Mercurial > pylearn
annotate dataset.py @ 353:47538a45b878
Cached dataset seems debug, using n_batches... is n_batches around to stay?
| author | Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> |
|---|---|
| date | Tue, 17 Jun 2008 17:12:43 -0400 |
| parents | 7545207466d4 |
| children | d580b3a369a4 |
| rev | line source |
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1 |
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2 from lookup_list import LookupList as Example |
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3 from misc import unique_elements_list_intersection |
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4 from string import join |
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5 from sys import maxint |
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6 import numpy, copy |
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| 166 | 8 from exceptions import * |
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9 |
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10 class AttributesHolder(object): |
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11 def __init__(self): pass |
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12 |
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13 def attributeNames(self): |
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14 raise AbstractFunction() |
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15 |
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16 def setAttributes(self,attribute_names,attribute_values,make_copies=False): |
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17 """ |
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18 Allow the attribute_values to not be a list (but a single value) if the attribute_names is of length 1. |
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19 """ |
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20 if len(attribute_names)==1 and not (isinstance(attribute_values,list) or isinstance(attribute_values,tuple) ): |
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21 attribute_values = [attribute_values] |
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22 if make_copies: |
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23 for name,value in zip(attribute_names,attribute_values): |
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24 self.__setattr__(name,copy.deepcopy(value)) |
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25 else: |
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26 for name,value in zip(attribute_names,attribute_values): |
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27 self.__setattr__(name,value) |
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28 |
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29 def getAttributes(self,attribute_names=None, return_copy=False): |
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30 """ |
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31 Return all (if attribute_names=None, in the order of attributeNames()) or a specified subset of attributes. |
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32 """ |
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33 if attribute_names is None: |
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34 attribute_names = self.attributeNames() |
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35 if return_copy: |
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36 return [copy.copy(self.__getattribute__(name)) for name in attribute_names] |
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37 else: |
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38 return [self.__getattribute__(name) for name in attribute_names] |
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39 |
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40 class DataSet(AttributesHolder): |
| 16 | 41 """A virtual base class for datasets. |
| 42 | |
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43 A DataSet can be seen as a generalization of a matrix, meant to be used in conjunction |
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44 with learning algorithms (for training and testing them): rows/records are called examples, and |
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45 columns/attributes are called fields. The field value for a particular example can be an arbitrary |
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46 python object, which depends on the particular dataset. |
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47 |
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48 We call a DataSet a 'stream' when its length is unbounded (in which case its __len__ method |
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49 should return sys.maxint). |
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50 |
| 16 | 51 A DataSet is a generator of iterators; these iterators can run through the |
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52 examples or the fields in a variety of ways. A DataSet need not necessarily have a finite |
| 16 | 53 or known length, so this class can be used to interface to a 'stream' which |
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54 feeds on-line learning (however, as noted below, some operations are not |
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55 feasible or not recommended on streams). |
| 16 | 56 |
| 57 To iterate over examples, there are several possibilities: | |
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58 - for example in dataset: |
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59 - for val1,val2,... in dataset: |
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60 - for example in dataset(field1, field2,field3, ...): |
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61 - for val1,val2,val3 in dataset(field1, field2,field3): |
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62 - for minibatch in dataset.minibatches([field1, field2, ...],minibatch_size=N): |
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63 - for mini1,mini2,mini3 in dataset.minibatches([field1, field2, field3], minibatch_size=N): |
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64 Each of these is documented below. All of these iterators are expected |
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65 to provide, in addition to the usual 'next()' method, a 'next_index()' method |
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66 which returns a non-negative integer pointing to the position of the next |
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67 example that will be returned by 'next()' (or of the first example in the |
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68 next minibatch returned). This is important because these iterators |
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69 can wrap around the dataset in order to do multiple passes through it, |
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70 in possibly unregular ways if the minibatch size is not a divisor of the |
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71 dataset length. |
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72 |
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73 To iterate over fields, one can do |
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74 - for field in dataset.fields(): |
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75 for field_value in field: # iterate over the values associated to that field for all the dataset examples |
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76 - for field in dataset(field1,field2,...).fields() to select a subset of fields |
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77 - for field in dataset.fields(field1,field2,...) to select a subset of fields |
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78 and each of these fields is iterable over the examples: |
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79 - for field_examples in dataset.fields(): |
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80 for example_value in field_examples: |
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81 ... |
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82 but when the dataset is a stream (unbounded length), it is not recommended to do |
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83 such things because the underlying dataset may refuse to access the different fields in |
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84 an unsynchronized ways. Hence the fields() method is illegal for streams, by default. |
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85 The result of fields() is a L{DataSetFields} object, which iterates over fields, |
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86 and whose elements are iterable over examples. A DataSetFields object can |
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87 be turned back into a DataSet with its examples() method:: |
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88 dataset2 = dataset1.fields().examples() |
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89 and dataset2 should behave exactly like dataset1 (in fact by default dataset2==dataset1). |
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90 |
| 16 | 91 Note: Fields are not mutually exclusive, i.e. two fields can overlap in their actual content. |
| 92 | |
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93 Note: The content of a field can be of any type. Field values can also be 'missing' |
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94 (e.g. to handle semi-supervised learning), and in the case of numeric (numpy array) |
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95 fields (i.e. an ArrayFieldsDataSet), NaN plays the role of a missing value. |
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96 What about non-numeric values? None. |
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97 |
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98 Dataset elements can be indexed and sub-datasets (with a subset |
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99 of examples) can be extracted. These operations are not supported |
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100 by default in the case of streams. |
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101 |
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102 - dataset[:n] returns an Example with the n first examples. |
| 16 | 103 |
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104 - dataset[i1:i2:s] returns an Example with the examples i1,i1+s,...i2-s. |
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105 |
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106 - dataset[i] returns an Example. |
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107 |
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108 - dataset[[i1,i2,...in]] returns a. Example with examples i1,i2,...in. |
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109 |
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110 A similar command gives you a DataSet instead of Examples : |
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111 |
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112 - dataset.subset[:n] returns a DataSet with the n first examples. |
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113 |
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114 - dataset.subset[i1:i2:s] returns a DataSet with the examples i1,i1+s,...i2-s. |
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115 |
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116 - dataset.subset[i] returns a DataSet. |
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117 |
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118 - dataset.subset[[i1,i2,...in]] returns a DataSet with examples i1,i2,...in. |
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119 |
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120 |
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121 - dataset.<property> returns the value of a property associated with |
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122 the name <property>. The following properties should be supported: |
| 41 | 123 - 'description': a textual description or name for the dataset |
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124 - 'fieldtypes': a list of types (one per field) |
| 78 | 125 A DataSet may have other attributes that it makes visible to other objects. These are |
| 126 used to store information that is not example-wise but global to the dataset. | |
| 127 The list of names of these attributes is given by the attribute_names() method. | |
| 41 | 128 |
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129 Datasets can be concatenated either vertically (increasing the length) or |
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130 horizontally (augmenting the set of fields), if they are compatible, using |
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131 the following operations (with the same basic semantics as numpy.hstack |
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132 and numpy.vstack): |
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133 |
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134 - dataset1 | dataset2 | dataset3 == dataset.hstack([dataset1,dataset2,dataset3]) |
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135 |
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136 creates a new dataset whose list of fields is the concatenation of the list of |
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137 fields of the argument datasets. This only works if they all have the same length. |
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138 |
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139 - dataset1 & dataset2 & dataset3 == dataset.vstack([dataset1,dataset2,dataset3]) |
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140 |
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141 creates a new dataset that concatenates the examples from the argument datasets |
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142 (and whose length is the sum of the length of the argument datasets). This only |
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143 works if they all have the same fields. |
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144 |
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145 According to the same logic, and viewing a DataSetFields object associated to |
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146 a DataSet as a kind of transpose of it, fields1 & fields2 concatenates fields of |
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147 a DataSetFields fields1 and fields2, and fields1 | fields2 concatenates their |
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148 examples. |
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149 |
| 41 | 150 A dataset can hold arbitrary key-value pairs that may be used to access meta-data |
| 151 or other properties of the dataset or associated with the dataset or the result | |
| 152 of a computation stored in a dataset. These can be accessed through the [key] syntax | |
| 153 when key is a string (or more specifically, neither an integer, a slice, nor a list). | |
| 78 | 154 |
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155 A DataSet sub-class should always redefine the following methods: |
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156 - __len__ if it is not a stream |
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157 - fieldNames |
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158 - minibatches_nowrap (called by DataSet.minibatches()) |
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159 For efficiency of implementation, a sub-class might also want to redefine |
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160 - valuesHStack |
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161 - valuesVStack |
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162 - hasFields |
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163 - __getitem__ may not be feasible with some streams |
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164 - __iter__ |
| 78 | 165 A sub-class should also append attributes to self._attribute_names |
| 166 (the default value returned by attributeNames()). | |
| 167 By convention, attributes not in attributeNames() should have a name | |
| 168 starting with an underscore. | |
| 169 @todo enforce/test that convention! | |
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170 """ |
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171 |
| 83 | 172 numpy_vstack = lambda fieldname,values: numpy.vstack(values) |
| 173 numpy_hstack = lambda fieldnames,values: numpy.hstack(values) | |
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174 |
| 292 | 175 def __init__(self, description=None, fieldnames=None, fieldtypes=None): |
| 176 """ | |
| 177 @type fieldnames: list of strings | |
| 178 @type fieldtypes: list of python types, same length as fieldnames | |
| 179 @type description: string | |
| 180 @param description: description/name for this dataset | |
| 181 """ | |
| 182 def default_desc(): | |
| 183 return type(self).__name__ \ | |
| 184 + " ( " + join([x.__name__ for x in type(self).__bases__]) + " )" | |
| 185 | |
| 186 #self.fieldnames = fieldnames | |
| 187 | |
| 188 self.fieldtypes = fieldtypes if fieldtypes is not None \ | |
| 189 else [None]*1 #len(fieldnames) | |
| 190 | |
| 191 self.description = default_desc() if description is None \ | |
| 192 else description | |
| 78 | 193 self._attribute_names = ["description"] |
| 292 | 194 |
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195 |
| 292 | 196 attributeNames = property(lambda self: copy.copy(self._attribute_names)) |
| 197 | |
| 198 def __contains__(self, fieldname): | |
| 199 return (fieldname in self.fieldNames()) \ | |
| 200 or (fieldname in self.attributeNames()) | |
| 201 | |
| 202 def __iter__(self): | |
| 203 """Supports the syntax "for i in dataset: ..." | |
| 78 | 204 |
| 292 | 205 Using this syntax, "i" will be an Example instance (or equivalent) with |
| 206 all the fields of DataSet self. Every field of "i" will give access to | |
| 207 a field of a single example. Fields should be accessible via | |
| 208 i["fielname"] or i[3] (in the order defined by the elements of the | |
| 209 Example returned by this iterator), but the derived class is free | |
| 210 to accept any type of identifier, and add extra functionality to the iterator. | |
| 211 | |
| 212 The default implementation calls the minibatches iterator and extracts the first example of each field. | |
| 213 """ | |
| 214 return DataSet.MinibatchToSingleExampleIterator(self.minibatches(None, minibatch_size = 1)) | |
| 215 | |
| 216 def __len__(self): | |
| 217 """ | |
| 218 len(dataset) returns the number of examples in the dataset. | |
| 219 By default, a DataSet is a 'stream', i.e. it has an unbounded length (sys.maxint). | |
| 220 Sub-classes which implement finite-length datasets should redefine this method. | |
| 221 Some methods only make sense for finite-length datasets. | |
| 222 """ | |
| 223 return None | |
| 224 | |
| 78 | 225 |
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226 class MinibatchToSingleExampleIterator(object): |
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227 """ |
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228 Converts the result of minibatch iterator with minibatch_size==1 into |
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229 single-example values in the result. Therefore the result of |
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230 iterating on the dataset itself gives a sequence of single examples |
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231 (whereas the result of iterating over minibatches gives in each |
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232 Example field an iterable object over the individual examples in |
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233 the minibatch). |
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234 """ |
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235 def __init__(self, minibatch_iterator): |
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236 self.minibatch_iterator = minibatch_iterator |
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237 self.minibatch = None |
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238 def __iter__(self): #makes for loop work |
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239 return self |
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240 def next(self): |
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241 size1_minibatch = self.minibatch_iterator.next() |
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242 if not self.minibatch: |
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243 names = size1_minibatch.keys() |
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244 # next lines are a hack, but there was problem when we were getting [array(327)] for instance |
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245 try: |
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246 values = [value[0] for value in size1_minibatch.values()] |
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247 except : |
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248 values = [value for value in size1_minibatch.values()] |
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249 self.minibatch = Example(names,values) |
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250 else: |
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251 self.minibatch._values = [value[0] for value in size1_minibatch.values()] |
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252 return self.minibatch |
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253 |
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254 def next_index(self): |
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255 return self.minibatch_iterator.next_index() |
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256 |
|
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257 class MinibatchWrapAroundIterator(object): |
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258 """ |
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259 An iterator for minibatches that handles the case where we need to wrap around the |
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260 dataset because n_batches*minibatch_size > len(dataset). It is constructed from |
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261 a dataset that provides a minibatch iterator that does not need to handle that problem. |
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262 This class is a utility for dataset subclass writers, so that they do not have to handle |
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263 this issue multiple times, nor check that fieldnames are valid, nor handle the |
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264 empty fieldnames (meaning 'use all the fields'). |
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265 """ |
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266 def __init__(self,dataset,fieldnames,minibatch_size,n_batches,offset): |
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267 self.dataset=dataset |
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268 self.fieldnames=fieldnames |
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269 self.minibatch_size=minibatch_size |
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270 self.n_batches=n_batches |
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271 self.n_batches_done=0 |
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272 self.next_row=offset |
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273 self.L=len(dataset) |
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274 self.offset=offset % self.L |
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275 ds_nbatches = (self.L-self.next_row)/self.minibatch_size |
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276 if n_batches is not None: |
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277 ds_nbatches = min(n_batches,ds_nbatches) |
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278 if fieldnames: |
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279 assert dataset.hasFields(*fieldnames) |
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280 else: |
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281 self.fieldnames=dataset.fieldNames() |
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282 self.iterator = self.dataset.minibatches_nowrap(self.fieldnames,self.minibatch_size, ds_nbatches,self.next_row) |
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283 |
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284 def __iter__(self): |
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285 return self |
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286 |
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287 def next_index(self): |
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288 return self.next_row |
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289 |
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290 def next(self): |
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291 if self.n_batches and self.n_batches_done==self.n_batches: |
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292 raise StopIteration |
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293 elif not self.n_batches and self.next_row ==self.L: |
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294 raise StopIteration |
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295 upper = self.next_row+self.minibatch_size |
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296 if upper <=self.L: |
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297 minibatch = self.iterator.next() |
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298 else: |
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299 if not self.n_batches: |
|
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300 upper=min(upper, self.L) |
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301 # if their is not a fixed number of batch, we continue to the end of the dataset. |
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302 # this can create a minibatch that is smaller then the minibatch_size |
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303 assert (self.L-self.next_row)<=self.minibatch_size |
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304 minibatch = self.dataset.minibatches_nowrap(self.fieldnames,self.L-self.next_row,1,self.next_row).next() |
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305 else: |
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306 # we must concatenate (vstack) the bottom and top parts of our minibatch |
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307 # first get the beginning of our minibatch (top of dataset) |
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308 first_part = self.dataset.minibatches_nowrap(self.fieldnames,self.L-self.next_row,1,self.next_row).next() |
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309 second_part = self.dataset.minibatches_nowrap(self.fieldnames,upper-self.L,1,0).next() |
|
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310 minibatch = Example(self.fieldnames, |
|
268
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311 [self.dataset.valuesVStack(name,[first_part[name],second_part[name]]) |
|
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312 for name in self.fieldnames]) |
|
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313 self.next_row=upper |
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314 self.n_batches_done+=1 |
|
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315 if upper >= self.L and self.n_batches: |
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316 self.next_row -= self.L |
|
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317 ds_nbatches = (self.L-self.next_row)/self.minibatch_size |
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318 if self.n_batches is not None: |
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319 ds_nbatches = min(self.n_batches,ds_nbatches) |
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320 self.iterator = self.dataset.minibatches_nowrap(self.fieldnames,self.minibatch_size, |
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321 ds_nbatches,self.next_row) |
|
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322 return DataSetFields(MinibatchDataSet(minibatch,self.dataset.valuesVStack, |
|
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323 self.dataset.valuesHStack), |
|
74
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324 minibatch.keys()) |
|
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325 |
|
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326 |
|
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327 minibatches_fieldnames = None |
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328 minibatches_minibatch_size = 1 |
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329 minibatches_n_batches = None |
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330 def minibatches(self, |
|
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331 fieldnames = minibatches_fieldnames, |
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332 minibatch_size = minibatches_minibatch_size, |
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333 n_batches = minibatches_n_batches, |
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334 offset = 0): |
|
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335 """ |
|
36
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336 Return an iterator that supports three forms of syntax: |
|
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337 |
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338 for i in dataset.minibatches(None,**kwargs): ... |
| 16 | 339 |
|
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340 for i in dataset.minibatches([f1, f2, f3],**kwargs): ... |
| 16 | 341 |
|
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342 for i1, i2, i3 in dataset.minibatches([f1, f2, f3],**kwargs): ... |
| 16 | 343 |
|
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344 Using the first two syntaxes, "i" will be an indexable object, such as a list, |
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345 tuple, or Example instance. In both cases, i[k] is a list-like container |
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346 of a batch of current examples. In the second case, i[0] is |
|
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347 list-like container of the f1 field of a batch current examples, i[1] is |
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348 a list-like container of the f2 field, etc. |
|
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349 |
|
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350 Using the first syntax, all the fields will be returned in "i". |
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351 Using the third syntax, i1, i2, i3 will be list-like containers of the |
|
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352 f1, f2, and f3 fields of a batch of examples on each loop iteration. |
|
11
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Debugged (to the extent of my tests) the new version of dataset
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353 |
|
36
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354 The minibatches iterator is expected to return upon each call to next() |
|
290
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355 a DataSetFields object, which is a Example (indexed by the field names) whose |
| 80 | 356 elements are iterable and indexable over the minibatch examples, and which keeps a pointer to |
|
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357 a sub-dataset that can be used to iterate over the individual examples |
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358 in the minibatch. Hence a minibatch can be converted back to a regular |
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359 dataset or its fields can be looked at individually (and possibly iterated over). |
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360 |
|
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361 PARAMETERS |
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362 - fieldnames (list of any type, default None): |
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363 The loop variables i1, i2, i3 (in the example above) should contain the |
|
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364 f1, f2, and f3 fields of the current batch of examples. If None, the |
|
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365 derived class can choose a default, e.g. all fields. |
| 16 | 366 |
|
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367 - minibatch_size (integer, default 1) |
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368 On every iteration, the variables i1, i2, i3 will have |
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369 exactly minibatch_size elements. e.g. len(i1) == minibatch_size |
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370 |
|
331
52aa031e1fe3
IMPORTANT: minibatches now returns minibatch_nowrap with a minimum of assert before. Should implement the good behavior, e.g. returning only complete batches and let the user figure out what he wants.
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330
diff
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|
371 @DEPRECATED n_batches : not used anywhere |
|
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372 - n_batches (integer, default None) |
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373 The iterator will loop exactly this many times, and then stop. If None, |
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374 the derived class can choose a default. If (-1), then the returned |
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375 iterator should support looping indefinitely. |
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376 |
|
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377 - offset (integer, default 0) |
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378 The iterator will start at example 'offset' in the dataset, rather than the default. |
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379 |
|
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380 Note: A list-like container is something like a tuple, list, numpy.ndarray or |
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381 any other object that supports integer indexing and slicing. |
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382 |
|
331
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383 @ATTENTION: now minibatches returns minibatches_nowrap, which is supposed to return complete |
|
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384 batches only, raise StopIteration. |
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385 @ATTENTION: minibatches returns a LookupList, we can't iterate over examples on it. |
|
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386 |
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387 """ |
|
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388 #return DataSet.MinibatchWrapAroundIterator(self,fieldnames,minibatch_size,n_batches,offset)\ |
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389 assert offset >= 0 |
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390 assert offset < len(self) |
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391 assert offset + minibatch_size -1 < len(self) |
|
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392 if fieldnames == None : |
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393 fieldnames = self.fieldNames() |
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394 return self.minibatches_nowrap(fieldnames,minibatch_size,n_batches,offset) |
|
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395 |
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396 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
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397 """ |
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398 This is the minibatches iterator generator that sub-classes must define. |
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399 It does not need to worry about wrapping around multiple times across the dataset, |
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400 as this is handled by MinibatchWrapAroundIterator when DataSet.minibatches() is called. |
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401 The next() method of the returned iterator does not even need to worry about |
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402 the termination condition (as StopIteration will be raised by DataSet.minibatches |
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403 before an improper call to minibatches_nowrap's next() is made). |
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404 That next() method can assert that its next row will always be within [0,len(dataset)). |
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405 The iterator returned by minibatches_nowrap does not need to implement |
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406 a next_index() method either, as this will be provided by MinibatchWrapAroundIterator. |
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407 """ |
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408 raise AbstractFunction() |
|
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409 |
|
48
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410 def is_unbounded(self): |
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411 """ |
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412 Tests whether a dataset is unbounded (e.g. a stream). |
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413 """ |
| 123 | 414 return len(self)==maxint |
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415 |
|
26
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416 def hasFields(self,*fieldnames): |
|
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417 """ |
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418 Return true if the given field name (or field names, if multiple arguments are |
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419 given) is recognized by the DataSet (i.e. can be used as a field name in one |
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420 of the iterators). |
|
29
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421 |
|
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422 The default implementation may be inefficient (O(# fields in dataset)), as it calls the fieldNames() |
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423 method. Many datasets may store their field names in a dictionary, which would allow more efficiency. |
|
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424 """ |
|
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425 return len(unique_elements_list_intersection(fieldnames,self.fieldNames()))>0 |
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426 |
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427 def fieldNames(self): |
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428 """ |
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429 Return the list of field names that are supported by the iterators, |
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430 and for which hasFields(fieldname) would return True. |
|
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431 """ |
|
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432 raise AbstractFunction() |
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433 |
|
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434 def __call__(self,*fieldnames): |
|
23
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Working on ApplyFunctionDataSet, added constraint that
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435 """ |
|
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436 Return a dataset that sees only the fields whose name are specified. |
|
20
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437 """ |
|
42
9b68774fcc6b
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438 assert self.hasFields(*fieldnames) |
|
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439 return self.fields(*fieldnames).examples() |
|
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440 |
|
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441 def fields(self,*fieldnames): |
|
29
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442 """ |
|
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443 Return a DataSetFields object associated with this dataset. |
|
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444 """ |
|
74
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Fixed errors raised by test_dataset
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445 return DataSetFields(self,fieldnames) |
|
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446 |
|
269
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447 def getitem_key(self, fieldname): |
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448 """A not-so-well thought-out place to put code that used to be in |
|
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449 getitem. |
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450 """ |
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451 #removing as per discussion June 4. --JSB |
|
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452 |
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453 i = fieldname |
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454 # else check for a fieldname |
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455 if self.hasFields(i): |
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456 return self.minibatches(fieldnames=[i],minibatch_size=len(self),n_batches=1,offset=0).next()[0] |
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457 # else we are trying to access a property of the dataset |
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458 assert i in self.__dict__ # else it means we are trying to access a non-existing property |
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459 return self.__dict__[i] |
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460 |
|
2
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Rewrote DataSet interface and created FiniteDataSet interface.
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461 def __getitem__(self,i): |
|
28
541a273bc89f
Removed __array__ method from dataset, whose
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462 """ |
|
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463 @rtype: Example |
|
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464 @returns: single or multiple examples |
|
1
2cd82666b9a7
Added statscollector and started writing dataset and learner.
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465 |
|
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466 @type i: integer or slice or <iterable> of integers |
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467 @param i: |
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468 dataset[i] returns the (i+1)-th example of the dataset. |
|
309
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469 dataset[i:j] returns a LookupList with examples i,i+1,...,j-1. |
|
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470 dataset[i:j:s] returns a LookupList with examples i,i+2,i+4...,j-2. |
|
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471 dataset[[i1,i2,..,in]] returns a LookupList with examples i1,i2,...,in. |
|
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472 |
|
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473 @note: |
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474 Some stream datasets may be unable to implement random access, i.e. |
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475 arbitrary slicing/indexing because they can only iterate through |
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476 examples one or a minibatch at a time and do not actually store or keep |
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477 past (or future) examples. |
|
40
88fd1cce08b9
replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
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|
478 |
|
88fd1cce08b9
replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
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|
479 The default implementation of getitem uses the minibatches iterator |
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480 to obtain one example, one slice, or a list of examples. It may not |
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481 always be the most efficient way to obtain the result, especially if |
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482 the data are actually stored in a memory array. |
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483 """ |
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484 |
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485 if type(i) is int: |
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486 assert i >= 0 # TBM: see if someone complains and want negative i |
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487 if i >= len(self) : |
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488 raise IndexError |
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489 i_batch = self.minibatches_nowrap(self.fieldNames(), |
| 293 | 490 minibatch_size=1, n_batches=1, offset=i) |
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491 return DataSet.MinibatchToSingleExampleIterator(i_batch).next() |
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492 |
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493 #if i is a contiguous slice |
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494 if type(i) is slice and (i.step in (None, 1)): |
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495 offset = 0 if i.start is None else i.start |
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496 upper_bound = len(self) if i.stop is None else i.stop |
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497 upper_bound = min(len(self) , upper_bound) |
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498 #return MinibatchDataSet(self.minibatches_nowrap(self.fieldNames(), |
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499 # minibatch_size=upper_bound - offset, |
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500 # n_batches=1, |
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501 # offset=offset).next()) |
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502 # now returns a LookupList |
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503 return self.minibatches_nowrap(self.fieldNames(), |
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504 minibatch_size=upper_bound - offset, |
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505 n_batches=1, |
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506 offset=offset).next() |
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507 |
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508 # if slice has a step param, convert it to list and handle it with the |
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509 # list code |
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510 if type(i) is slice: |
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511 offset = 0 if i.start is None else i.start |
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512 upper_bound = len(self) if i.stop is None else i.stop |
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513 upper_bound = min(len(self) , upper_bound) |
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514 i = list(range(offset, upper_bound, i.step)) |
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515 |
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516 # handle tuples, arrays, lists |
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517 if hasattr(i, '__getitem__'): |
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518 for idx in i: |
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519 #dis-allow nested slices |
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520 if not isinstance(idx, int): |
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521 raise TypeError(idx) |
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522 if idx >= len(self) : |
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523 raise IndexError |
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524 # call back into self.__getitem__ |
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525 examples = [self.minibatches_nowrap(self.fieldNames(), |
| 293 | 526 minibatch_size=1, n_batches=1, offset=ii).next() |
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527 for ii in i] |
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528 # re-index the fields in each example by field instead of by example |
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529 field_values = [[] for blah in self.fieldNames()] |
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530 for e in examples: |
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531 for f,v in zip(field_values, e): |
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532 f.append(v) |
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533 #build them into a LookupList (a.ka. Example) |
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534 zz = zip(self.fieldNames(),field_values) |
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535 vst = [self.valuesVStack(fieldname,field_values) for fieldname,field_values in zz] |
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536 example = Example(self.fieldNames(), vst) |
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537 #return MinibatchDataSet(example, self.valuesVStack, self.valuesHStack) |
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538 # now returns a LookupList |
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539 return example |
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540 |
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541 # what in the world is i? |
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542 raise TypeError(i, type(i)) |
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543 |
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544 |
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545 """ |
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546 Enables the call dataset.subset[a:b:c] that will return a DataSet |
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547 around the examples returned by __getitem__(slice(a,b,c)) |
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548 |
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549 @SEE DataSet.__getsubset(self) |
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550 """ |
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551 subset = property(lambda s : s.__getsubset(),doc="returns a subset as a DataSet") |
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552 |
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553 |
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554 def __getsubset(self) : |
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555 """ |
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556 Enables the call data.subset[a:b:c], returns a DataSet. |
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557 Default implementation is a simple wrap around __getitem__() using MinibatchDataSet. |
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558 |
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559 @RETURN DataSet |
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560 @SEE DataSet.subset = property(lambda s : s.__getsubset()) |
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561 """ |
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562 _self = self |
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563 class GetSliceReturnsDataSet(object) : |
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564 def __getitem__(self,slice) : |
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565 return MinibatchDataSet(_self.__getitem__(slice)) |
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566 return GetSliceReturnsDataSet() |
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567 |
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568 |
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569 |
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570 def valuesHStack(self,fieldnames,fieldvalues): |
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571 """ |
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572 Return a value that corresponds to concatenating (horizontally) several field values. |
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573 This can be useful to merge some fields. The implementation of this operation is likely |
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574 to involve a copy of the original values. When the values are numpy arrays, the |
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575 result should be numpy.hstack(values). If it makes sense, this operation should |
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576 work as well when each value corresponds to multiple examples in a minibatch |
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577 e.g. if each value is a Ni-vector and a minibatch of length L is a LxNi matrix, |
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578 then the result should be a Lx(N1+N2+..) matrix equal to numpy.hstack(values). |
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579 The default is to use numpy.hstack for numpy.ndarray values, and a list |
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580 pointing to the original values for other data types. |
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581 """ |
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582 all_numpy=True |
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583 for value in fieldvalues: |
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584 if not type(value) is numpy.ndarray: |
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585 all_numpy=False |
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586 if all_numpy: |
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587 return numpy.hstack(fieldvalues) |
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588 # the default implementation of horizontal stacking is to put values in a list |
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589 return fieldvalues |
|
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590 |
|
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591 def valuesVStack(self,fieldname,values): |
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592 """ |
|
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593 @param fieldname: the name of the field from which the values were taken |
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594 @type fieldname: any type |
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595 |
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596 @param values: bits near the beginning or end of the dataset |
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597 @type values: list of minibatches (returned by minibatch_nowrap) |
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598 |
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599 @return: the concatenation (stacking) of the values |
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600 @rtype: something suitable as a minibatch field |
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601 """ |
|
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602 rval = [] |
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603 for v in values: |
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604 rval.extend(v) |
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605 return rval |
|
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606 |
|
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607 def __or__(self,other): |
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608 """ |
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609 dataset1 | dataset2 returns a dataset whose list of fields is the concatenation of the list of |
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610 fields of the argument datasets. This only works if they all have the same length. |
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611 """ |
|
135
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612 return HStackedDataSet([self,other]) |
|
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613 |
|
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614 def __and__(self,other): |
|
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615 """ |
|
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616 dataset1 & dataset2 is a dataset that concatenates the examples from the argument datasets |
|
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617 (and whose length is the sum of the length of the argument datasets). This only |
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618 works if they all have the same fields. |
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619 """ |
|
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620 return VStackedDataSet([self,other]) |
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621 |
|
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622 def hstack(datasets): |
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623 """ |
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624 hstack(dataset1,dataset2,...) returns dataset1 | datataset2 | ... |
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625 which is a dataset whose fields list is the concatenation of the fields |
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626 of the individual datasets. |
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627 """ |
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628 assert len(datasets)>0 |
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629 if len(datasets)==1: |
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630 return datasets[0] |
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631 return HStackedDataSet(datasets) |
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632 |
|
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633 def vstack(datasets): |
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634 """ |
|
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635 vstack(dataset1,dataset2,...) returns dataset1 & datataset2 & ... |
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636 which is a dataset which iterates first over the examples of dataset1, then |
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637 over those of dataset2, etc. |
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638 """ |
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639 assert len(datasets)>0 |
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640 if len(datasets)==1: |
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641 return datasets[0] |
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642 return VStackedDataSet(datasets) |
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|
643 |
|
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644 class FieldsSubsetDataSet(DataSet): |
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645 """ |
| 167 | 646 A sub-class of L{DataSet} that selects a subset of the fields. |
|
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647 """ |
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648 def __init__(self,src,fieldnames): |
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649 self.src=src |
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650 self.fieldnames=fieldnames |
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651 assert src.hasFields(*fieldnames) |
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652 self.valuesHStack = src.valuesHStack |
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653 self.valuesVStack = src.valuesVStack |
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654 |
|
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655 def __len__(self): return len(self.src) |
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656 |
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657 def fieldNames(self): |
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658 return self.fieldnames |
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659 |
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|
660 def __iter__(self): |
|
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661 class FieldsSubsetIterator(object): |
|
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662 def __init__(self,ds): |
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663 self.ds=ds |
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664 self.src_iter=ds.src.__iter__() |
|
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665 self.example=None |
|
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666 def __iter__(self): return self |
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667 def next(self): |
|
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668 complete_example = self.src_iter.next() |
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669 if self.example: |
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670 self.example._values=[complete_example[field] |
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671 for field in self.ds.fieldnames] |
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672 else: |
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673 self.example=Example(self.ds.fieldnames, |
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674 [complete_example[field] for field in self.ds.fieldnames]) |
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675 return self.example |
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676 return FieldsSubsetIterator(self) |
|
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677 |
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678 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
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679 assert self.hasFields(*fieldnames) |
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680 return self.src.minibatches_nowrap(fieldnames,minibatch_size,n_batches,offset) |
|
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681 def dontuse__getitem__(self,i): |
|
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682 return FieldsSubsetDataSet(self.src[i],self.fieldnames) |
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683 |
|
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684 class RenamedFieldsDataSet(DataSet): |
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|
685 """ |
|
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|
686 A sub-class of L{DataSet} that selects and renames a subset of the fields. |
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|
687 """ |
|
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688 def __init__(self,src,src_fieldnames,new_fieldnames): |
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689 self.src=src |
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690 self.src_fieldnames=src_fieldnames |
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691 self.new_fieldnames=new_fieldnames |
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692 assert src.hasFields(*src_fieldnames) |
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693 assert len(src_fieldnames)==len(new_fieldnames) |
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694 self.valuesHStack = src.valuesHStack |
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|
695 self.valuesVStack = src.valuesVStack |
|
351
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|
696 self.lookup_fields = Example(new_fieldnames,src_fieldnames) |
|
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|
697 |
|
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|
698 def __len__(self): return len(self.src) |
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|
699 |
|
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700 def fieldNames(self): |
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701 return self.new_fieldnames |
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|
702 |
|
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|
703 def __iter__(self): |
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|
704 class FieldsSubsetIterator(object): |
|
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705 def __init__(self,ds): |
|
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|
706 self.ds=ds |
|
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|
707 self.src_iter=ds.src.__iter__() |
|
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|
708 self.example=None |
|
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|
709 def __iter__(self): return self |
|
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|
710 def next(self): |
|
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diff
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|
711 complete_example = self.src_iter.next() |
|
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|
712 if self.example: |
|
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|
713 self.example._values=[complete_example[field] |
|
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|
714 for field in self.ds.src_fieldnames] |
|
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|
715 else: |
|
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|
716 self.example=Example(self.ds.new_fieldnames, |
|
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|
717 [complete_example[field] |
|
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|
718 for field in self.ds.src_fieldnames]) |
|
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|
719 return self.example |
|
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|
720 return FieldsSubsetIterator(self) |
|
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|
721 |
|
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|
722 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
|
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|
723 assert self.hasFields(*fieldnames) |
|
351
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diff
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|
724 cursor = Example(fieldnames,[0]*len(fieldnames)) |
|
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|
725 for batch in self.src.minibatches_nowrap([self.lookup_fields[f] for f in fieldnames],minibatch_size,n_batches,offset): |
|
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|
726 cursor._values=batch._values |
|
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|
727 yield cursor |
|
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|
728 |
|
328
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|
729 def __getitem__(self,i): |
|
333
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|
730 # return FieldsSubsetDataSet(self.src[i],self.new_fieldnames) |
|
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|
731 complete_example = self.src[i] |
|
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|
732 return Example(self.new_fieldnames, |
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|
733 [complete_example[field] |
|
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|
734 for field in self.src_fieldnames]) |
|
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|
735 |
|
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|
736 |
|
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|
737 |
|
290
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|
738 class DataSetFields(Example): |
|
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|
739 """ |
| 167 | 740 Although a L{DataSet} iterates over examples (like rows of a matrix), an associated |
|
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|
741 DataSetFields iterates over fields (like columns of a matrix), and can be understood |
|
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742 as a transpose of the associated dataset. |
|
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|
743 |
|
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|
744 To iterate over fields, one can do |
|
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|
745 * for fields in dataset.fields() |
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|
746 * for fields in dataset(field1,field2,...).fields() to select a subset of fields |
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|
747 * for fields in dataset.fields(field1,field2,...) to select a subset of fields |
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|
748 and each of these fields is iterable over the examples: |
|
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|
749 * for field_examples in dataset.fields(): |
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|
750 for example_value in field_examples: |
|
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|
751 ... |
|
241
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If I understand properly, the length of an unbounded stream is sys.maxint
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parents:
231
diff
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|
752 but when the dataset is a stream (unbounded length), it is not recommended to do |
|
36
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|
753 such things because the underlying dataset may refuse to access the different fields in |
|
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|
754 an unsynchronized ways. Hence the fields() method is illegal for streams, by default. |
|
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|
755 The result of fields() is a DataSetFields object, which iterates over fields, |
|
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|
756 and whose elements are iterable over examples. A DataSetFields object can |
|
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|
757 be turned back into a DataSet with its examples() method: |
|
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|
758 dataset2 = dataset1.fields().examples() |
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|
759 and dataset2 should behave exactly like dataset1 (in fact by default dataset2==dataset1). |
|
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diff
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|
760 |
|
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diff
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|
761 DataSetFields can be concatenated vertically or horizontally. To be consistent with |
|
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diff
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|
762 the syntax used for DataSets, the | concatenates the fields and the & concatenates |
|
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|
763 the examples. |
|
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|
764 """ |
|
74
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diff
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|
765 def __init__(self,dataset,fieldnames): |
|
65
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diff
changeset
|
766 original_dataset=dataset |
|
40
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|
767 if not fieldnames: |
|
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|
768 fieldnames=dataset.fieldNames() |
|
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diff
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|
769 elif not list(fieldnames)==list(dataset.fieldNames()): |
|
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diff
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|
770 #we must cast to list, othersize('x','y')!=['x','y'] |
|
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diff
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|
771 dataset = FieldsSubsetDataSet(dataset,fieldnames) |
|
37
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|
772 assert dataset.hasFields(*fieldnames) |
|
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diff
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|
773 self.dataset=dataset |
|
66
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diff
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|
774 |
|
64
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|
775 if isinstance(dataset,MinibatchDataSet): |
|
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|
776 Example.__init__(self,fieldnames,list(dataset._fields)) |
|
65
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|
777 elif isinstance(original_dataset,MinibatchDataSet): |
|
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|
778 Example.__init__(self,fieldnames, |
|
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diff
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|
779 [original_dataset._fields[field] |
|
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|
780 for field in fieldnames]) |
|
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|
781 else: |
|
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|
782 minibatch_iterator = dataset.minibatches(fieldnames, |
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diff
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|
783 minibatch_size=len(dataset), |
|
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|
784 n_batches=1) |
|
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diff
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|
785 minibatch=minibatch_iterator.next() |
|
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|
786 Example.__init__(self,fieldnames,minibatch) |
|
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|
787 |
|
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|
788 def examples(self): |
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|
789 return self.dataset |
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|
790 |
|
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|
791 def __or__(self,other): |
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|
792 """ |
|
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|
793 fields1 | fields2 is a DataSetFields that whose list of examples is the concatenation |
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794 of the list of examples of DataSetFields fields1 and fields2. |
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|
795 """ |
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|
796 return (self.examples() + other.examples()).fields() |
|
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diff
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|
797 |
|
40
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|
798 def __and__(self,other): |
|
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changeset
|
799 """ |
|
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|
800 fields1 + fields2 is a DataSetFields that whose list of fields is the concatenation |
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|
801 of the fields of DataSetFields fields1 and fields2. |
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|
802 """ |
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|
803 return (self.examples() | other.examples()).fields() |
|
17
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|
804 |
|
37
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diff
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|
805 |
|
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|
806 class MinibatchDataSet(DataSet): |
|
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|
807 """ |
|
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|
808 Turn a L{Example} of same-length (iterable) fields into an example-iterable dataset. |
|
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|
809 Each element of the lookup-list should be an iterable and sliceable, all of the same length. |
|
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|
810 """ |
|
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|
811 def __init__(self,fields_lookuplist,values_vstack=DataSet().valuesVStack, |
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812 values_hstack=DataSet().valuesHStack): |
|
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|
813 """ |
|
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|
814 The user can (and generally should) also provide values_vstack(fieldname,fieldvalues) |
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815 and a values_hstack(fieldnames,fieldvalues) functions behaving with the same |
|
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|
816 semantics as the DataSet methods of the same name (but without the self argument). |
|
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817 """ |
|
211
bd728c83faff
in __get__, problem if the i.stop was None, i being the slice, added one line replacing None by the len(self)
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|
818 |
|
61
a8b70a9117ad
bugfix: in MinibatchDataSet renamed the class variable fields to _fields as parent class have a function called field.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
60
diff
changeset
|
819 self._fields=fields_lookuplist |
|
36
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
820 assert len(fields_lookuplist)>0 |
|
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Rewriting dataset.py completely
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parents:
29
diff
changeset
|
821 self.length=len(fields_lookuplist[0]) |
|
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parents:
29
diff
changeset
|
822 for field in fields_lookuplist[1:]: |
|
223
517364d48ae0
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Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
823 if self.length != len(field) : |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
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parents:
218
diff
changeset
|
824 print 'self.length = ',self.length |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
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parents:
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diff
changeset
|
825 print 'len(field) = ', len(field) |
|
517364d48ae0
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parents:
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diff
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|
826 print 'self._fields.keys() = ', self._fields.keys() |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
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parents:
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diff
changeset
|
827 print 'field=',field |
|
290
9b533cc7874a
trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
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diff
changeset
|
828 print 'fields_lookuplist=', fields_lookuplist |
|
36
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parents:
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diff
changeset
|
829 assert self.length==len(field) |
|
290
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parents:
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diff
changeset
|
830 self.valuesVStack=values_vstack |
|
9b533cc7874a
trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
274
diff
changeset
|
831 self.valuesHStack=values_hstack |
|
3
378b68d5c4ad
Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents:
2
diff
changeset
|
832 |
|
378b68d5c4ad
Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents:
2
diff
changeset
|
833 def __len__(self): |
|
36
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parents:
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diff
changeset
|
834 return self.length |
|
28
541a273bc89f
Removed __array__ method from dataset, whose
bengioy@grenat.iro.umontreal.ca
parents:
26
diff
changeset
|
835 |
|
290
9b533cc7874a
trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
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diff
changeset
|
836 def dontuse__getitem__(self,i): |
| 80 | 837 if type(i) in (slice,list): |
|
48
b6730f9a336d
Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents:
46
diff
changeset
|
838 return DataSetFields(MinibatchDataSet( |
| 80 | 839 Example(self._fields.keys(),[field[i] for field in self._fields])),self.fieldNames()) |
| 840 if type(i) is int: | |
| 85 | 841 return Example(self._fields.keys(),[field[i] for field in self._fields]) |
|
48
b6730f9a336d
Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents:
46
diff
changeset
|
842 if self.hasFields(i): |
|
61
a8b70a9117ad
bugfix: in MinibatchDataSet renamed the class variable fields to _fields as parent class have a function called field.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
60
diff
changeset
|
843 return self._fields[i] |
|
55
66619ce44497
Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
48
diff
changeset
|
844 assert i in self.__dict__ # else it means we are trying to access a non-existing property |
|
48
b6730f9a336d
Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents:
46
diff
changeset
|
845 return self.__dict__[i] |
|
11
be128b9127c8
Debugged (to the extent of my tests) the new version of dataset
bengioy@esprit.iro.umontreal.ca
parents:
9
diff
changeset
|
846 |
|
29
46c5c90019c2
Changed apply_function so that it propagates methods of the source.
bengioy@grenat.iro.umontreal.ca
parents:
28
diff
changeset
|
847 def fieldNames(self): |
|
61
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bugfix: in MinibatchDataSet renamed the class variable fields to _fields as parent class have a function called field.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
60
diff
changeset
|
848 return self._fields.keys() |
|
36
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diff
changeset
|
849 |
|
37
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
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36
diff
changeset
|
850 def hasFields(self,*fieldnames): |
|
36
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diff
changeset
|
851 for fieldname in fieldnames: |
|
61
a8b70a9117ad
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Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
60
diff
changeset
|
852 if fieldname not in self._fields.keys(): |
|
36
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Rewriting dataset.py completely
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diff
changeset
|
853 return False |
|
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Rewriting dataset.py completely
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diff
changeset
|
854 return True |
|
20
266c68cb6136
Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents:
19
diff
changeset
|
855 |
|
37
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
856 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
|
223
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
857 #@TODO bug somewhere here, fieldnames doesnt seem to be well handled |
|
36
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parents:
29
diff
changeset
|
858 class Iterator(object): |
|
223
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
859 def __init__(self,ds,fieldnames): |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
860 # tbm: added two next lines to handle fieldnames |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
861 if fieldnames is None: fieldnames = ds._fields.keys() |
|
517364d48ae0
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Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
862 self.fieldnames = fieldnames |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
863 |
|
36
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
864 self.ds=ds |
|
37
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
865 self.next_example=offset |
|
290
9b533cc7874a
trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
274
diff
changeset
|
866 assert minibatch_size >= 0 |
| 41 | 867 if offset+minibatch_size > ds.length: |
|
36
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
868 raise NotImplementedError() |
|
20
266c68cb6136
Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents:
19
diff
changeset
|
869 def __iter__(self): |
|
266c68cb6136
Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents:
19
diff
changeset
|
870 return self |
|
266c68cb6136
Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents:
19
diff
changeset
|
871 def next(self): |
|
61
a8b70a9117ad
bugfix: in MinibatchDataSet renamed the class variable fields to _fields as parent class have a function called field.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
60
diff
changeset
|
872 upper = self.next_example+minibatch_size |
|
353
47538a45b878
Cached dataset seems debug, using n_batches... is n_batches around to stay?
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
351
diff
changeset
|
873 if upper > len(self.ds) : |
|
47538a45b878
Cached dataset seems debug, using n_batches... is n_batches around to stay?
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
351
diff
changeset
|
874 raise StopIteration() |
|
47538a45b878
Cached dataset seems debug, using n_batches... is n_batches around to stay?
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
351
diff
changeset
|
875 assert upper<=len(self.ds) # instead of self.ds.length |
|
223
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
876 #minibatch = Example(self.ds._fields.keys(), |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
877 # [field[self.next_example:upper] |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
878 # for field in self.ds._fields]) |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
879 # tbm: modif to use fieldnames |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
880 values = [] |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
881 for f in self.fieldnames : |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
882 #print 'we have field',f,'in fieldnames' |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
883 values.append( self.ds._fields[f][self.next_example:upper] ) |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
884 minibatch = Example(self.fieldnames,values) |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
885 #print minibatch |
|
36
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
886 self.next_example+=minibatch_size |
|
73
69f97aad3faf
Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents:
72
diff
changeset
|
887 return minibatch |
|
20
266c68cb6136
Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents:
19
diff
changeset
|
888 |
|
223
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
889 # tbm: added fieldnames to handle subset of fieldnames |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
890 return Iterator(self,fieldnames) |
|
20
266c68cb6136
Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents:
19
diff
changeset
|
891 |
|
36
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
892 class HStackedDataSet(DataSet): |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
893 """ |
| 167 | 894 A L{DataSet} that wraps several datasets and shows a view that includes all their fields, |
|
36
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
895 i.e. whose list of fields is the concatenation of their lists of fields. |
|
438440ba0627
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bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
896 |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
897 If a field name is found in more than one of the datasets, then either an error is |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
898 raised or the fields are renamed (either by prefixing the __name__ attribute |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
899 of the dataset + ".", if it exists, or by suffixing the dataset index in the argument list). |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
900 |
| 167 | 901 @todo: automatically detect a chain of stacked datasets due to A | B | C | D ... |
|
36
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
902 """ |
| 41 | 903 def __init__(self,datasets,accept_nonunique_names=False,description=None,field_types=None): |
| 904 DataSet.__init__(self,description,field_types) | |
|
36
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
905 self.datasets=datasets |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
906 self.accept_nonunique_names=accept_nonunique_names |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
907 self.fieldname2dataset={} |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
908 |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
909 def rename_field(fieldname,dataset,i): |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
910 if hasattr(dataset,"__name__"): |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
911 return dataset.__name__ + "." + fieldname |
|
438440ba0627
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parents:
29
diff
changeset
|
912 return fieldname+"."+str(i) |
|
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parents:
29
diff
changeset
|
913 |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
914 # make sure all datasets have the same length and unique field names |
|
438440ba0627
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bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
915 self.length=None |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
916 names_to_change=[] |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
917 for i in xrange(len(datasets)): |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
918 dataset = datasets[i] |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
919 length=len(dataset) |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
920 if self.length: |
|
438440ba0627
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parents:
29
diff
changeset
|
921 assert self.length==length |
|
438440ba0627
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parents:
29
diff
changeset
|
922 else: |
|
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Rewriting dataset.py completely
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parents:
29
diff
changeset
|
923 self.length=length |
|
438440ba0627
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parents:
29
diff
changeset
|
924 for fieldname in dataset.fieldNames(): |
|
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parents:
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diff
changeset
|
925 if fieldname in self.fieldname2dataset: # name conflict! |
|
438440ba0627
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parents:
29
diff
changeset
|
926 if accept_nonunique_names: |
|
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parents:
29
diff
changeset
|
927 fieldname=rename_field(fieldname,dataset,i) |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
928 names2change.append((fieldname,i)) |
|
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Rewriting dataset.py completely
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parents:
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diff
changeset
|
929 else: |
|
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parents:
29
diff
changeset
|
930 raise ValueError("Incompatible datasets: non-unique field name = "+fieldname) |
|
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parents:
29
diff
changeset
|
931 self.fieldname2dataset[fieldname]=i |
|
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Rewriting dataset.py completely
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29
diff
changeset
|
932 for fieldname,i in names_to_change: |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
933 del self.fieldname2dataset[fieldname] |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
934 self.fieldname2dataset[rename_field(fieldname,self.datasets[i],i)]=i |
|
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Rewriting dataset.py completely
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parents:
29
diff
changeset
|
935 |
|
37
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
936 def hasFields(self,*fieldnames): |
|
36
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
937 for fieldname in fieldnames: |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
938 if not fieldname in self.fieldname2dataset: |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
939 return False |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
940 return True |
|
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Rewriting dataset.py completely
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parents:
29
diff
changeset
|
941 |
|
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Rewriting dataset.py completely
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parents:
29
diff
changeset
|
942 def fieldNames(self): |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
943 return self.fieldname2dataset.keys() |
|
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Rewriting dataset.py completely
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parents:
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diff
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|
944 |
| 41 | 945 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
|
36
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Rewriting dataset.py completely
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parents:
29
diff
changeset
|
946 |
|
44
5a85fda9b19b
Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents:
43
diff
changeset
|
947 class HStackedIterator(object): |
|
36
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Rewriting dataset.py completely
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29
diff
changeset
|
948 def __init__(self,hsds,iterators): |
|
438440ba0627
Rewriting dataset.py completely
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29
diff
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|
949 self.hsds=hsds |
|
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Rewriting dataset.py completely
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parents:
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diff
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|
950 self.iterators=iterators |
|
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Rewriting dataset.py completely
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diff
changeset
|
951 def __iter__(self): |
|
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diff
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|
952 return self |
|
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diff
changeset
|
953 def next(self): |
|
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diff
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|
954 # concatenate all the fields of the minibatches |
|
290
9b533cc7874a
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James Bergstra <bergstrj@iro.umontreal.ca>
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diff
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|
955 l=Example() |
| 140 | 956 for iter in self.iterators: |
| 957 l.append_lookuplist(iter.next()) | |
| 958 return l | |
|
36
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Rewriting dataset.py completely
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diff
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|
959 |
| 125 | 960 assert self.hasFields(*fieldnames) |
|
36
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Rewriting dataset.py completely
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diff
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|
961 # find out which underlying datasets are necessary to service the required fields |
|
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Rewriting dataset.py completely
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diff
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|
962 # and construct corresponding minibatch iterators |
| 140 | 963 if fieldnames and fieldnames!=self.fieldNames(): |
|
36
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Rewriting dataset.py completely
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diff
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|
964 datasets=set([]) |
|
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Rewriting dataset.py completely
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diff
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|
965 fields_in_dataset=dict([(dataset,[]) for dataset in datasets]) |
|
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Rewriting dataset.py completely
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diff
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|
966 for fieldname in fieldnames: |
| 136 | 967 dataset=self.datasets[self.fieldname2dataset[fieldname]] |
|
36
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Rewriting dataset.py completely
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diff
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|
968 datasets.add(dataset) |
|
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diff
changeset
|
969 fields_in_dataset[dataset].append(fieldname) |
|
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|
970 datasets=list(datasets) |
|
37
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Factored the minibatch-writing code into an iterator class inside DataSet
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|
971 iterators=[dataset.minibatches(fields_in_dataset[dataset],minibatch_size,n_batches,offset) |
|
36
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diff
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|
972 for dataset in datasets] |
|
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diff
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|
973 else: |
|
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diff
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|
974 datasets=self.datasets |
|
37
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Factored the minibatch-writing code into an iterator class inside DataSet
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diff
changeset
|
975 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
|
976 return HStackedIterator(self,iterators) |
|
36
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diff
changeset
|
977 |
|
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diff
changeset
|
978 |
|
290
9b533cc7874a
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diff
changeset
|
979 def untested_valuesVStack(self,fieldname,fieldvalues): |
|
36
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diff
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|
980 return self.datasets[self.fieldname2dataset[fieldname]].valuesVStack(fieldname,fieldvalues) |
|
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diff
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|
981 |
|
290
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diff
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|
982 def untested_valuesHStack(self,fieldnames,fieldvalues): |
|
36
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Rewriting dataset.py completely
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diff
changeset
|
983 """ |
|
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29
diff
changeset
|
984 We will use the sub-dataset associated with the first fieldname in the fieldnames list |
|
438440ba0627
Rewriting dataset.py completely
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29
diff
changeset
|
985 to do the work, hoping that it can cope with the other values (i.e. won't care |
|
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Rewriting dataset.py completely
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29
diff
changeset
|
986 about the incompatible fieldnames). Hence this heuristic will always work if |
|
438440ba0627
Rewriting dataset.py completely
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29
diff
changeset
|
987 all the fieldnames are of the same sub-dataset. |
|
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diff
changeset
|
988 """ |
|
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diff
changeset
|
989 return self.datasets[self.fieldname2dataset[fieldnames[0]]].valuesHStack(fieldnames,fieldvalues) |
|
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diff
changeset
|
990 |
|
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diff
changeset
|
991 class VStackedDataSet(DataSet): |
|
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Rewriting dataset.py completely
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diff
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|
992 """ |
| 167 | 993 A L{DataSet} that wraps several datasets and shows a view that includes all their examples, |
|
36
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Rewriting dataset.py completely
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29
diff
changeset
|
994 in the order provided. This clearly assumes that they all have the same field names |
|
438440ba0627
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29
diff
changeset
|
995 and all (except possibly the last one) are of finite length. |
|
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diff
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|
996 |
| 167 | 997 @todo: automatically detect a chain of stacked datasets due to A + B + C + D ... |
|
36
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diff
changeset
|
998 """ |
|
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29
diff
changeset
|
999 def __init__(self,datasets): |
|
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29
diff
changeset
|
1000 self.datasets=datasets |
|
438440ba0627
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diff
changeset
|
1001 self.length=0 |
|
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29
diff
changeset
|
1002 self.index2dataset={} |
|
37
73c4212ba5b3
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bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
1003 assert len(datasets)>0 |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
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parents:
36
diff
changeset
|
1004 fieldnames = datasets[-1].fieldNames() |
|
38
d637ad8f7352
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parents:
37
diff
changeset
|
1005 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
|
1006 # 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
|
1007 # to avoid having to search for the appropriate dataset each time and slice is asked for. |
|
36
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parents:
29
diff
changeset
|
1008 for dataset,k in enumerate(datasets[0:-1]): |
|
48
b6730f9a336d
Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents:
46
diff
changeset
|
1009 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
|
1010 L=len(dataset) |
|
36
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Rewriting dataset.py completely
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parents:
29
diff
changeset
|
1011 for i in xrange(L): |
|
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parents:
29
diff
changeset
|
1012 self.index2dataset[self.length+i]=k |
|
38
d637ad8f7352
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bengioy@esprit.iro.umontreal.ca
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37
diff
changeset
|
1013 self.datasets_start_row.append(self.length) |
|
36
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diff
changeset
|
1014 self.length+=L |
|
37
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bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
1015 assert dataset.fieldNames()==fieldnames |
|
38
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Finished first untested version of VStackedDataset
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diff
changeset
|
1016 self.datasets_start_row.append(self.length) |
|
36
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diff
changeset
|
1017 self.length+=len(datasets[-1]) |
|
37
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bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
1018 # If length is very large, we should use a more memory-efficient mechanism |
|
73c4212ba5b3
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bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
1019 # 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
|
1020 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
|
1021 # 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
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36
diff
changeset
|
1022 # TODO |
|
73c4212ba5b3
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bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
1023 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
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36
diff
changeset
|
1024 |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
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36
diff
changeset
|
1025 def __len__(self): |
|
73c4212ba5b3
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bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
1026 return self.length |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
1027 |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
1028 def fieldNames(self): |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
1029 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
|
1030 |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
1031 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
|
1032 return self.datasets[0].hasFields(*fieldnames) |
|
73c4212ba5b3
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bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
1033 |
|
38
d637ad8f7352
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bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
1034 def locate_row(self,row): |
|
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
1035 """Return (dataset_index, row_within_dataset) for global row number""" |
|
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
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37
diff
changeset
|
1036 dataset_index = self.index2dataset[row] |
|
d637ad8f7352
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parents:
37
diff
changeset
|
1037 row_within_dataset = self.datasets_start_row[dataset_index] |
|
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parents:
37
diff
changeset
|
1038 return dataset_index, row_within_dataset |
|
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
1039 |
| 41 | 1040 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
|
44
5a85fda9b19b
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bengioy@grenat.iro.umontreal.ca
parents:
43
diff
changeset
|
1041 |
|
5a85fda9b19b
Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents:
43
diff
changeset
|
1042 class VStackedIterator(object): |
|
37
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Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
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diff
changeset
|
1043 def __init__(self,vsds): |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
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parents:
36
diff
changeset
|
1044 self.vsds=vsds |
|
73c4212ba5b3
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parents:
36
diff
changeset
|
1045 self.next_row=offset |
|
38
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bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
1046 self.next_dataset_index,self.next_dataset_row=self.vsds.locate_row(offset) |
|
37
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bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
1047 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
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parents:
36
diff
changeset
|
1048 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
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36
diff
changeset
|
1049 |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
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36
diff
changeset
|
1050 def next_iterator(self,dataset,starting_offset,batches_left): |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
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diff
changeset
|
1051 L=len(dataset) |
|
73c4212ba5b3
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parents:
36
diff
changeset
|
1052 ds_nbatches = (L-starting_offset)/minibatch_size |
|
73c4212ba5b3
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diff
changeset
|
1053 if batches_left is not None: |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
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diff
changeset
|
1054 ds_nbatches = max(batches_left,ds_nbatches) |
|
73c4212ba5b3
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36
diff
changeset
|
1055 if minibatch_size>L: |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
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diff
changeset
|
1056 ds_minibatch_size=L |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
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parents:
36
diff
changeset
|
1057 n_left_in_mb=minibatch_size-L |
|
38
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
1058 ds_nbatches=1 |
|
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
1059 else: |
|
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
1060 n_left_in_mb=0 |
|
37
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
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36
diff
changeset
|
1061 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
|
1062 L-(starting_offset+ds_nbatches*minibatch_size), n_left_in_mb |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
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parents:
36
diff
changeset
|
1063 |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
1064 def move_to_next_dataset(self): |
|
38
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
1065 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
|
1066 self.current_iterator,self.n_left_at_the_end_of_ds,self.n_left_in_mb= \ |
|
d637ad8f7352
Finished first untested version of VStackedDataset
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parents:
37
diff
changeset
|
1067 self.next_iterator(vsds.datasets[self.next_dataset_index], |
|
d637ad8f7352
Finished first untested version of VStackedDataset
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parents:
37
diff
changeset
|
1068 self.n_left_at_the_end_of_ds,1) |
|
d637ad8f7352
Finished first untested version of VStackedDataset
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37
diff
changeset
|
1069 else: |
|
d637ad8f7352
Finished first untested version of VStackedDataset
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parents:
37
diff
changeset
|
1070 self.next_dataset_index +=1 |
|
d637ad8f7352
Finished first untested version of VStackedDataset
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parents:
37
diff
changeset
|
1071 if self.next_dataset_index==len(self.vsds.datasets): |
|
d637ad8f7352
Finished first untested version of VStackedDataset
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parents:
37
diff
changeset
|
1072 self.next_dataset_index = 0 |
|
d637ad8f7352
Finished first untested version of VStackedDataset
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37
diff
changeset
|
1073 self.current_iterator,self.n_left_at_the_end_of_ds,self.n_left_in_mb= \ |
|
d637ad8f7352
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37
diff
changeset
|
1074 self.next_iterator(vsds.datasets[self.next_dataset_index],starting_offset,n_batches) |
|
37
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Factored the minibatch-writing code into an iterator class inside DataSet
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36
diff
changeset
|
1075 |
|
73c4212ba5b3
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diff
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|
1076 def __iter__(self): |
|
73c4212ba5b3
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diff
changeset
|
1077 return self |
|
73c4212ba5b3
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36
diff
changeset
|
1078 |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
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36
diff
changeset
|
1079 def next(self): |
|
73c4212ba5b3
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diff
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|
1080 dataset=self.vsds.datasets[self.next_dataset_index] |
|
73c4212ba5b3
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diff
changeset
|
1081 mb = self.next_iterator.next() |
|
73c4212ba5b3
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diff
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|
1082 if self.n_left_in_mb: |
|
73c4212ba5b3
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diff
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|
1083 extra_mb = [] |
|
73c4212ba5b3
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36
diff
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|
1084 while self.n_left_in_mb>0: |
|
73c4212ba5b3
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diff
changeset
|
1085 self.move_to_next_dataset() |
|
73c4212ba5b3
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parents:
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diff
changeset
|
1086 extra_mb.append(self.next_iterator.next()) |
|
73
69f97aad3faf
Coded untested ApplyFunctionDataSet and CacheDataSet
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parents:
72
diff
changeset
|
1087 mb = Example(fieldnames, |
|
40
88fd1cce08b9
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bengioy@esprit.iro.umontreal.ca
parents:
39
diff
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|
1088 [dataset.valuesVStack(name, |
|
88fd1cce08b9
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bengioy@esprit.iro.umontreal.ca
parents:
39
diff
changeset
|
1089 [mb[name]]+[b[name] for b in extra_mb]) |
|
88fd1cce08b9
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bengioy@esprit.iro.umontreal.ca
parents:
39
diff
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|
1090 for name in fieldnames]) |
|
88fd1cce08b9
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bengioy@esprit.iro.umontreal.ca
parents:
39
diff
changeset
|
1091 |
|
37
73c4212ba5b3
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36
diff
changeset
|
1092 self.next_row+=minibatch_size |
|
38
d637ad8f7352
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37
diff
changeset
|
1093 self.next_dataset_row+=minibatch_size |
|
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37
diff
changeset
|
1094 if self.next_row+minibatch_size>len(dataset): |
|
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parents:
37
diff
changeset
|
1095 self.move_to_next_dataset() |
|
44
5a85fda9b19b
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43
diff
changeset
|
1096 return examples |
|
5a85fda9b19b
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parents:
43
diff
changeset
|
1097 return VStackedIterator(self) |
|
37
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diff
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|
1098 |
| 41 | 1099 class ArrayFieldsDataSet(DataSet): |
| 1100 """ | |
| 1101 Virtual super-class of datasets whose field values are numpy array, | |
| 1102 thus defining valuesHStack and valuesVStack for sub-classes. | |
| 1103 """ | |
|
268
3f1cd8897fda
reverting dataset
James Bergstra <bergstrj@iro.umontreal.ca>
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266
diff
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|
1104 def __init__(self,description=None,field_types=None): |
|
3f1cd8897fda
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266
diff
changeset
|
1105 DataSet.__init__(self,description,field_types) |
|
290
9b533cc7874a
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James Bergstra <bergstrj@iro.umontreal.ca>
parents:
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diff
changeset
|
1106 def untested_valuesHStack(self,fieldnames,fieldvalues): |
| 41 | 1107 """Concatenate field values horizontally, e.g. two vectors |
| 1108 become a longer vector, two matrices become a wider matrix, etc.""" | |
| 1109 return numpy.hstack(fieldvalues) | |
|
290
9b533cc7874a
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parents:
274
diff
changeset
|
1110 def untested_valuesVStack(self,fieldname,values): |
| 41 | 1111 """Concatenate field values vertically, e.g. two vectors |
| 1112 become a two-row matrix, two matrices become a longer matrix, etc.""" | |
| 1113 return numpy.vstack(values) | |
| 1114 | |
|
316
5fe6d0c93109
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314
diff
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|
1115 |
|
5fe6d0c93109
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diff
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|
1116 |
|
5fe6d0c93109
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314
diff
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|
1117 class NArraysDataSet(ArrayFieldsDataSet) : |
|
5fe6d0c93109
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diff
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|
1118 """ |
|
5fe6d0c93109
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diff
changeset
|
1119 An NArraysDataSet stores fields that are numpy tensor, whose first axis |
|
5fe6d0c93109
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314
diff
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|
1120 iterates over examples. It's a generalization of ArrayDataSet. |
|
5fe6d0c93109
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diff
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|
1121 """ |
|
5fe6d0c93109
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314
diff
changeset
|
1122 #@TODO not completely implemented yet |
|
5fe6d0c93109
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diff
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|
1123 def __init__(self, data_arrays, fieldnames, **kwargs) : |
|
5fe6d0c93109
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diff
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|
1124 """ |
|
5fe6d0c93109
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314
diff
changeset
|
1125 Construct an NArraysDataSet from a list of numpy tensor (data_arrays) and a list |
|
5fe6d0c93109
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314
diff
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|
1126 of fieldnames. The number of arrays must be the same as the number of |
|
5fe6d0c93109
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diff
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|
1127 fieldnames. Each set of numpy tensor must have the same first dimension (first |
|
5fe6d0c93109
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|
1128 axis) corresponding to the number of examples. |
|
5fe6d0c93109
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|
1129 |
|
321
f03ae06fadc8
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parents:
320
diff
changeset
|
1130 Every tensor is treated as a numpy array (using numpy.asarray) |
|
316
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314
diff
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|
1131 """ |
|
318
e2eab74b6a28
NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
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317
diff
changeset
|
1132 ArrayFieldsDataSet.__init__(self,**kwargs) |
|
316
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|
1133 assert len(data_arrays) == len(fieldnames) |
|
5fe6d0c93109
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diff
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|
1134 assert len(fieldnames) > 0 |
|
322
ad8be93b3c55
small bugs fixed with NArrayDataSet
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parents:
321
diff
changeset
|
1135 ndarrays = [numpy.asarray(a) for a in data_arrays] |
|
321
f03ae06fadc8
NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes
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320
diff
changeset
|
1136 lens = [a.shape[0] for a in ndarrays] |
|
f03ae06fadc8
NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes
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diff
changeset
|
1137 num_examples = lens[0] #they must all be equal anyway |
|
316
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|
1138 self._fieldnames = fieldnames |
|
322
ad8be93b3c55
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diff
changeset
|
1139 for k in ndarrays : |
|
321
f03ae06fadc8
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diff
changeset
|
1140 assert k.shape[0] == num_examples |
|
f03ae06fadc8
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diff
changeset
|
1141 self._datas = ndarrays |
|
f03ae06fadc8
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diff
changeset
|
1142 # create dict |
|
f03ae06fadc8
NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes
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diff
changeset
|
1143 self.map_field_idx = dict() |
|
f03ae06fadc8
NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes
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diff
changeset
|
1144 for k in range(len(fieldnames)): |
|
f03ae06fadc8
NArraysDataSet improved, use arrays instead of matrix, also a dictionnary of field indexes
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diff
changeset
|
1145 self.map_field_idx[fieldnames[k]] = k |
|
316
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|
1146 |
|
5fe6d0c93109
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|
1147 |
|
5fe6d0c93109
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|
1148 def __len__(self) : |
|
5fe6d0c93109
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|
1149 """ |
|
5fe6d0c93109
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|
1150 Length of the dataset is based on the first array = data_arrays[0], using its shape |
|
5fe6d0c93109
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|
1151 """ |
|
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1152 return self._datas[0].shape[0] |
|
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1153 |
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1154 def fieldNames(self) : |
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1155 """ |
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1156 Returns the fieldnames as set in self.__init__ |
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1157 """ |
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1158 return self._fieldnames |
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1159 |
|
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1160 def field_pos(self,fieldname) : |
|
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1161 """ |
|
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1162 Returns the index of a given fieldname. Fieldname must exists! see fieldNames(). |
|
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1163 """ |
|
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1164 return self.map_field_idx[fieldname] |
|
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1165 |
|
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|
1166 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
|
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1167 cursor = Example(fieldnames,[0]*len(fieldnames)) |
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1168 fieldnames = self.fieldNames() if fieldnames is None else fieldnames |
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1169 for n in xrange(n_batches): |
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1170 if offset == len(self): |
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|
1171 break |
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1172 for f in range(len(cursor._names)) : |
|
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1173 idx = self.field_pos(cursor._names[f]) |
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|
1174 sub_data = self._datas[idx][offset : offset+minibatch_size] |
|
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1175 cursor._values[f] = sub_data |
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1176 offset += len(sub_data) #can be less than minibatch_size at end |
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1177 yield cursor |
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1178 |
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|
1179 #return ArrayDataSetIterator(self,fieldnames,minibatch_size,n_batches,offset) |
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1180 |
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1181 |
|
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1182 |
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1183 |
| 41 | 1184 class ArrayDataSet(ArrayFieldsDataSet): |
| 1185 """ | |
| 1186 An ArrayDataSet stores the fields as groups of columns in a numpy tensor, | |
| 1187 whose first axis iterates over examples, second axis determines fields. | |
| 1188 If the underlying array is N-dimensional (has N axes), then the field | |
| 1189 values are (N-2)-dimensional objects (i.e. ordinary numbers if N=2). | |
| 1190 """ | |
| 1191 | |
|
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|
1192 def __init__(self, data_array, fields_columns, **kwargs): |
|
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1193 """ |
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|
1194 Construct an ArrayDataSet from the underlying numpy array (data) and |
|
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|
1195 a map (fields_columns) from fieldnames to field columns. The columns of a field are specified |
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|
1196 using the standard arguments for indexing/slicing: integer for a column index, |
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|
1197 slice for an interval of columns (with possible stride), or iterable of column indices. |
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|
1198 """ |
|
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|
1199 ArrayFieldsDataSet.__init__(self, **kwargs) |
| 41 | 1200 self.data=data_array |
|
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diff
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|
1201 self.fields_columns=fields_columns |
| 41 | 1202 |
| 1203 # check consistency and complete slices definitions | |
|
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Testing basic functionality and removing obvious bugs
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diff
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|
1204 for fieldname, fieldcolumns in self.fields_columns.items(): |
| 41 | 1205 if type(fieldcolumns) is int: |
| 1206 assert fieldcolumns>=0 and fieldcolumns<data_array.shape[1] | |
|
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1207 if 1: |
|
227
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|
1208 #I changed this because it didn't make sense to me, |
|
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|
1209 # and it made it more difficult to write my learner. |
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|
1210 # If it breaks stuff, let's talk about it. |
|
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|
1211 # - James 22/05/2008 |
|
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|
1212 self.fields_columns[fieldname]=[fieldcolumns] |
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|
1213 else: |
|
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|
1214 self.fields_columns[fieldname]=fieldcolumns |
| 41 | 1215 elif type(fieldcolumns) is slice: |
| 1216 start,step=None,None | |
| 1217 if not fieldcolumns.start: | |
| 1218 start=0 | |
| 1219 if not fieldcolumns.step: | |
| 1220 step=1 | |
| 1221 if start or step: | |
|
42
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diff
changeset
|
1222 self.fields_columns[fieldname]=slice(start,fieldcolumns.stop,step) |
| 41 | 1223 elif hasattr(fieldcolumns,"__iter__"): # something like a list |
| 1224 for i in fieldcolumns: | |
| 1225 assert i>=0 and i<data_array.shape[1] | |
| 1226 | |
|
42
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diff
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|
1227 def fieldNames(self): |
|
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diff
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|
1228 return self.fields_columns.keys() |
| 41 | 1229 |
|
42
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diff
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|
1230 def __len__(self): |
|
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diff
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|
1231 return len(self.data) |
| 41 | 1232 |
|
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|
1233 def __getitem__(self,key): |
|
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|
1234 """More efficient implementation than the default __getitem__""" |
|
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|
1235 fieldnames=self.fields_columns.keys() |
|
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|
1236 values=self.fields_columns.values() |
| 80 | 1237 if type(key) is int: |
|
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|
1238 return Example(fieldnames, |
|
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|
1239 [self.data[key,col] for col in values]) |
| 80 | 1240 if type(key) is slice: |
|
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|
1241 return Example(fieldnames,[self.data[key,col] for col in values]) |
| 80 | 1242 if type(key) is list: |
| 1243 for i in range(len(key)): | |
| 1244 if self.hasFields(key[i]): | |
| 1245 key[i]=self.fields_columns[key[i]] | |
|
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|
1246 return Example(fieldnames, |
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|
1247 #we must separate differently for list as numpy |
|
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|
1248 # doesn't support self.data[[i1,...],[i2,...]] |
|
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|
1249 # when their is more then two i1 and i2 |
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|
1250 [self.data[key,:][:,col] |
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|
1251 if isinstance(col,list) else |
|
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|
1252 self.data[key,col] for col in values]) |
| 80 | 1253 |
|
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|
1254 # else check for a fieldname |
| 80 | 1255 if self.hasFields(key): |
|
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diff
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|
1256 return self.data[:,self.fields_columns[key]] |
|
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|
1257 # else we are trying to access a property of the dataset |
| 80 | 1258 assert key in self.__dict__ # else it means we are trying to access a non-existing property |
| 1259 return self.__dict__[key] | |
|
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|
1260 |
|
290
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|
1261 def dontuse__iter__(self): |
|
270
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|
1262 class ArrayDataSetIteratorIter(object): |
|
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|
1263 def __init__(self,dataset,fieldnames): |
|
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|
1264 if fieldnames is None: fieldnames = dataset.fieldNames() |
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|
1265 # store the resulting minibatch in a lookup-list of values |
|
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|
1266 self.minibatch = Example(fieldnames,[0]*len(fieldnames)) |
|
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|
1267 self.dataset=dataset |
|
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|
1268 self.current=0 |
|
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|
1269 self.columns = [self.dataset.fields_columns[f] |
|
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|
1270 for f in self.minibatch._names] |
|
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|
1271 self.l = self.dataset.data.shape[0] |
|
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|
1272 def __iter__(self): |
|
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|
1273 return self |
|
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|
1274 def next(self): |
|
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|
1275 #@todo: we suppose that we need to stop only when minibatch_size == 1. |
|
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|
1276 # Otherwise, MinibatchWrapAroundIterator do it. |
|
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|
1277 if self.current>=self.l: |
|
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|
1278 raise StopIteration |
|
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|
1279 sub_data = self.dataset.data[self.current] |
|
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|
1280 self.minibatch._values = [sub_data[c] for c in self.columns] |
|
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|
1281 |
|
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|
1282 self.current+=1 |
|
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|
1283 return self.minibatch |
|
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|
1284 |
|
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|
1285 return ArrayDataSetIteratorIter(self,self.fieldNames()) |
|
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|
1286 |
|
42
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diff
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|
1287 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
|
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|
1288 cursor = Example(fieldnames,[0]*len(fieldnames)) |
|
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|
1289 fieldnames = self.fieldNames() if fieldnames is None else fieldnames |
|
339
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n_minibatches in ArrayDataSet automatically computed
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diff
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|
1290 if n_batches == None: |
|
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|
1291 n_batches = (len(self) - offset) / minibatch_size |
|
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|
1292 for n in xrange(n_batches): |
|
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|
1293 if offset == len(self): |
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|
1294 break |
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|
1295 sub_data = self.data[offset : offset+minibatch_size] |
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|
1296 offset += len(sub_data) #can be less than minibatch_size at end |
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|
1297 cursor._values = [sub_data[:,self.fields_columns[f]] for f in cursor._names] |
|
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|
1298 yield cursor |
|
42
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diff
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|
1299 |
|
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|
1300 #return ArrayDataSetIterator(self,fieldnames,minibatch_size,n_batches,offset) |
|
57
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diff
changeset
|
1301 |
|
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diff
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|
1302 |
|
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diff
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|
1303 class CachedDataSet(DataSet): |
|
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diff
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|
1304 """ |
| 167 | 1305 Wrap a L{DataSet} whose values are computationally expensive to obtain |
|
57
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diff
changeset
|
1306 (e.g. because they involve some computation, or disk access), |
|
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56
diff
changeset
|
1307 so that repeated accesses to the same example are done cheaply, |
|
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diff
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|
1308 by caching every example value that has been accessed at least once. |
|
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diff
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|
1309 |
|
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diff
changeset
|
1310 Optionally, for finite-length dataset, all the values can be computed |
|
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diff
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|
1311 (and cached) upon construction of the CachedDataSet, rather at the |
|
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diff
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|
1312 first access. |
|
73
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diff
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|
1313 |
| 167 | 1314 @todo: when cache_all_upon_construction create mini-batches that are as |
|
77
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diff
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|
1315 large as possible but not so large as to fill up memory. |
|
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|
1316 |
| 167 | 1317 @todo: add disk-buffering capability, so that when the cache becomes too |
|
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diff
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|
1318 big for memory, we cache things on disk, trying to keep in memory only |
|
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diff
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|
1319 the record most likely to be accessed next. |
|
57
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diff
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|
1320 """ |
|
73
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|
1321 def __init__(self,source_dataset,cache_all_upon_construction=False): |
|
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|
1322 self.source_dataset=source_dataset |
|
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diff
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|
1323 self.cache_all_upon_construction=cache_all_upon_construction |
|
152
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diff
changeset
|
1324 self.cached_examples = [] |
|
73
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|
1325 if cache_all_upon_construction: |
|
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|
1326 # this potentially brings all the source examples |
|
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|
1327 # into memory at once, which may be too much |
|
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|
1328 # the work could possibly be done by minibatches |
|
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|
1329 # that are as large as possible but no more than what memory allows. |
|
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|
1330 # |
|
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|
1331 # field_values is supposed to be an DataSetFields, that inherits from LookupList |
|
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|
1332 #fields_values = source_dataset.minibatches(minibatch_size=len(source_dataset)).__iter__().next() |
|
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|
1333 fields_values = DataSetFields(source_dataset,None) |
|
152
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diff
changeset
|
1334 assert all([len(self)==len(field_values) for field_values in fields_values]) |
|
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diff
changeset
|
1335 for example in fields_values.examples(): |
|
171
895b4b60f5e8
bugfix. Otherwise the example was writed over and not a new one was returned
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
167
diff
changeset
|
1336 self.cached_examples.append(copy.copy(example)) |
|
57
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diff
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|
1337 |
|
73
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diff
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|
1338 self.fieldNames = source_dataset.fieldNames |
|
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diff
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|
1339 self.hasFields = source_dataset.hasFields |
|
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|
1340 self.valuesHStack = source_dataset.valuesHStack |
|
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|
1341 self.valuesVStack = source_dataset.valuesVStack |
|
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diff
changeset
|
1342 |
|
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changeset
|
1343 def __len__(self): |
|
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diff
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|
1344 return len(self.source_dataset) |
|
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diff
changeset
|
1345 |
|
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diff
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|
1346 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
|
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diff
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|
1347 class CacheIterator(object): |
|
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diff
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|
1348 def __init__(self,dataset): |
|
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diff
changeset
|
1349 self.dataset=dataset |
|
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|
1350 self.current=offset |
|
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|
1351 self.all_fields = self.dataset.fieldNames()==fieldnames |
|
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|
1352 self.n_batches = n_batches |
|
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|
1353 self.batch_counter = 0 |
|
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|
1354 def __iter__(self): return self |
|
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|
1355 def next(self): |
|
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|
1356 self.batch_counter += 1 |
|
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|
1357 if self.n_batches and self.batch_counter > self.n_batches : |
|
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|
1358 raise StopIteration() |
|
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diff
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|
1359 upper = self.current+minibatch_size |
|
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|
1360 if upper > len(self.dataset.source_dataset): |
|
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|
1361 raise StopIteration() |
|
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|
1362 cache_len = len(self.dataset.cached_examples) |
|
135
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Fixed bugs in dataset to make test_mlp.py work
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134
diff
changeset
|
1363 if upper>cache_len: # whole minibatch is not already in cache |
|
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|
1364 # cache everything from current length to upper |
|
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|
1365 #for example in self.dataset.source_dataset[cache_len:upper]: |
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|
1366 for example in self.dataset.source_dataset.subset[cache_len:upper]: |
|
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|
1367 self.dataset.cached_examples.append(example) |
|
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|
1368 all_fields_minibatch = Example(self.dataset.fieldNames(), |
|
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changeset
|
1369 zip(*self.dataset.cached_examples[self.current:self.current+minibatch_size])) |
|
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|
1370 |
|
163
d7d67651d67c
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diff
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|
1371 self.current+=minibatch_size |
|
254
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|
1372 if self.all_fields: |
|
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|
1373 return all_fields_minibatch |
|
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diff
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|
1374 return Example(fieldnames,[all_fields_minibatch[name] for name in fieldnames]) |
|
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|
1375 return CacheIterator(self) |
|
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diff
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|
1376 |
|
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|
1377 def dontuse__getitem__(self,i): |
| 153 | 1378 if type(i)==int and len(self.cached_examples)>i: |
| 1379 return self.cached_examples[i] | |
| 1380 else: | |
|
251
7e6edee187e3
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Frederic Bastien <bastienf@iro.umontreal.ca>
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243
diff
changeset
|
1381 return self.source_dataset[i] |
|
252
856d14dc4468
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1382 |
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1383 def __iter__(self): |
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1384 class CacheIteratorIter(object): |
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1385 def __init__(self,dataset): |
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1386 self.dataset=dataset |
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1387 self.l = len(dataset) |
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1388 self.current = 0 |
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1389 self.fieldnames = self.dataset.fieldNames() |
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1390 self.example = Example(self.fieldnames,[0]*len(self.fieldnames)) |
|
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1391 def __iter__(self): return self |
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1392 def next(self): |
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1393 if self.current>=self.l: |
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1394 raise StopIteration |
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1395 cache_len = len(self.dataset.cached_examples) |
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1396 if self.current>=cache_len: # whole minibatch is not already in cache |
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1397 # cache everything from current length to upper |
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1398 self.dataset.cached_examples.append( |
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1399 self.dataset.source_dataset[self.current]) |
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1400 self.example._values = self.dataset.cached_examples[self.current] |
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1401 self.current+=1 |
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1402 return self.example |
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1403 |
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1404 return CacheIteratorIter(self) |
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1405 |
|
57
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|
1406 class ApplyFunctionDataSet(DataSet): |
|
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1407 """ |
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1408 A L{DataSet} that contains as fields the results of applying a |
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1409 given function example-wise or minibatch-wise to all the fields of |
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1410 an input dataset. The output of the function should be an iterable |
|
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1411 (e.g. a list or a LookupList) over the resulting values. |
|
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1412 |
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1413 The function take as input the fields of the dataset, not the examples. |
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1414 |
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1415 In minibatch mode, the function is expected to work on minibatches |
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1416 (takes a minibatch in input and returns a minibatch in output). More |
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1417 precisely, it means that each element of the input or output list |
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1418 should be iterable and indexable over the individual example values |
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1419 (typically these elements will be numpy arrays). All of the elements |
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1420 in the input and output lists should have the same length, which is |
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|
1421 the length of the minibatch. |
|
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|
1422 |
|
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|
1423 The function is applied each time an example or a minibatch is accessed. |
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|
1424 To avoid re-doing computation, wrap this dataset inside a CachedDataSet. |
|
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|
1425 |
|
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|
1426 If the values_{h,v}stack functions are not provided, then |
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|
1427 the input_dataset.values{H,V}Stack functions are used by default. |
|
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|
1428 |
|
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|
1429 """ |
|
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|
1430 |
|
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|
1431 def __init__(self,input_dataset,function,output_names,minibatch_mode=True, |
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|
1432 values_hstack=None,values_vstack=None, |
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|
1433 description=None,fieldtypes=None): |
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|
1434 """ |
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|
1435 Constructor takes an input dataset that has as many fields as the function |
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|
1436 expects as inputs. The resulting dataset has as many fields as the function |
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|
1437 produces as outputs, and that should correspond to the number of output names |
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|
1438 (provided in a list). |
|
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|
1439 |
|
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|
1440 Note that the expected semantics of the function differs in minibatch mode |
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|
1441 (it takes minibatches of inputs and produces minibatches of outputs, as |
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|
1442 documented in the class comment). |
|
211
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in __get__, problem if the i.stop was None, i being the slice, added one line replacing None by the len(self)
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diff
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|
1443 |
|
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|
1444 TBM: are filedtypes the old field types (from input_dataset) or the new ones |
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|
1445 (for the new dataset created)? |
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|
1446 """ |
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|
1447 self.input_dataset=input_dataset |
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|
1448 self.function=function |
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|
1449 self.output_names=output_names |
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|
1450 self.minibatch_mode=minibatch_mode |
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|
1451 DataSet.__init__(self,description,fieldtypes) |
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|
1452 self.valuesHStack = values_hstack if values_hstack else input_dataset.valuesHStack |
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|
1453 self.valuesVStack = values_vstack if values_vstack else input_dataset.valuesVStack |
|
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|
1454 |
|
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|
1455 def __len__(self): |
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|
1456 return len(self.input_dataset) |
|
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|
1457 |
|
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|
1458 def fieldNames(self): |
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|
1459 return self.output_names |
|
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|
1460 |
|
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diff
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|
1461 def minibatches_nowrap(self, fieldnames, *args, **kwargs): |
|
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|
1462 all_input_fieldNames = self.input_dataset.fieldNames() |
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diff
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|
1463 mbnw = self.input_dataset.minibatches_nowrap |
|
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|
1464 |
|
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|
1465 for input_fields in mbnw(all_input_fieldNames, *args, **kwargs): |
|
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|
1466 if self.minibatch_mode: |
|
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|
1467 all_output_fields = self.function(*input_fields) |
|
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|
1468 else: |
|
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|
1469 input_examples = zip(*input_fields) #makes so that [i] means example i |
|
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|
1470 output_examples = [self.function(*input_example) |
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|
1471 for input_example in input_examples] |
|
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|
1472 all_output_fields = zip(*output_examples) |
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|
1473 |
|
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|
1474 all_outputs = Example(self.output_names, all_output_fields) |
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|
1475 #print 'input_fields', input_fields |
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|
1476 #print 'all_outputs', all_outputs |
|
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|
1477 if fieldnames==self.output_names: |
| 293 | 1478 rval = all_outputs |
|
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|
1479 else: |
| 293 | 1480 rval = Example(fieldnames,[all_outputs[name] for name in fieldnames]) |
|
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|
1481 #print 'rval', rval |
|
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diff
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|
1482 #print '--------' |
| 293 | 1483 yield rval |
|
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|
1484 |
|
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|
1485 def untested__iter__(self): # only implemented for increased efficiency |
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|
1486 class ApplyFunctionSingleExampleIterator(object): |
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|
1487 def __init__(self,output_dataset): |
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|
1488 self.current=0 |
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|
1489 self.output_dataset=output_dataset |
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|
1490 self.input_iterator=output_dataset.input_dataset.__iter__() |
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|
1491 def __iter__(self): return self |
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1492 def next(self): |
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1493 if self.output_dataset.minibatch_mode: |
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1494 function_inputs = [[input] for input in self.input_iterator.next()] |
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1495 outputs = self.output_dataset.function(*function_inputs) |
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1496 assert all([hasattr(output,'__iter__') for output in outputs]) |
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1497 function_outputs = [output[0] for output in outputs] |
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1498 else: |
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1499 function_inputs = self.input_iterator.next() |
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1500 function_outputs = self.output_dataset.function(*function_inputs) |
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1501 return Example(self.output_dataset.output_names,function_outputs) |
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1502 return ApplyFunctionSingleExampleIterator(self) |
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1503 |
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1504 def supervised_learning_dataset(src_dataset,input_fields,target_fields,weight_field=None): |
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1505 """ |
| 167 | 1506 Wraps an arbitrary L{DataSet} into one for supervised learning tasks |
| 1507 by forcing the user to define a set of fields as the 'input' field | |
| 1508 and a set of fields as the 'target' field. Optionally, a single | |
| 1509 weight_field can also be defined. | |
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1510 """ |
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1511 args = ((input_fields,'input'),(output_fields,'target')) |
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1512 if weight_field: args+=(([weight_field],'weight')) |
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1513 return src_dataset.merge_fields(*args) |
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1514 |
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1515 |
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1516 |
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1517 |