all the fields will be returned in "i". |
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292 Using the third syntax, i1, i2, i3 will be list-like containers of the |
|
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293 f1, f2, and f3 fields of a batch of examples on each loop iteration. |
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294 |
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295 The minibatches iterator is expected to return upon each call to next() |
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296 a DataSetFields object, which is a LookupList (indexed by the field names) whose |
| 80 | 297 elements are iterable and indexable over the minibatch examples, and which keeps a pointer to |
|
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298 a sub-dataset that can be used to iterate over the individual examples |
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299 in the minibatch. Hence a minibatch can be converted back to a regular |
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300 dataset or its fields can be looked at individually (and possibly iterated over). |
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301 |
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302 PARAMETERS |
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303 - fieldnames (list of any type, default None): |
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304 The loop variables i1, i2, i3 (in the example above) should contain the |
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305 f1, f2, and f3 fields of the current batch of examples. If None, the |
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306 derived class can choose a default, e.g. all fields. |
| 16 | 307 |
|
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308 - minibatch_size (integer, default 1) |
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309 On every iteration, the variables i1, i2, i3 will have |
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310 exactly minibatch_size elements. e.g. len(i1) == minibatch_size |
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311 |
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312 - n_batches (integer, default None) |
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313 The iterator will loop exactly this many times, and then stop. If None, |
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314 the derived class can choose a default. If (-1), then the returned |
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315 iterator should support looping indefinitely. |
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316 |
|
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317 - offset (integer, default 0) |
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318 The iterator will start at example 'offset' in the dataset, rather than the default. |
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319 |
|
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320 Note: A list-like container is something like a tuple, list, numpy.ndarray or |
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321 any other object that supports integer indexing and slicing. |
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322 |
|
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323 """ |
|
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324 return DataSet.MinibatchWrapAroundIterator(self,fieldnames,minibatch_size,n_batches,offset) |
|
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325 |
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326 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
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327 """ |
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328 This is the minibatches iterator generator that sub-classes must define. |
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329 It does not need to worry about wrapping around multiple times across the dataset, |
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330 as this is handled by MinibatchWrapAroundIterator when DataSet.minibatches() is called. |
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331 The next() method of the returned iterator does not even need to worry about |
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332 the termination condition (as StopIteration will be raised by DataSet.minibatches |
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333 before an improper call to minibatches_nowrap's next() is made). |
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334 That next() method can assert that its next row will always be within [0,len(dataset)). |
|
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335 The iterator returned by minibatches_nowrap does not need to implement |
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336 a next_index() method either, as this will be provided by MinibatchWrapAroundIterator. |
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337 """ |
|
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338 raise AbstractFunction() |
|
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339 |
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340 def __len__(self): |
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341 """ |
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342 len(dataset) returns the number of examples in the dataset. |
|
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343 By default, a DataSet is a 'stream', i.e. it has an unbounded length (sys.maxint). |
|
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344 Sub-classes which implement finite-length datasets should redefine this method. |
|
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345 Some methods only make sense for finite-length datasets. |
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346 """ |
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347 return sys.maxint |
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348 |
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349 def is_unbounded(self): |
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350 """ |
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351 Tests whether a dataset is unbounded (e.g. a stream). |
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352 """ |
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353 return len(self)==sys.maxint |
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354 |
|
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355 def hasFields(self,*fieldnames): |
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356 """ |
|
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357 Return true if the given field name (or field names, if multiple arguments are |
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358 given) is recognized by the DataSet (i.e. can be used as a field name in one |
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359 of the iterators). |
|
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360 |
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361 The default implementation may be inefficient (O(# fields in dataset)), as it calls the fieldNames() |
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362 method. Many datasets may store their field names in a dictionary, which would allow more efficiency. |
|
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363 """ |
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364 return len(unique_elements_list_intersection(fieldnames,self.fieldNames()))>0 |
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365 |
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366 def fieldNames(self): |
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367 """ |
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368 Return the list of field names that are supported by the iterators, |
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369 and for which hasFields(fieldname) would return True. |
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370 """ |
|
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371 raise AbstractFunction() |
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372 |
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373 def __call__(self,*fieldnames): |
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374 """ |
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375 Return a dataset that sees only the fields whose name are specified. |
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376 """ |
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377 assert self.hasFields(*fieldnames) |
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378 return self.fields(*fieldnames).examples() |
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379 |
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380 def fields(self,*fieldnames): |
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381 """ |
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382 Return a DataSetFields object associated with this dataset. |
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383 """ |
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384 return DataSetFields(self,fieldnames) |
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385 |
|
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386 def __getitem__(self,i): |
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387 """ |
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388 dataset[i] returns the (i+1)-th example of the dataset. |
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389 dataset[i:j] returns the subdataset with examples i,i+1,...,j-1. |
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390 dataset[i:j:s] returns the subdataset with examples i,i+2,i+4...,j-2. |
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391 dataset[[i1,i2,..,in]] returns the subdataset with examples i1,i2,...,in. |
| 41 | 392 dataset['key'] returns a property associated with the given 'key' string. |
| 393 If 'key' is a fieldname, then the VStacked field values (iterable over | |
| 394 field values) for that field is returned. Other keys may be supported | |
| 395 by different dataset subclasses. The following key names are encouraged: | |
| 396 - 'description': a textual description or name for the dataset | |
| 397 - '<fieldname>.type': a type name or value for a given <fieldname> | |
|
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398 |
| 39 | 399 Note that some stream datasets may be unable to implement random access, i.e. |
| 400 arbitrary slicing/indexing | |
|
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401 because they can only iterate through examples one or a minibatch at a time |
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402 and do not actually store or keep past (or future) examples. |
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403 |
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404 The default implementation of getitem uses the minibatches iterator |
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405 to obtain one example, one slice, or a list of examples. It may not |
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406 always be the most efficient way to obtain the result, especially if |
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407 the data are actually stored in a memory array. |
|
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408 """ |
| 41 | 409 # check for an index |
|
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410 if type(i) is int: |
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411 return DataSet.MinibatchToSingleExampleIterator( |
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412 self.minibatches(minibatch_size=1,n_batches=1,offset=i)).next() |
| 41 | 413 rows=None |
| 414 # or a slice | |
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415 if type(i) is slice: |
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416 if not i.start: i.start=0 |
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417 if not i.step: i.step=1 |
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418 if i.step is 1: |
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419 return self.minibatches(minibatch_size=i.stop-i.start,n_batches=1,offset=i.start).next().examples() |
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420 rows = range(i.start,i.stop,i.step) |
| 41 | 421 # or a list of indices |
| 422 elif type(i) is list: | |
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423 rows = i |
| 41 | 424 if rows is not None: |
|
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425 examples = [self[row] for row in rows] |
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426 fields_values = zip(*examples) |
|
45
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427 return MinibatchDataSet( |
| 41 | 428 Example(self.fieldNames(),[ self.valuesVStack(fieldname,field_values) |
| 429 for fieldname,field_values | |
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430 in zip(self.fieldNames(),fields_values)]), |
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431 self.valuesVStack,self.valuesHStack) |
| 41 | 432 # else check for a fieldname |
| 433 if self.hasFields(i): | |
| 434 return self.minibatches(fieldnames=[i],minibatch_size=len(self),n_batches=1,offset=0).next()[0] | |
| 435 # else we are trying to access a property of the dataset | |
| 436 assert i in self.__dict__ # else it means we are trying to access a non-existing property | |
| 437 return self.__dict__[i] | |
|
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438 |
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439 def valuesHStack(self,fieldnames,fieldvalues): |
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440 """ |
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441 Return a value that corresponds to concatenating (horizontally) several field values. |
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442 This can be useful to merge some fields. The implementation of this operation is likely |
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443 to involve a copy of the original values. When the values are numpy arrays, the |
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444 result should be numpy.hstack(values). If it makes sense, this operation should |
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445 work as well when each value corresponds to multiple examples in a minibatch |
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446 e.g. if each value is a Ni-vector and a minibatch of length L is a LxNi matrix, |
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447 then the result should be a Lx(N1+N2+..) matrix equal to numpy.hstack(values). |
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448 The default is to use numpy.hstack for numpy.ndarray values, and a list |
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449 pointing to the original values for other data types. |
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450 """ |
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451 all_numpy=True |
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452 for value in fieldvalues: |
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453 if not type(value) is numpy.ndarray: |
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454 all_numpy=False |
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455 if all_numpy: |
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456 return numpy.hstack(fieldvalues) |
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457 # the default implementation of horizontal stacking is to put values in a list |
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458 return fieldvalues |
|
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459 |
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460 |
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461 def valuesVStack(self,fieldname,values): |
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462 """ |
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463 Return a value that corresponds to concatenating (vertically) several values of the |
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464 same field. This can be important to build a minibatch out of individual examples. This |
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465 is likely to involve a copy of the original values. When the values are numpy arrays, the |
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466 result should be numpy.vstack(values). |
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467 The default is to use numpy.vstack for numpy.ndarray values, and a list |
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468 pointing to the original values for other data types. |
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469 """ |
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470 all_numpy=True |
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471 for value in values: |
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472 if not type(value) is numpy.ndarray: |
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473 all_numpy=False |
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474 if all_numpy: |
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475 return numpy.vstack(values) |
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476 # the default implementation of vertical stacking is to put values in a list |
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477 return values |
|
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478 |
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479 def __or__(self,other): |
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480 """ |
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481 dataset1 | dataset2 returns a dataset whose list of fields is the concatenation of the list of |
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482 fields of the argument datasets. This only works if they all have the same length. |
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483 """ |
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484 return HStackedDataSet(self,other) |
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485 |
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486 def __and__(self,other): |
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487 """ |
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488 dataset1 & dataset2 is a dataset that concatenates the examples from the argument datasets |
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489 (and whose length is the sum of the length of the argument datasets). This only |
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490 works if they all have the same fields. |
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491 """ |
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492 return VStackedDataSet(self,other) |
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493 |
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494 def hstack(datasets): |
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495 """ |
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496 hstack(dataset1,dataset2,...) returns dataset1 | datataset2 | ... |
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497 which is a dataset whose fields list is the concatenation of the fields |
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498 of the individual datasets. |
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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 HStackedDataSet(datasets) |
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504 |
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505 def vstack(datasets): |
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506 """ |
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507 vstack(dataset1,dataset2,...) returns dataset1 & datataset2 & ... |
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508 which is a dataset which iterates first over the examples of dataset1, then |
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509 over those of dataset2, etc. |
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510 """ |
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511 assert len(datasets)>0 |
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512 if len(datasets)==1: |
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513 return datasets[0] |
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514 return VStackedDataSet(datasets) |
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515 |
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516 class FieldsSubsetDataSet(DataSet): |
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517 """ |
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518 A sub-class of DataSet that selects a subset of the fields. |
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519 """ |
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520 def __init__(self,src,fieldnames): |
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521 self.src=src |
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522 self.fieldnames=fieldnames |
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523 assert src.hasFields(*fieldnames) |
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524 self.valuesHStack = src.valuesHStack |
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525 self.valuesVStack = src.valuesVStack |
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526 |
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527 def __len__(self): return len(self.src) |
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528 |
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529 def fieldNames(self): |
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530 return self.fieldnames |
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531 |
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532 def __iter__(self): |
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533 class FieldsSubsetIterator(object): |
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534 def __init__(self,ds): |
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535 self.ds=ds |
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536 self.src_iter=ds.src.__iter__() |
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537 self.example=None |
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538 def __iter__(self): return self |
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539 def next(self): |
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540 complete_example = self.src_iter.next() |
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541 if self.example: |
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542 self.example._values=[complete_example[field] |
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543 for field in self.ds.fieldnames] |
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544 else: |
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545 self.example=Example(self.ds.fieldnames, |
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546 [complete_example[field] for field in self.ds.fieldnames]) |
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547 return self.example |
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548 return FieldsSubsetIterator(self) |
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549 |
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550 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
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551 assert self.hasFields(*fieldnames) |
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552 return self.src.minibatches_nowrap(fieldnames,minibatch_size,n_batches,offset) |
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553 def __getitem__(self,i): |
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554 return FieldsSubsetDataSet(self.src[i],self.fieldnames) |
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555 |
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|
556 |
|
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557 class DataSetFields(LookupList): |
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558 """ |
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559 Although a DataSet iterates over examples (like rows of a matrix), an associated |
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560 DataSetFields iterates over fields (like columns of a matrix), and can be understood |
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561 as a transpose of the associated dataset. |
|
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|
562 |
|
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563 To iterate over fields, one can do |
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564 * for fields in dataset.fields() |
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565 * for fields in dataset(field1,field2,...).fields() to select a subset of fields |
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566 * for fields in dataset.fields(field1,field2,...) to select a subset of fields |
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567 and each of these fields is iterable over the examples: |
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568 * for field_examples in dataset.fields(): |
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569 for example_value in field_examples: |
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570 ... |
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571 but when the dataset is a stream (unbounded length), it is not recommanded to do |
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572 such things because the underlying dataset may refuse to access the different fields in |
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573 an unsynchronized ways. Hence the fields() method is illegal for streams, by default. |
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574 The result of fields() is a DataSetFields object, which iterates over fields, |
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575 and whose elements are iterable over examples. A DataSetFields object can |
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576 be turned back into a DataSet with its examples() method: |
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577 dataset2 = dataset1.fields().examples() |
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578 and dataset2 should behave exactly like dataset1 (in fact by default dataset2==dataset1). |
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579 |
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|
580 DataSetFields can be concatenated vertically or horizontally. To be consistent with |
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581 the syntax used for DataSets, the | concatenates the fields and the & concatenates |
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582 the examples. |
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583 """ |
|
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584 def __init__(self,dataset,fieldnames): |
|
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585 original_dataset=dataset |
|
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586 if not fieldnames: |
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587 fieldnames=dataset.fieldNames() |
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588 elif not fieldnames==dataset.fieldNames(): |
|
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589 dataset = FieldsSubsetDataSet(dataset,fieldnames) |
|
37
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590 assert dataset.hasFields(*fieldnames) |
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591 self.dataset=dataset |
|
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592 |
|
64
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593 if isinstance(dataset,MinibatchDataSet): |
|
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594 LookupList.__init__(self,fieldnames,list(dataset._fields)) |
|
65
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595 elif isinstance(original_dataset,MinibatchDataSet): |
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596 LookupList.__init__(self,fieldnames, |
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597 [original_dataset._fields[field] |
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598 for field in fieldnames]) |
|
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599 else: |
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600 minibatch_iterator = dataset.minibatches(fieldnames, |
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601 minibatch_size=len(dataset), |
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602 n_batches=1) |
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603 minibatch=minibatch_iterator.next() |
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604 LookupList.__init__(self,fieldnames,minibatch) |
|
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605 |
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606 def examples(self): |
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607 return self.dataset |
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608 |
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609 def __or__(self,other): |
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610 """ |
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611 fields1 | fields2 is a DataSetFields that whose list of examples is the concatenation |
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612 of the list of examples of DataSetFields fields1 and fields2. |
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613 """ |
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614 return (self.examples() + other.examples()).fields() |
|
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615 |
|
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616 def __and__(self,other): |
|
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617 """ |
|
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618 fields1 + fields2 is a DataSetFields that whose list of fields is the concatenation |
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619 of the fields of DataSetFields fields1 and fields2. |
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620 """ |
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621 return (self.examples() | other.examples()).fields() |
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622 |
|
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623 |
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624 class MinibatchDataSet(DataSet): |
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625 """ |
| 85 | 626 Turn a LookupList of same-length (iterable) fields into an example-iterable dataset. |
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627 Each element of the lookup-list should be an iterable and sliceable, all of the same length. |
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628 """ |
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629 def __init__(self,fields_lookuplist,values_vstack=DataSet().valuesVStack, |
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630 values_hstack=DataSet().valuesHStack): |
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631 """ |
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632 The user can (and generally should) also provide values_vstack(fieldname,fieldvalues) |
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633 and a values_hstack(fieldnames,fieldvalues) functions behaving with the same |
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634 semantics as the DataSet methods of the same name (but without the self argument). |
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635 """ |
|
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636 self._fields=fields_lookuplist |
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637 assert len(fields_lookuplist)>0 |
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638 self.length=len(fields_lookuplist[0]) |
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639 for field in fields_lookuplist[1:]: |
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640 assert self.length==len(field) |
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641 self.values_vstack=values_vstack |
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642 self.values_hstack=values_hstack |
|
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643 |
|
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644 def __len__(self): |
|
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645 return self.length |
|
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646 |
|
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647 def __getitem__(self,i): |
| 80 | 648 if type(i) in (slice,list): |
|
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649 return DataSetFields(MinibatchDataSet( |
| 80 | 650 Example(self._fields.keys(),[field[i] for field in self._fields])),self.fieldNames()) |
| 651 if type(i) is int: | |
| 85 | 652 return Example(self._fields.keys(),[field[i] for field in self._fields]) |
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653 if self.hasFields(i): |
|
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654 return self._fields[i] |
|
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655 assert i in self.__dict__ # else it means we are trying to access a non-existing property |
|
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656 return self.__dict__[i] |
|
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657 |
|
29
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658 def fieldNames(self): |
|
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659 return self._fields.keys() |
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660 |
|
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661 def hasFields(self,*fieldnames): |
|
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662 for fieldname in fieldnames: |
|
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663 if fieldname not in self._fields.keys(): |
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664 return False |
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665 return True |
|
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666 |
|
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667 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
|
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668 class Iterator(object): |
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669 def __init__(self,ds): |
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670 self.ds=ds |
|
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671 self.next_example=offset |
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672 assert minibatch_size > 0 |
| 41 | 673 if offset+minibatch_size > ds.length: |
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674 raise NotImplementedError() |
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675 def __iter__(self): |
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676 return self |
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677 def next(self): |
|
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678 upper = self.next_example+minibatch_size |
|
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679 assert upper<=self.ds.length |
|
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680 minibatch = Example(self.ds._fields.keys(), |
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681 [field[self.next_example:upper] |
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682 for field in self.ds._fields]) |
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683 self.next_example+=minibatch_size |
|
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684 return minibatch |
|
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685 |
|
40
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686 return Iterator(self) |
|
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687 |
|
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688 def valuesVStack(self,fieldname,fieldvalues): |
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689 return self.values_vstack(fieldname,fieldvalues) |
|
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690 |
|
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691 def valuesHStack(self,fieldnames,fieldvalues): |
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692 return self.values_hstack(fieldnames,fieldvalues) |
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693 |
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694 class HStackedDataSet(DataSet): |
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695 """ |
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696 A DataSet that wraps several datasets and shows a view that includes all their fields, |
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697 i.e. whose list of fields is the concatenation of their lists of fields. |
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698 |
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699 If a field name is found in more than one of the datasets, then either an error is |
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700 raised or the fields are renamed (either by prefixing the __name__ attribute |
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701 of the dataset + ".", if it exists, or by suffixing the dataset index in the argument list). |
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702 |
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703 TODO: automatically detect a chain of stacked datasets due to A | B | C | D ... |
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704 """ |
| 41 | 705 def __init__(self,datasets,accept_nonunique_names=False,description=None,field_types=None): |
| 706 DataSet.__init__(self,description,field_types) | |
|
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707 self.datasets=datasets |
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708 self.accept_nonunique_names=accept_nonunique_names |
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709 self.fieldname2dataset={} |
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710 |
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711 def rename_field(fieldname,dataset,i): |
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712 if hasattr(dataset,"__name__"): |
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713 return dataset.__name__ + "." + fieldname |
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|
714 return fieldname+"."+str(i) |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
715 |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
716 # make sure all datasets have the same length and unique field names |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
717 self.length=None |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
718 names_to_change=[] |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
719 for i in xrange(len(datasets)): |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
720 dataset = datasets[i] |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
721 length=len(dataset) |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
722 if self.length: |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
723 assert self.length==length |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
724 else: |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
725 self.length=length |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
726 for fieldname in dataset.fieldNames(): |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
727 if fieldname in self.fieldname2dataset: # name conflict! |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
728 if accept_nonunique_names: |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
729 fieldname=rename_field(fieldname,dataset,i) |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
730 names2change.append((fieldname,i)) |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
731 else: |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
732 raise ValueError("Incompatible datasets: non-unique field name = "+fieldname) |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
733 self.fieldname2dataset[fieldname]=i |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
734 for fieldname,i in names_to_change: |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
735 del self.fieldname2dataset[fieldname] |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
736 self.fieldname2dataset[rename_field(fieldname,self.datasets[i],i)]=i |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
737 |
|
37
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
738 def hasFields(self,*fieldnames): |
|
36
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
739 for fieldname in fieldnames: |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
740 if not fieldname in self.fieldname2dataset: |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
741 return False |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
742 return True |
|
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Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
743 |
|
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Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
744 def fieldNames(self): |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
745 return self.fieldname2dataset.keys() |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
746 |
| 41 | 747 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
|
36
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
748 |
|
44
5a85fda9b19b
Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents:
43
diff
changeset
|
749 class HStackedIterator(object): |
|
36
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
750 def __init__(self,hsds,iterators): |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
751 self.hsds=hsds |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
752 self.iterators=iterators |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
753 def __iter__(self): |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
754 return self |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
755 def next(self): |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
756 # concatenate all the fields of the minibatches |
|
73
69f97aad3faf
Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents:
72
diff
changeset
|
757 return reduce(LookupList.__add__,[iterator.next() for iterator in self.iterators]) |
|
36
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
758 |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
759 assert self.hasfields(fieldnames) |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
760 # find out which underlying datasets are necessary to service the required fields |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
761 # and construct corresponding minibatch iterators |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
762 if fieldnames: |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
763 datasets=set([]) |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
764 fields_in_dataset=dict([(dataset,[]) for dataset in datasets]) |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
765 for fieldname in fieldnames: |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
766 dataset=self.datasets[self.fieldnames2dataset[fieldname]] |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
767 datasets.add(dataset) |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
768 fields_in_dataset[dataset].append(fieldname) |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
769 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
|
770 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
|
771 for dataset in datasets] |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
772 else: |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
773 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
|
774 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
|
775 return HStackedIterator(self,iterators) |
|
36
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
776 |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
777 |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
778 def valuesVStack(self,fieldname,fieldvalues): |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
779 return self.datasets[self.fieldname2dataset[fieldname]].valuesVStack(fieldname,fieldvalues) |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
780 |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
781 def valuesHStack(self,fieldnames,fieldvalues): |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
782 """ |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
783 We will use the sub-dataset associated with the first fieldname in the fieldnames list |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
784 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
|
785 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
|
786 all the fieldnames are of the same sub-dataset. |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
787 """ |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
788 return self.datasets[self.fieldname2dataset[fieldnames[0]]].valuesHStack(fieldnames,fieldvalues) |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
789 |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
790 class VStackedDataSet(DataSet): |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
791 """ |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
792 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
|
793 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
|
794 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
|
795 |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
796 TODO: automatically detect a chain of stacked datasets due to A + B + C + D ... |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
797 """ |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
798 def __init__(self,datasets): |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
799 self.datasets=datasets |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
800 self.length=0 |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
801 self.index2dataset={} |
|
37
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
802 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
|
803 fieldnames = datasets[-1].fieldNames() |
|
38
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
804 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
|
805 # 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
|
806 # 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
|
807 for dataset,k in enumerate(datasets[0:-1]): |
|
48
b6730f9a336d
Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents:
46
diff
changeset
|
808 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
|
809 L=len(dataset) |
|
36
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
810 for i in xrange(L): |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
811 self.index2dataset[self.length+i]=k |
|
38
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
812 self.datasets_start_row.append(self.length) |
|
36
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
813 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
|
814 assert dataset.fieldNames()==fieldnames |
|
38
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
815 self.datasets_start_row.append(self.length) |
|
36
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
816 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
|
817 # 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
|
818 # 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
|
819 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
|
820 # 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
|
821 # TODO |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
822 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
|
823 |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
824 def __len__(self): |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
825 return self.length |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
826 |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
827 def fieldNames(self): |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
828 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
|
829 |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
830 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
|
831 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
|
832 |
|
38
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
833 def locate_row(self,row): |
|
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
834 """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
|
835 dataset_index = self.index2dataset[row] |
|
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
836 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
|
837 return dataset_index, row_within_dataset |
|
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
838 |
| 41 | 839 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
|
840 |
|
5a85fda9b19b
Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents:
43
diff
changeset
|
841 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
|
842 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
|
843 self.vsds=vsds |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
844 self.next_row=offset |
|
38
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
845 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
|
846 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
|
847 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
|
848 |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
849 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
|
850 L=len(dataset) |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
851 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
|
852 if batches_left is not None: |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
853 ds_nbatches = max(batches_left,ds_nbatches) |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
854 if minibatch_size>L: |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
855 ds_minibatch_size=L |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
856 n_left_in_mb=minibatch_size-L |
|
38
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
857 ds_nbatches=1 |
|
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
858 else: |
|
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
859 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
|
860 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
|
861 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
|
862 |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
863 def move_to_next_dataset(self): |
|
38
d637ad8f7352
Finished first untested version of VStackedDataset
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parents:
37
diff
changeset
|
864 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
|
865 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
|
866 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
|
867 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
|
868 else: |
|
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
869 self.next_dataset_index +=1 |
|
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
870 if self.next_dataset_index==len(self.vsds.datasets): |
|
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
871 self.next_dataset_index = 0 |
|
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
872 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
|
873 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
|
874 |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
875 def __iter__(self): |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
876 return self |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
877 |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
878 def next(self): |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
879 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
|
880 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
|
881 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
|
882 extra_mb = [] |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
883 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
|
884 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
|
885 extra_mb.append(self.next_iterator.next()) |
|
73
69f97aad3faf
Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents:
72
diff
changeset
|
886 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
|
887 [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
|
888 [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
|
889 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
|
890 |
|
37
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
891 self.next_row+=minibatch_size |
|
38
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
892 self.next_dataset_row+=minibatch_size |
|
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
893 if self.next_row+minibatch_size>len(dataset): |
|
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
894 self.move_to_next_dataset() |
|
44
5a85fda9b19b
Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents:
43
diff
changeset
|
895 return examples |
|
5a85fda9b19b
Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents:
43
diff
changeset
|
896 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
|
897 |
| 41 | 898 class ArrayFieldsDataSet(DataSet): |
| 899 """ | |
| 900 Virtual super-class of datasets whose field values are numpy array, | |
| 901 thus defining valuesHStack and valuesVStack for sub-classes. | |
| 902 """ | |
| 903 def __init__(self,description=None,field_types=None): | |
| 904 DataSet.__init__(self,description,field_types) | |
| 905 def valuesHStack(self,fieldnames,fieldvalues): | |
| 906 """Concatenate field values horizontally, e.g. two vectors | |
| 907 become a longer vector, two matrices become a wider matrix, etc.""" | |
| 908 return numpy.hstack(fieldvalues) | |
| 909 def valuesVStack(self,fieldname,values): | |
| 910 """Concatenate field values vertically, e.g. two vectors | |
| 911 become a two-row matrix, two matrices become a longer matrix, etc.""" | |
| 912 return numpy.vstack(values) | |
| 913 | |
| 914 class ArrayDataSet(ArrayFieldsDataSet): | |
| 915 """ | |
| 916 An ArrayDataSet stores the fields as groups of columns in a numpy tensor, | |
| 917 whose first axis iterates over examples, second axis determines fields. | |
| 918 If the underlying array is N-dimensional (has N axes), then the field | |
| 919 values are (N-2)-dimensional objects (i.e. ordinary numbers if N=2). | |
| 920 """ | |
| 921 | |
|
42
9b68774fcc6b
Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents:
41
diff
changeset
|
922 def __init__(self, data_array, fields_columns): |
|
55
66619ce44497
Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
48
diff
changeset
|
923 """ |
|
66619ce44497
Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
48
diff
changeset
|
924 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
|
925 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
|
926 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
|
927 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
|
928 """ |
| 41 | 929 self.data=data_array |
|
42
9b68774fcc6b
Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents:
41
diff
changeset
|
930 self.fields_columns=fields_columns |
| 41 | 931 |
| 932 # check consistency and complete slices definitions | |
|
42
9b68774fcc6b
Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents:
41
diff
changeset
|
933 for fieldname, fieldcolumns in self.fields_columns.items(): |
| 41 | 934 if type(fieldcolumns) is int: |
| 935 assert fieldcolumns>=0 and fieldcolumns<data_array.shape[1] | |
|
99
a8da709eb6a9
in ArrayDataSet.__init__ if a columns is an index, we change it to be a list that containt only this index. This way, we remove the special case where the columns is an index for all subsequent call.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
98
diff
changeset
|
936 self.fields_columns[fieldname]=[fieldcolumns] |
| 41 | 937 elif type(fieldcolumns) is slice: |
| 938 start,step=None,None | |
| 939 if not fieldcolumns.start: | |
| 940 start=0 | |
| 941 if not fieldcolumns.step: | |
| 942 step=1 | |
| 943 if start or step: | |
|
42
9b68774fcc6b
Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents:
41
diff
changeset
|
944 self.fields_columns[fieldname]=slice(start,fieldcolumns.stop,step) |
| 41 | 945 elif hasattr(fieldcolumns,"__iter__"): # something like a list |
| 946 for i in fieldcolumns: | |
| 947 assert i>=0 and i<data_array.shape[1] | |
| 948 | |
|
42
9b68774fcc6b
Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents:
41
diff
changeset
|
949 def fieldNames(self): |
|
9b68774fcc6b
Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents:
41
diff
changeset
|
950 return self.fields_columns.keys() |
| 41 | 951 |
|
42
9b68774fcc6b
Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents:
41
diff
changeset
|
952 def __len__(self): |
|
9b68774fcc6b
Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents:
41
diff
changeset
|
953 return len(self.data) |
| 41 | 954 |
| 80 | 955 def __getitem__(self,key): |
|
55
66619ce44497
Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
48
diff
changeset
|
956 """More efficient implementation than the default __getitem__""" |
|
66619ce44497
Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
48
diff
changeset
|
957 fieldnames=self.fields_columns.keys() |
| 80 | 958 if type(key) is int: |
|
55
66619ce44497
Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
48
diff
changeset
|
959 return Example(fieldnames, |
| 80 | 960 [self.data[key,self.fields_columns[f]] for f in fieldnames]) |
| 961 if type(key) is slice: | |
|
55
66619ce44497
Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
48
diff
changeset
|
962 return MinibatchDataSet(Example(fieldnames, |
| 80 | 963 [self.data[key,self.fields_columns[f]] for f in fieldnames])) |
| 964 if type(key) is list: | |
| 965 for i in range(len(key)): | |
| 966 if self.hasFields(key[i]): | |
| 967 key[i]=self.fields_columns[key[i]] | |
| 968 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
|
969 #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
|
970 # 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
|
971 # 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
|
972 [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
|
973 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
|
974 self.data[key,self.fields_columns[f]] |
|
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|
975 for f in fieldnames]), |
|
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976 self.valuesVStack,self.valuesHStack) |
| 80 | 977 |
|
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|
978 # else check for a fieldname |
| 80 | 979 if self.hasFields(key): |
|
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980 return self.data[:,self.fields_columns[key]] |
|
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|
981 # else we are trying to access a property of the dataset |
| 80 | 982 assert key in self.__dict__ # else it means we are trying to access a non-existing property |
| 983 return self.__dict__[key] | |
|
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|
984 |
| 41 | 985 |
|
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|
986 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
|
44
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|
987 class ArrayDataSetIterator(object): |
|
42
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988 def __init__(self,dataset,fieldnames,minibatch_size,n_batches,offset): |
|
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|
989 if fieldnames is None: fieldnames = dataset.fieldNames() |
|
44
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990 # store the resulting minibatch in a lookup-list of values |
|
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991 self.minibatch = LookupList(fieldnames,[0]*len(fieldnames)) |
|
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992 self.dataset=dataset |
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993 self.minibatch_size=minibatch_size |
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994 assert offset>=0 and offset<len(dataset.data) |
|
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|
995 assert offset+minibatch_size<=len(dataset.data) |
|
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|
996 self.current=offset |
|
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997 def __iter__(self): |
|
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|
998 return self |
|
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|
999 def next(self): |
|
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|
1000 sub_data = self.dataset.data[self.current:self.current+self.minibatch_size] |
|
44
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|
1001 self.minibatch._values = [sub_data[:,self.dataset.fields_columns[f]] for f in self.minibatch._names] |
|
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|
1002 self.current+=self.minibatch_size |
|
44
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|
1003 return self.minibatch |
|
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|
1004 |
|
44
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|
1005 return ArrayDataSetIterator(self,fieldnames,minibatch_size,n_batches,offset) |
|
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|
1006 |
|
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diff
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|
1007 |
|
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|
1008 class CachedDataSet(DataSet): |
|
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|
1009 """ |
|
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diff
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|
1010 Wrap a dataset whose values are computationally expensive to obtain |
|
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|
1011 (e.g. because they involve some computation, or disk access), |
|
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diff
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|
1012 so that repeated accesses to the same example are done cheaply, |
|
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|
1013 by caching every example value that has been accessed at least once. |
|
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|
1014 |
|
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|
1015 Optionally, for finite-length dataset, all the values can be computed |
|
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diff
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|
1016 (and cached) upon construction of the CachedDataSet, rather at the |
|
1aabd2e2bb5f
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|
1017 first access. |
|
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|
1018 |
|
77
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|
1019 @todo when cache_all_upon_construction create mini-batches that are as |
|
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|
1020 large as possible but not so large as to fill up memory. |
|
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|
1021 |
|
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|
1022 @todo add disk-buffering capability, so that when the cache becomes too |
|
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|
1023 big for memory, we cache things on disk, trying to keep in memory only |
|
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|
1024 the record most likely to be accessed next. |
|
57
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|
1025 """ |
|
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|
1026 def __init__(self,source_dataset,cache_all_upon_construction=False): |
|
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|
1027 self.source_dataset=source_dataset |
|
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|
1028 self.cache_all_upon_construction=cache_all_upon_construction |
|
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|
1029 if cache_all_upon_construction: |
|
77
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|
1030 # this potentially brings all the source examples |
|
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|
1031 # into memory at once, which may be too much |
|
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|
1032 # the work could possibly be done by minibatches |
|
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|
1033 # that are as large as possible but no more than what memory allows. |
|
73
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|
1034 self.cached_examples = zip(*source_dataset.minibatches(minibatch_size=len(source_dataset)).__iter__().next()) |
|
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|
1035 else: |
|
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|
1036 self.cached_examples = [] |
|
57
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|
1037 |
|
73
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|
1038 self.fieldNames = source_dataset.fieldNames |
|
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|
1039 self.hasFields = source_dataset.hasFields |
|
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|
1040 self.valuesHStack = source_dataset.valuesHStack |
|
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|
1041 self.valuesVStack = source_dataset.valuesVStack |
|
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|
1042 |
|
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|
1043 def __len__(self): |
|
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|
1044 return len(self.source_dataset) |
|
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|
1045 |
|
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|
1046 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
|
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|
1047 class CacheIterator(object): |
|
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|
1048 def __init__(self,dataset): |
|
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|
1049 self.dataset=dataset |
|
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|
1050 self.current=offset |
|
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|
1051 def __iter__(self): return self |
|
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|
1052 def next(self): |
|
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|
1053 upper = self.current+minibatch_size |
|
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|
1054 cache_len = len(self.dataset.cached_examples) |
|
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|
1055 if upper>=cache_len: # whole minibatch is not already in cache |
|
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|
1056 # cache everything from current length to upper |
|
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|
1057 for example in self.dataset.source_dataset[cache_len:upper]: |
|
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|
1058 self.dataset.cached_examples.append(example) |
|
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|
1059 all_fields_minibatch = Example(self.dataset.fieldNames(), |
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|
1060 self.dataset.cached_examples[self.current:self.current+minibatch_size]) |
|
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|
1061 if self.dataset.fieldNames()==fieldnames: |
|
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|
1062 return all_fields_minibatch |
|
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|
1063 return Example(fieldnames,[all_fields_minibatch[name] for name in fieldnames]) |
|
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|
1064 return CacheIterator(self) |
|
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|
1065 |
|
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|
1066 |
|
57
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|
1067 class ApplyFunctionDataSet(DataSet): |
|
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|
1068 """ |
|
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|
1069 A dataset that contains as fields the results of applying a given function |
|
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|
1070 example-wise or minibatch-wise to all the fields of an input dataset. |
|
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|
1071 The output of the function should be an iterable (e.g. a list or a LookupList) |
|
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|
1072 over the resulting values. |
|
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|
1073 |
|
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|
1074 In minibatch mode, the function is expected to work on minibatches (takes |
|
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|
1075 a minibatch in input and returns a minibatch in output). More precisely, |
|
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|
1076 it means that each element of the input or output list should be iterable |
|
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|
1077 and indexable over the individual example values (typically these |
|
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|
1078 elements will be numpy arrays). All of the elements in the input and |
|
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|
1079 output lists should have the same length, which is the length of the |
|
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|
1080 minibatch. |
|
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|
1081 |
|
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|
1082 The function is applied each time an example or a minibatch is accessed. |
|
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|
1083 To avoid re-doing computation, wrap this dataset inside a CachedDataSet. |
|
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|
1084 |
|
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|
1085 If the values_{h,v}stack functions are not provided, then |
|
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1086 the input_dataset.values{H,V}Stack functions are used by default. |
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1087 """ |
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1088 def __init__(self,input_dataset,function,output_names,minibatch_mode=True, |
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1089 values_hstack=None,values_vstack=None, |
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1090 description=None,fieldtypes=None): |
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1091 """ |
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1092 Constructor takes an input dataset that has as many fields as the function |
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1093 expects as inputs. The resulting dataset has as many fields as the function |
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1094 produces as outputs, and that should correspond to the number of output names |
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1095 (provided in a list). |
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1096 |
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1097 Note that the expected semantics of the function differs in minibatch mode |
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1098 (it takes minibatches of inputs and produces minibatches of outputs, as |
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1099 documented in the class comment). |
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1100 """ |
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1101 self.input_dataset=input_dataset |
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1102 self.function=function |
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1103 self.output_names=output_names |
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1104 self.minibatch_mode=minibatch_mode |
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1105 DataSet.__init__(description,fieldtypes) |
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1106 self.valuesHStack = values_hstack if values_hstack else input_dataset.valuesHStack |
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1107 self.valuesVStack = values_vstack if values_vstack else input_dataset.valuesVStack |
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1108 |
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1109 def __len__(self): |
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1110 return len(self.input_dataset) |
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1111 |
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1112 def fieldnames(self): |
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1113 return self.output_names |
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1114 |
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1115 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
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1116 class ApplyFunctionIterator(object): |
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1117 def __init__(self,output_dataset): |
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1118 self.input_dataset=output_dataset.input_dataset |
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1119 self.output_dataset=output_dataset |
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1120 self.input_iterator=input_dataset.minibatches(minibatch_size=minibatch_size, |
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1121 n_batches=n_batches,offset=offset).__iter__() |
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1122 |
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1123 def __iter__(self): return self |
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1124 |
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1125 def next(self): |
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1126 function_inputs = self.input_iterator.next() |
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1127 all_output_names = self.output_dataset.output_names |
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1128 if self.output_dataset.minibatch_mode: |
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1129 function_outputs = self.output_dataset.function(function_inputs) |
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1130 else: |
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1131 input_examples = zip(*function_inputs) |
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1132 output_examples = [self.output_dataset.function(input_example) |
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1133 for input_example in input_examples] |
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1134 function_outputs = [self.output_dataset.valuesVStack(name,values) |
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1135 for name,values in zip(all_output_names, |
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1136 zip(*output_examples))] |
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1137 all_outputs = Example(all_output_names,function_outputs) |
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1138 if fieldnames==all_output_names: |
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1139 return all_outputs |
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1140 return Example(fieldnames,[all_outputs[name] for name in fieldnames]) |
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1141 |
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1142 return ApplyFunctionIterator(self.input_dataset,self) |
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1143 |
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1144 def __iter__(self): # only implemented for increased efficiency |
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1145 class ApplyFunctionSingleExampleIterator(object): |
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1146 def __init__(self,output_dataset): |
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1147 self.current=0 |
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1148 self.output_dataset=output_dataset |
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1149 self.input_iterator=output_dataset.input_dataset.__iter__() |
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1150 def __iter__(self): return self |
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1151 def next(self): |
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1152 function_inputs = self.input_iterator.next() |
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1153 if self.output_dataset.minibatch_mode: |
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1154 function_outputs = [output[0] for output in self.output_dataset.function(function_inputs)] |
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1155 else: |
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1156 function_outputs = self.output_dataset.function(function_inputs) |
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1157 return Example(self.output_dataset.output_names,function_outputs) |
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1158 return ApplyFunctionSingleExampleIterator(self) |
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1159 |
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1160 |
|
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1161 def supervised_learning_dataset(src_dataset,input_fields,target_fields,weight_field=None): |
|
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1162 """ |
|
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1163 Wraps an arbitrary DataSet into one for supervised learning tasks by forcing the |
|
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1164 user to define a set of fields as the 'input' field and a set of fields |
|
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1165 as the 'target' field. Optionally, a single weight_field can also be defined. |
|
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|
1166 """ |
|
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|
1167 args = ((input_fields,'input'),(output_fields,'target')) |
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1168 if weight_field: args+=(([weight_field],'weight')) |
|
36
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|
1169 return src_dataset.merge_fields(*args) |
|
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|
1170 |
|
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|
1171 |
|
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|
1172 |
|
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1173 |