Mercurial > pylearn
annotate dataset.py @ 318:e2eab74b6a28
NArraysDataSet, a generalization ArrayDataSet where every field is a ndarray, is implemented. Not really tested aside basic stuff...
| author | Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca> |
|---|---|
| date | Wed, 11 Jun 2008 16:59:03 -0400 |
| parents | 14081904d8f3 |
| children | 6441e568745e |
| rev | line source |
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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 |
| 195 attributeNames = property(lambda self: copy.copy(self._attribute_names)) | |
| 196 | |
| 197 def __contains__(self, fieldname): | |
| 198 return (fieldname in self.fieldNames()) \ | |
| 199 or (fieldname in self.attributeNames()) | |
| 200 | |
| 201 def __iter__(self): | |
| 202 """Supports the syntax "for i in dataset: ..." | |
| 78 | 203 |
| 292 | 204 Using this syntax, "i" will be an Example instance (or equivalent) with |
| 205 all the fields of DataSet self. Every field of "i" will give access to | |
| 206 a field of a single example. Fields should be accessible via | |
| 207 i["fielname"] or i[3] (in the order defined by the elements of the | |
| 208 Example returned by this iterator), but the derived class is free | |
| 209 to accept any type of identifier, and add extra functionality to the iterator. | |
| 210 | |
| 211 The default implementation calls the minibatches iterator and extracts the first example of each field. | |
| 212 """ | |
| 213 return DataSet.MinibatchToSingleExampleIterator(self.minibatches(None, minibatch_size = 1)) | |
| 214 | |
| 215 def __len__(self): | |
| 216 """ | |
| 217 len(dataset) returns the number of examples in the dataset. | |
| 218 By default, a DataSet is a 'stream', i.e. it has an unbounded length (sys.maxint). | |
| 219 Sub-classes which implement finite-length datasets should redefine this method. | |
| 220 Some methods only make sense for finite-length datasets. | |
| 221 """ | |
| 222 return None | |
| 223 | |
| 78 | 224 |
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225 class MinibatchToSingleExampleIterator(object): |
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226 """ |
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227 Converts the result of minibatch iterator with minibatch_size==1 into |
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228 single-example values in the result. Therefore the result of |
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229 iterating on the dataset itself gives a sequence of single examples |
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230 (whereas the result of iterating over minibatches gives in each |
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231 Example field an iterable object over the individual examples in |
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232 the minibatch). |
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233 """ |
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234 def __init__(self, minibatch_iterator): |
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235 self.minibatch_iterator = minibatch_iterator |
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236 self.minibatch = None |
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237 def __iter__(self): #makes for loop work |
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238 return self |
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239 def next(self): |
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240 size1_minibatch = self.minibatch_iterator.next() |
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241 if not self.minibatch: |
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242 self.minibatch = Example(size1_minibatch.keys(),[value[0] for value in size1_minibatch.values()]) |
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243 else: |
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244 self.minibatch._values = [value[0] for value in size1_minibatch.values()] |
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245 return self.minibatch |
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246 |
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247 def next_index(self): |
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248 return self.minibatch_iterator.next_index() |
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249 |
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250 class MinibatchWrapAroundIterator(object): |
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251 """ |
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252 An iterator for minibatches that handles the case where we need to wrap around the |
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253 dataset because n_batches*minibatch_size > len(dataset). It is constructed from |
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254 a dataset that provides a minibatch iterator that does not need to handle that problem. |
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255 This class is a utility for dataset subclass writers, so that they do not have to handle |
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256 this issue multiple times, nor check that fieldnames are valid, nor handle the |
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257 empty fieldnames (meaning 'use all the fields'). |
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258 """ |
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259 def __init__(self,dataset,fieldnames,minibatch_size,n_batches,offset): |
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260 self.dataset=dataset |
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261 self.fieldnames=fieldnames |
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262 self.minibatch_size=minibatch_size |
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263 self.n_batches=n_batches |
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264 self.n_batches_done=0 |
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265 self.next_row=offset |
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266 self.L=len(dataset) |
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267 self.offset=offset % self.L |
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268 ds_nbatches = (self.L-self.next_row)/self.minibatch_size |
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269 if n_batches is not None: |
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270 ds_nbatches = min(n_batches,ds_nbatches) |
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271 if fieldnames: |
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272 assert dataset.hasFields(*fieldnames) |
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273 else: |
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274 self.fieldnames=dataset.fieldNames() |
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275 self.iterator = self.dataset.minibatches_nowrap(self.fieldnames,self.minibatch_size, ds_nbatches,self.next_row) |
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276 |
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277 def __iter__(self): |
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278 return self |
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279 |
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280 def next_index(self): |
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281 return self.next_row |
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282 |
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283 def next(self): |
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284 if self.n_batches and self.n_batches_done==self.n_batches: |
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285 raise StopIteration |
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286 elif not self.n_batches and self.next_row ==self.L: |
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287 raise StopIteration |
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288 upper = self.next_row+self.minibatch_size |
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289 if upper <=self.L: |
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290 minibatch = self.iterator.next() |
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291 else: |
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292 if not self.n_batches: |
|
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293 upper=min(upper, self.L) |
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294 # if their is not a fixed number of batch, we continue to the end of the dataset. |
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295 # this can create a minibatch that is smaller then the minibatch_size |
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296 assert (self.L-self.next_row)<=self.minibatch_size |
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297 minibatch = self.dataset.minibatches_nowrap(self.fieldnames,self.L-self.next_row,1,self.next_row).next() |
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298 else: |
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299 # we must concatenate (vstack) the bottom and top parts of our minibatch |
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300 # first get the beginning of our minibatch (top of dataset) |
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301 first_part = self.dataset.minibatches_nowrap(self.fieldnames,self.L-self.next_row,1,self.next_row).next() |
|
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302 second_part = self.dataset.minibatches_nowrap(self.fieldnames,upper-self.L,1,0).next() |
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303 minibatch = Example(self.fieldnames, |
|
268
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304 [self.dataset.valuesVStack(name,[first_part[name],second_part[name]]) |
|
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305 for name in self.fieldnames]) |
|
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306 self.next_row=upper |
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307 self.n_batches_done+=1 |
|
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308 if upper >= self.L and self.n_batches: |
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309 self.next_row -= self.L |
|
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310 ds_nbatches = (self.L-self.next_row)/self.minibatch_size |
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311 if self.n_batches is not None: |
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312 ds_nbatches = min(self.n_batches,ds_nbatches) |
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313 self.iterator = self.dataset.minibatches_nowrap(self.fieldnames,self.minibatch_size, |
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314 ds_nbatches,self.next_row) |
|
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315 return DataSetFields(MinibatchDataSet(minibatch,self.dataset.valuesVStack, |
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316 self.dataset.valuesHStack), |
|
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317 minibatch.keys()) |
|
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318 |
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319 |
|
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320 minibatches_fieldnames = None |
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321 minibatches_minibatch_size = 1 |
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322 minibatches_n_batches = None |
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323 def minibatches(self, |
|
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324 fieldnames = minibatches_fieldnames, |
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325 minibatch_size = minibatches_minibatch_size, |
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326 n_batches = minibatches_n_batches, |
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327 offset = 0): |
|
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328 """ |
|
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329 Return an iterator that supports three forms of syntax: |
|
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330 |
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331 for i in dataset.minibatches(None,**kwargs): ... |
| 16 | 332 |
|
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333 for i in dataset.minibatches([f1, f2, f3],**kwargs): ... |
| 16 | 334 |
|
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335 for i1, i2, i3 in dataset.minibatches([f1, f2, f3],**kwargs): ... |
| 16 | 336 |
|
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337 Using the first two syntaxes, "i" will be an indexable object, such as a list, |
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338 tuple, or Example instance. In both cases, i[k] is a list-like container |
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339 of a batch of current examples. In the second case, i[0] is |
|
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340 list-like container of the f1 field of a batch current examples, i[1] is |
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341 a list-like container of the f2 field, etc. |
|
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342 |
|
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343 Using the first syntax, all the fields will be returned in "i". |
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344 Using the third syntax, i1, i2, i3 will be list-like containers of the |
|
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345 f1, f2, and f3 fields of a batch of examples on each loop iteration. |
|
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346 |
|
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347 The minibatches iterator is expected to return upon each call to next() |
|
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348 a DataSetFields object, which is a Example (indexed by the field names) whose |
| 80 | 349 elements are iterable and indexable over the minibatch examples, and which keeps a pointer to |
|
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350 a sub-dataset that can be used to iterate over the individual examples |
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351 in the minibatch. Hence a minibatch can be converted back to a regular |
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352 dataset or its fields can be looked at individually (and possibly iterated over). |
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353 |
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354 PARAMETERS |
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355 - fieldnames (list of any type, default None): |
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356 The loop variables i1, i2, i3 (in the example above) should contain the |
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357 f1, f2, and f3 fields of the current batch of examples. If None, the |
|
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358 derived class can choose a default, e.g. all fields. |
| 16 | 359 |
|
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360 - minibatch_size (integer, default 1) |
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361 On every iteration, the variables i1, i2, i3 will have |
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362 exactly minibatch_size elements. e.g. len(i1) == minibatch_size |
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363 |
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364 - n_batches (integer, default None) |
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365 The iterator will loop exactly this many times, and then stop. If None, |
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366 the derived class can choose a default. If (-1), then the returned |
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367 iterator should support looping indefinitely. |
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368 |
|
37
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369 - offset (integer, default 0) |
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370 The iterator will start at example 'offset' in the dataset, rather than the default. |
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371 |
|
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372 Note: A list-like container is something like a tuple, list, numpy.ndarray or |
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373 any other object that supports integer indexing and slicing. |
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374 |
|
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375 """ |
|
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376 return DataSet.MinibatchWrapAroundIterator(self,fieldnames,minibatch_size,n_batches,offset) |
|
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377 |
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378 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
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379 """ |
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380 This is the minibatches iterator generator that sub-classes must define. |
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381 It does not need to worry about wrapping around multiple times across the dataset, |
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382 as this is handled by MinibatchWrapAroundIterator when DataSet.minibatches() is called. |
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383 The next() method of the returned iterator does not even need to worry about |
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384 the termination condition (as StopIteration will be raised by DataSet.minibatches |
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385 before an improper call to minibatches_nowrap's next() is made). |
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386 That next() method can assert that its next row will always be within [0,len(dataset)). |
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387 The iterator returned by minibatches_nowrap does not need to implement |
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388 a next_index() method either, as this will be provided by MinibatchWrapAroundIterator. |
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389 """ |
|
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390 raise AbstractFunction() |
|
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391 |
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392 def is_unbounded(self): |
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393 """ |
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394 Tests whether a dataset is unbounded (e.g. a stream). |
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395 """ |
| 123 | 396 return len(self)==maxint |
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397 |
|
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398 def hasFields(self,*fieldnames): |
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399 """ |
|
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400 Return true if the given field name (or field names, if multiple arguments are |
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401 given) is recognized by the DataSet (i.e. can be used as a field name in one |
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402 of the iterators). |
|
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403 |
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404 The default implementation may be inefficient (O(# fields in dataset)), as it calls the fieldNames() |
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405 method. Many datasets may store their field names in a dictionary, which would allow more efficiency. |
|
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406 """ |
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407 return len(unique_elements_list_intersection(fieldnames,self.fieldNames()))>0 |
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408 |
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409 def fieldNames(self): |
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410 """ |
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411 Return the list of field names that are supported by the iterators, |
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412 and for which hasFields(fieldname) would return True. |
|
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413 """ |
|
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414 raise AbstractFunction() |
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415 |
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416 def __call__(self,*fieldnames): |
|
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417 """ |
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418 Return a dataset that sees only the fields whose name are specified. |
|
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419 """ |
|
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420 assert self.hasFields(*fieldnames) |
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421 return self.fields(*fieldnames).examples() |
|
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422 |
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423 def fields(self,*fieldnames): |
|
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424 """ |
|
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425 Return a DataSetFields object associated with this dataset. |
|
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426 """ |
|
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427 return DataSetFields(self,fieldnames) |
|
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428 |
|
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429 def getitem_key(self, fieldname): |
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430 """A not-so-well thought-out place to put code that used to be in |
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431 getitem. |
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432 """ |
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433 #removing as per discussion June 4. --JSB |
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434 |
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435 i = fieldname |
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436 # else check for a fieldname |
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437 if self.hasFields(i): |
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438 return self.minibatches(fieldnames=[i],minibatch_size=len(self),n_batches=1,offset=0).next()[0] |
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439 # else we are trying to access a property of the dataset |
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440 assert i in self.__dict__ # else it means we are trying to access a non-existing property |
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441 return self.__dict__[i] |
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442 |
|
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443 def __getitem__(self,i): |
|
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444 """ |
|
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445 @rtype: Example |
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446 @returns: single or multiple examples |
|
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447 |
|
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448 @type i: integer or slice or <iterable> of integers |
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449 @param i: |
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450 dataset[i] returns the (i+1)-th example of the dataset. |
|
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451 dataset[i:j] returns a LookupList with examples i,i+1,...,j-1. |
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452 dataset[i:j:s] returns a LookupList with examples i,i+2,i+4...,j-2. |
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453 dataset[[i1,i2,..,in]] returns a LookupList with examples i1,i2,...,in. |
|
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454 |
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455 @note: |
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456 Some stream datasets may be unable to implement random access, i.e. |
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457 arbitrary slicing/indexing because they can only iterate through |
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458 examples one or a minibatch at a time and do not actually store or keep |
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459 past (or future) examples. |
|
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460 |
|
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461 The default implementation of getitem uses the minibatches iterator |
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462 to obtain one example, one slice, or a list of examples. It may not |
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463 always be the most efficient way to obtain the result, especially if |
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464 the data are actually stored in a memory array. |
|
28
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465 """ |
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466 |
|
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467 if type(i) is int: |
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468 assert i >= 0 # TBM: see if someone complains and want negative i |
|
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469 if i >= len(self) : |
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470 raise IndexError |
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471 i_batch = self.minibatches_nowrap(self.fieldNames(), |
| 293 | 472 minibatch_size=1, n_batches=1, offset=i) |
|
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473 return DataSet.MinibatchToSingleExampleIterator(i_batch).next() |
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474 |
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475 #if i is a contiguous slice |
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476 if type(i) is slice and (i.step in (None, 1)): |
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477 offset = 0 if i.start is None else i.start |
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478 upper_bound = len(self) if i.stop is None else i.stop |
|
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479 upper_bound = min(len(self) , upper_bound) |
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480 #return MinibatchDataSet(self.minibatches_nowrap(self.fieldNames(), |
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481 # minibatch_size=upper_bound - offset, |
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482 # n_batches=1, |
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483 # offset=offset).next()) |
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484 # now returns a LookupList |
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485 return self.minibatches_nowrap(self.fieldNames(), |
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486 minibatch_size=upper_bound - offset, |
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487 n_batches=1, |
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488 offset=offset).next() |
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489 |
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490 # if slice has a step param, convert it to list and handle it with the |
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491 # list code |
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492 if type(i) is slice: |
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493 offset = 0 if i.start is None else i.start |
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494 upper_bound = len(self) if i.stop is None else i.stop |
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495 upper_bound = min(len(self) , upper_bound) |
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496 i = list(range(offset, upper_bound, i.step)) |
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497 |
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498 # handle tuples, arrays, lists |
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499 if hasattr(i, '__getitem__'): |
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500 for idx in i: |
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501 #dis-allow nested slices |
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502 if not isinstance(idx, int): |
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503 raise TypeError(idx) |
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504 if idx >= len(self) : |
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505 raise IndexError |
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506 # call back into self.__getitem__ |
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507 examples = [self.minibatches_nowrap(self.fieldNames(), |
| 293 | 508 minibatch_size=1, n_batches=1, offset=ii).next() |
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509 for ii in i] |
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510 # re-index the fields in each example by field instead of by example |
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511 field_values = [[] for blah in self.fieldNames()] |
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512 for e in examples: |
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513 for f,v in zip(field_values, e): |
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514 f.append(v) |
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515 #build them into a LookupList (a.ka. Example) |
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516 zz = zip(self.fieldNames(),field_values) |
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517 vst = [self.valuesVStack(fieldname,field_values) for fieldname,field_values in zz] |
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518 example = Example(self.fieldNames(), vst) |
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519 #return MinibatchDataSet(example, self.valuesVStack, self.valuesHStack) |
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520 # now returns a LookupList |
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521 return example |
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522 |
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523 # what in the world is i? |
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524 raise TypeError(i, type(i)) |
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525 |
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526 |
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527 """ |
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528 Enables the call dataset.subset[a:b:c] that will return a DataSet |
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529 around the examples returned by __getitem__(slice(a,b,c)) |
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530 |
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531 @SEE DataSet.__getsubset(self) |
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532 """ |
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533 subset = property(lambda s : s.__getsubset(),doc="returns a subset as a DataSet") |
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534 |
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535 |
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536 def __getsubset(self) : |
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537 """ |
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538 Enables the call data.subset[a:b:c], returns a DataSet. |
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539 Default implementation is a simple wrap around __getitem__() using MinibatchDataSet. |
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540 |
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541 @RETURN DataSet |
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542 @SEE DataSet.subset = property(lambda s : s.__getsubset()) |
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543 """ |
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544 _self = self |
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545 class GetSliceReturnsDataSet(object) : |
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546 def __getitem__(self,slice) : |
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547 return MinibatchDataSet(_self.__getitem__(slice)) |
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548 return GetSliceReturnsDataSet() |
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549 |
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550 |
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551 |
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552 def valuesHStack(self,fieldnames,fieldvalues): |
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553 """ |
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554 Return a value that corresponds to concatenating (horizontally) several field values. |
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555 This can be useful to merge some fields. The implementation of this operation is likely |
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556 to involve a copy of the original values. When the values are numpy arrays, the |
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557 result should be numpy.hstack(values). If it makes sense, this operation should |
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558 work as well when each value corresponds to multiple examples in a minibatch |
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559 e.g. if each value is a Ni-vector and a minibatch of length L is a LxNi matrix, |
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560 then the result should be a Lx(N1+N2+..) matrix equal to numpy.hstack(values). |
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561 The default is to use numpy.hstack for numpy.ndarray values, and a list |
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562 pointing to the original values for other data types. |
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563 """ |
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564 all_numpy=True |
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565 for value in fieldvalues: |
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566 if not type(value) is numpy.ndarray: |
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567 all_numpy=False |
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568 if all_numpy: |
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569 return numpy.hstack(fieldvalues) |
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570 # the default implementation of horizontal stacking is to put values in a list |
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571 return fieldvalues |
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572 |
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573 def valuesVStack(self,fieldname,values): |
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574 """ |
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575 @param fieldname: the name of the field from which the values were taken |
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576 @type fieldname: any type |
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577 |
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578 @param values: bits near the beginning or end of the dataset |
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579 @type values: list of minibatches (returned by minibatch_nowrap) |
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580 |
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581 @return: the concatenation (stacking) of the values |
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582 @rtype: something suitable as a minibatch field |
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583 """ |
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584 rval = [] |
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585 for v in values: |
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586 rval.extend(v) |
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587 return rval |
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588 |
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589 def __or__(self,other): |
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590 """ |
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591 dataset1 | dataset2 returns a dataset whose list of fields is the concatenation of the list of |
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592 fields of the argument datasets. This only works if they all have the same length. |
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593 """ |
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594 return HStackedDataSet([self,other]) |
|
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595 |
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596 def __and__(self,other): |
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597 """ |
|
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598 dataset1 & dataset2 is a dataset that concatenates the examples from the argument datasets |
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599 (and whose length is the sum of the length of the argument datasets). This only |
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600 works if they all have the same fields. |
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601 """ |
|
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602 return VStackedDataSet([self,other]) |
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603 |
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604 def hstack(datasets): |
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605 """ |
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606 hstack(dataset1,dataset2,...) returns dataset1 | datataset2 | ... |
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607 which is a dataset whose fields list is the concatenation of the fields |
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608 of the individual datasets. |
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609 """ |
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610 assert len(datasets)>0 |
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611 if len(datasets)==1: |
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612 return datasets[0] |
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613 return HStackedDataSet(datasets) |
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614 |
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615 def vstack(datasets): |
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616 """ |
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617 vstack(dataset1,dataset2,...) returns dataset1 & datataset2 & ... |
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618 which is a dataset which iterates first over the examples of dataset1, then |
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619 over those of dataset2, etc. |
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620 """ |
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621 assert len(datasets)>0 |
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622 if len(datasets)==1: |
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623 return datasets[0] |
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624 return VStackedDataSet(datasets) |
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625 |
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626 class FieldsSubsetDataSet(DataSet): |
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627 """ |
| 167 | 628 A sub-class of L{DataSet} that selects a subset of the fields. |
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629 """ |
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630 def __init__(self,src,fieldnames): |
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631 self.src=src |
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632 self.fieldnames=fieldnames |
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633 assert src.hasFields(*fieldnames) |
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634 self.valuesHStack = src.valuesHStack |
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635 self.valuesVStack = src.valuesVStack |
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636 |
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637 def __len__(self): return len(self.src) |
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638 |
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639 def fieldNames(self): |
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640 return self.fieldnames |
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641 |
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642 def __iter__(self): |
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643 class FieldsSubsetIterator(object): |
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644 def __init__(self,ds): |
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645 self.ds=ds |
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646 self.src_iter=ds.src.__iter__() |
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647 self.example=None |
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648 def __iter__(self): return self |
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649 def next(self): |
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650 complete_example = self.src_iter.next() |
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651 if self.example: |
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652 self.example._values=[complete_example[field] |
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653 for field in self.ds.fieldnames] |
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654 else: |
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655 self.example=Example(self.ds.fieldnames, |
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656 [complete_example[field] for field in self.ds.fieldnames]) |
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657 return self.example |
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658 return FieldsSubsetIterator(self) |
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659 |
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660 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
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661 assert self.hasFields(*fieldnames) |
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662 return self.src.minibatches_nowrap(fieldnames,minibatch_size,n_batches,offset) |
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663 def dontuse__getitem__(self,i): |
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664 return FieldsSubsetDataSet(self.src[i],self.fieldnames) |
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665 |
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666 |
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667 class DataSetFields(Example): |
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668 """ |
| 167 | 669 Although a L{DataSet} iterates over examples (like rows of a matrix), an associated |
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670 DataSetFields iterates over fields (like columns of a matrix), and can be understood |
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671 as a transpose of the associated dataset. |
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672 |
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673 To iterate over fields, one can do |
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674 * for fields in dataset.fields() |
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675 * for fields in dataset(field1,field2,...).fields() to select a subset of fields |
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676 * for fields in dataset.fields(field1,field2,...) to select a subset of fields |
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677 and each of these fields is iterable over the examples: |
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678 * for field_examples in dataset.fields(): |
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679 for example_value in field_examples: |
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680 ... |
|
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681 but when the dataset is a stream (unbounded length), it is not recommended to do |
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682 such things because the underlying dataset may refuse to access the different fields in |
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683 an unsynchronized ways. Hence the fields() method is illegal for streams, by default. |
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684 The result of fields() is a DataSetFields object, which iterates over fields, |
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685 and whose elements are iterable over examples. A DataSetFields object can |
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686 be turned back into a DataSet with its examples() method: |
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687 dataset2 = dataset1.fields().examples() |
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688 and dataset2 should behave exactly like dataset1 (in fact by default dataset2==dataset1). |
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689 |
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690 DataSetFields can be concatenated vertically or horizontally. To be consistent with |
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691 the syntax used for DataSets, the | concatenates the fields and the & concatenates |
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692 the examples. |
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693 """ |
|
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694 def __init__(self,dataset,fieldnames): |
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695 original_dataset=dataset |
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696 if not fieldnames: |
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697 fieldnames=dataset.fieldNames() |
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698 elif not list(fieldnames)==list(dataset.fieldNames()): |
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699 #we must cast to list, othersize('x','y')!=['x','y'] |
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700 dataset = FieldsSubsetDataSet(dataset,fieldnames) |
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701 assert dataset.hasFields(*fieldnames) |
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702 self.dataset=dataset |
|
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703 |
|
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704 if isinstance(dataset,MinibatchDataSet): |
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705 Example.__init__(self,fieldnames,list(dataset._fields)) |
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706 elif isinstance(original_dataset,MinibatchDataSet): |
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707 Example.__init__(self,fieldnames, |
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708 [original_dataset._fields[field] |
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709 for field in fieldnames]) |
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710 else: |
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711 minibatch_iterator = dataset.minibatches(fieldnames, |
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712 minibatch_size=len(dataset), |
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713 n_batches=1) |
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|
714 minibatch=minibatch_iterator.next() |
|
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715 Example.__init__(self,fieldnames,minibatch) |
|
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|
716 |
|
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|
717 def examples(self): |
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718 return self.dataset |
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|
719 |
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720 def __or__(self,other): |
|
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|
721 """ |
|
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|
722 fields1 | fields2 is a DataSetFields that whose list of examples is the concatenation |
|
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|
723 of the list of examples of DataSetFields fields1 and fields2. |
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724 """ |
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|
725 return (self.examples() + other.examples()).fields() |
|
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diff
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|
726 |
|
40
88fd1cce08b9
replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
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diff
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|
727 def __and__(self,other): |
|
17
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|
728 """ |
|
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729 fields1 + fields2 is a DataSetFields that whose list of fields is the concatenation |
|
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730 of the fields of DataSetFields fields1 and fields2. |
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731 """ |
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732 return (self.examples() | other.examples()).fields() |
|
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|
733 |
|
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|
734 |
|
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|
735 class MinibatchDataSet(DataSet): |
|
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736 """ |
|
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737 Turn a L{Example} of same-length (iterable) fields into an example-iterable dataset. |
|
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738 Each element of the lookup-list should be an iterable and sliceable, all of the same length. |
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739 """ |
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740 def __init__(self,fields_lookuplist,values_vstack=DataSet().valuesVStack, |
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741 values_hstack=DataSet().valuesHStack): |
|
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|
742 """ |
|
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743 The user can (and generally should) also provide values_vstack(fieldname,fieldvalues) |
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744 and a values_hstack(fieldnames,fieldvalues) functions behaving with the same |
|
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745 semantics as the DataSet methods of the same name (but without the self argument). |
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746 """ |
|
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|
747 |
|
61
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|
748 self._fields=fields_lookuplist |
|
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749 assert len(fields_lookuplist)>0 |
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750 self.length=len(fields_lookuplist[0]) |
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751 for field in fields_lookuplist[1:]: |
|
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752 if self.length != len(field) : |
|
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|
753 print 'self.length = ',self.length |
|
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|
754 print 'len(field) = ', len(field) |
|
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|
755 print 'self._fields.keys() = ', self._fields.keys() |
|
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|
756 print 'field=',field |
|
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|
757 print 'fields_lookuplist=', fields_lookuplist |
|
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|
758 assert self.length==len(field) |
|
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|
759 self.valuesVStack=values_vstack |
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|
760 self.valuesHStack=values_hstack |
|
3
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|
761 |
|
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|
762 def __len__(self): |
|
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763 return self.length |
|
28
541a273bc89f
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diff
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|
764 |
|
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|
765 def dontuse__getitem__(self,i): |
| 80 | 766 if type(i) in (slice,list): |
|
48
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Fixing MinibatchDataSet getitem
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parents:
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|
767 return DataSetFields(MinibatchDataSet( |
| 80 | 768 Example(self._fields.keys(),[field[i] for field in self._fields])),self.fieldNames()) |
| 769 if type(i) is int: | |
| 85 | 770 return Example(self._fields.keys(),[field[i] for field in self._fields]) |
|
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|
771 if self.hasFields(i): |
|
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Frederic Bastien <bastienf@iro.umontreal.ca>
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diff
changeset
|
772 return self._fields[i] |
|
55
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Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
48
diff
changeset
|
773 assert i in self.__dict__ # else it means we are trying to access a non-existing property |
|
48
b6730f9a336d
Fixing MinibatchDataSet getitem
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parents:
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diff
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|
774 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
|
775 |
|
29
46c5c90019c2
Changed apply_function so that it propagates methods of the source.
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parents:
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diff
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|
776 def fieldNames(self): |
|
61
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|
777 return self._fields.keys() |
|
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|
778 |
|
37
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|
779 def hasFields(self,*fieldnames): |
|
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780 for fieldname in fieldnames: |
|
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|
781 if fieldname not in self._fields.keys(): |
|
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|
782 return False |
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|
783 return True |
|
20
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diff
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|
784 |
|
37
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Factored the minibatch-writing code into an iterator class inside DataSet
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diff
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|
785 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
|
223
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|
786 #@TODO bug somewhere here, fieldnames doesnt seem to be well handled |
|
36
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|
787 class Iterator(object): |
|
223
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|
788 def __init__(self,ds,fieldnames): |
|
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diff
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|
789 # tbm: added two next lines to handle fieldnames |
|
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|
790 if fieldnames is None: fieldnames = ds._fields.keys() |
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|
791 self.fieldnames = fieldnames |
|
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|
792 |
|
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|
793 self.ds=ds |
|
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|
794 self.next_example=offset |
|
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|
795 assert minibatch_size >= 0 |
| 41 | 796 if offset+minibatch_size > ds.length: |
|
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|
797 raise NotImplementedError() |
|
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diff
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|
798 def __iter__(self): |
|
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diff
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|
799 return self |
|
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diff
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|
800 def next(self): |
|
61
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Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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diff
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|
801 upper = self.next_example+minibatch_size |
|
37
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
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diff
changeset
|
802 assert upper<=self.ds.length |
|
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|
803 #minibatch = Example(self.ds._fields.keys(), |
|
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|
804 # [field[self.next_example:upper] |
|
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|
805 # for field in self.ds._fields]) |
|
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|
806 # tbm: modif to use fieldnames |
|
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|
807 values = [] |
|
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|
808 for f in self.fieldnames : |
|
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|
809 #print 'we have field',f,'in fieldnames' |
|
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|
810 values.append( self.ds._fields[f][self.next_example:upper] ) |
|
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|
811 minibatch = Example(self.fieldnames,values) |
|
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|
812 #print minibatch |
|
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|
813 self.next_example+=minibatch_size |
|
73
69f97aad3faf
Coded untested ApplyFunctionDataSet and CacheDataSet
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72
diff
changeset
|
814 return minibatch |
|
20
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|
815 |
|
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|
816 # tbm: added fieldnames to handle subset of fieldnames |
|
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|
817 return Iterator(self,fieldnames) |
|
20
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|
818 |
|
36
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diff
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|
819 class HStackedDataSet(DataSet): |
|
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diff
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|
820 """ |
| 167 | 821 A L{DataSet} that wraps several datasets and shows a view that includes all their fields, |
|
36
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|
822 i.e. whose list of fields is the concatenation of their lists of fields. |
|
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|
823 |
|
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changeset
|
824 If a field name is found in more than one of the datasets, then either an error is |
|
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diff
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|
825 raised or the fields are renamed (either by prefixing the __name__ attribute |
|
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Rewriting dataset.py completely
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diff
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|
826 of the dataset + ".", if it exists, or by suffixing the dataset index in the argument list). |
|
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diff
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|
827 |
| 167 | 828 @todo: automatically detect a chain of stacked datasets due to A | B | C | D ... |
|
36
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diff
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|
829 """ |
| 41 | 830 def __init__(self,datasets,accept_nonunique_names=False,description=None,field_types=None): |
| 831 DataSet.__init__(self,description,field_types) | |
|
36
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diff
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|
832 self.datasets=datasets |
|
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|
833 self.accept_nonunique_names=accept_nonunique_names |
|
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diff
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|
834 self.fieldname2dataset={} |
|
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|
835 |
|
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diff
changeset
|
836 def rename_field(fieldname,dataset,i): |
|
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diff
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|
837 if hasattr(dataset,"__name__"): |
|
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diff
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|
838 return dataset.__name__ + "." + fieldname |
|
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diff
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|
839 return fieldname+"."+str(i) |
|
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diff
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|
840 |
|
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|
841 # make sure all datasets have the same length and unique field names |
|
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842 self.length=None |
|
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|
843 names_to_change=[] |
|
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|
844 for i in xrange(len(datasets)): |
|
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|
845 dataset = datasets[i] |
|
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|
846 length=len(dataset) |
|
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|
847 if self.length: |
|
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|
848 assert self.length==length |
|
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diff
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|
849 else: |
|
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|
850 self.length=length |
|
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|
851 for fieldname in dataset.fieldNames(): |
|
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|
852 if fieldname in self.fieldname2dataset: # name conflict! |
|
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diff
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|
853 if accept_nonunique_names: |
|
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diff
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|
854 fieldname=rename_field(fieldname,dataset,i) |
|
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diff
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|
855 names2change.append((fieldname,i)) |
|
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|
856 else: |
|
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|
857 raise ValueError("Incompatible datasets: non-unique field name = "+fieldname) |
|
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diff
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|
858 self.fieldname2dataset[fieldname]=i |
|
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diff
changeset
|
859 for fieldname,i in names_to_change: |
|
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29
diff
changeset
|
860 del self.fieldname2dataset[fieldname] |
|
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diff
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|
861 self.fieldname2dataset[rename_field(fieldname,self.datasets[i],i)]=i |
|
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diff
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|
862 |
|
37
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
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diff
changeset
|
863 def hasFields(self,*fieldnames): |
|
36
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29
diff
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|
864 for fieldname in fieldnames: |
|
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parents:
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diff
changeset
|
865 if not fieldname in self.fieldname2dataset: |
|
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parents:
29
diff
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|
866 return False |
|
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parents:
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diff
changeset
|
867 return True |
|
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parents:
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diff
changeset
|
868 |
|
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29
diff
changeset
|
869 def fieldNames(self): |
|
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Rewriting dataset.py completely
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parents:
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diff
changeset
|
870 return self.fieldname2dataset.keys() |
|
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Rewriting dataset.py completely
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diff
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|
871 |
| 41 | 872 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
|
36
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29
diff
changeset
|
873 |
|
44
5a85fda9b19b
Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
parents:
43
diff
changeset
|
874 class HStackedIterator(object): |
|
36
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Rewriting dataset.py completely
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parents:
29
diff
changeset
|
875 def __init__(self,hsds,iterators): |
|
438440ba0627
Rewriting dataset.py completely
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29
diff
changeset
|
876 self.hsds=hsds |
|
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Rewriting dataset.py completely
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29
diff
changeset
|
877 self.iterators=iterators |
|
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Rewriting dataset.py completely
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diff
changeset
|
878 def __iter__(self): |
|
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diff
changeset
|
879 return self |
|
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29
diff
changeset
|
880 def next(self): |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
881 # concatenate all the fields of the minibatches |
|
290
9b533cc7874a
trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
274
diff
changeset
|
882 l=Example() |
| 140 | 883 for iter in self.iterators: |
| 884 l.append_lookuplist(iter.next()) | |
| 885 return l | |
|
36
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Rewriting dataset.py completely
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parents:
29
diff
changeset
|
886 |
| 125 | 887 assert self.hasFields(*fieldnames) |
|
36
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
888 # find out which underlying datasets are necessary to service the required fields |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
889 # and construct corresponding minibatch iterators |
| 140 | 890 if fieldnames and fieldnames!=self.fieldNames(): |
|
36
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
891 datasets=set([]) |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
892 fields_in_dataset=dict([(dataset,[]) for dataset in datasets]) |
|
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Rewriting dataset.py completely
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parents:
29
diff
changeset
|
893 for fieldname in fieldnames: |
| 136 | 894 dataset=self.datasets[self.fieldname2dataset[fieldname]] |
|
36
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
895 datasets.add(dataset) |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
896 fields_in_dataset[dataset].append(fieldname) |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
897 datasets=list(datasets) |
|
37
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
898 iterators=[dataset.minibatches(fields_in_dataset[dataset],minibatch_size,n_batches,offset) |
|
36
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
899 for dataset in datasets] |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
900 else: |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
901 datasets=self.datasets |
|
37
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
902 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
|
903 return HStackedIterator(self,iterators) |
|
36
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
904 |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
905 |
|
290
9b533cc7874a
trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
274
diff
changeset
|
906 def untested_valuesVStack(self,fieldname,fieldvalues): |
|
36
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
907 return self.datasets[self.fieldname2dataset[fieldname]].valuesVStack(fieldname,fieldvalues) |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
908 |
|
290
9b533cc7874a
trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
274
diff
changeset
|
909 def untested_valuesHStack(self,fieldnames,fieldvalues): |
|
36
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Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
910 """ |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
911 We will use the sub-dataset associated with the first fieldname in the fieldnames list |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
912 to do the work, hoping that it can cope with the other values (i.e. won't care |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
913 about the incompatible fieldnames). Hence this heuristic will always work if |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
914 all the fieldnames are of the same sub-dataset. |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
915 """ |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
916 return self.datasets[self.fieldname2dataset[fieldnames[0]]].valuesHStack(fieldnames,fieldvalues) |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
917 |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
918 class VStackedDataSet(DataSet): |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
919 """ |
| 167 | 920 A L{DataSet} that wraps several datasets and shows a view that includes all their examples, |
|
36
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
921 in the order provided. This clearly assumes that they all have the same field names |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
922 and all (except possibly the last one) are of finite length. |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
923 |
| 167 | 924 @todo: automatically detect a chain of stacked datasets due to A + B + C + D ... |
|
36
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
925 """ |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
926 def __init__(self,datasets): |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
927 self.datasets=datasets |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
928 self.length=0 |
|
438440ba0627
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bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
929 self.index2dataset={} |
|
37
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
930 assert len(datasets)>0 |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
931 fieldnames = datasets[-1].fieldNames() |
|
38
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
932 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
|
933 # 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
|
934 # to avoid having to search for the appropriate dataset each time and slice is asked for. |
|
36
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
935 for dataset,k in enumerate(datasets[0:-1]): |
|
48
b6730f9a336d
Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents:
46
diff
changeset
|
936 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
|
937 L=len(dataset) |
|
36
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
938 for i in xrange(L): |
|
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parents:
29
diff
changeset
|
939 self.index2dataset[self.length+i]=k |
|
38
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
940 self.datasets_start_row.append(self.length) |
|
36
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29
diff
changeset
|
941 self.length+=L |
|
37
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
942 assert dataset.fieldNames()==fieldnames |
|
38
d637ad8f7352
Finished first untested version of VStackedDataset
bengioy@esprit.iro.umontreal.ca
parents:
37
diff
changeset
|
943 self.datasets_start_row.append(self.length) |
|
36
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parents:
29
diff
changeset
|
944 self.length+=len(datasets[-1]) |
|
37
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
945 # If length is very large, we should use a more memory-efficient mechanism |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
946 # 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
|
947 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
|
948 # 1 million entries would require about 60 meg for the index2dataset map |
|
73c4212ba5b3
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diff
changeset
|
949 # TODO |
|
73c4212ba5b3
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36
diff
changeset
|
950 print "A more efficient mechanism for index2dataset should be implemented" |
|
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bengioy@esprit.iro.umontreal.ca
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diff
changeset
|
951 |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
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parents:
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diff
changeset
|
952 def __len__(self): |
|
73c4212ba5b3
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parents:
36
diff
changeset
|
953 return self.length |
|
73c4212ba5b3
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36
diff
changeset
|
954 |
|
73c4212ba5b3
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parents:
36
diff
changeset
|
955 def fieldNames(self): |
|
73c4212ba5b3
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bengioy@esprit.iro.umontreal.ca
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diff
changeset
|
956 return self.datasets[0].fieldNames() |
|
73c4212ba5b3
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bengioy@esprit.iro.umontreal.ca
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36
diff
changeset
|
957 |
|
73c4212ba5b3
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parents:
36
diff
changeset
|
958 def hasFields(self,*fieldnames): |
|
73c4212ba5b3
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parents:
36
diff
changeset
|
959 return self.datasets[0].hasFields(*fieldnames) |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
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parents:
36
diff
changeset
|
960 |
|
38
d637ad8f7352
Finished first untested version of VStackedDataset
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parents:
37
diff
changeset
|
961 def locate_row(self,row): |
|
d637ad8f7352
Finished first untested version of VStackedDataset
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parents:
37
diff
changeset
|
962 """Return (dataset_index, row_within_dataset) for global row number""" |
|
d637ad8f7352
Finished first untested version of VStackedDataset
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diff
changeset
|
963 dataset_index = self.index2dataset[row] |
|
d637ad8f7352
Finished first untested version of VStackedDataset
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diff
changeset
|
964 row_within_dataset = self.datasets_start_row[dataset_index] |
|
d637ad8f7352
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diff
changeset
|
965 return dataset_index, row_within_dataset |
|
d637ad8f7352
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changeset
|
966 |
| 41 | 967 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
|
44
5a85fda9b19b
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diff
changeset
|
968 |
|
5a85fda9b19b
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bengioy@grenat.iro.umontreal.ca
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diff
changeset
|
969 class VStackedIterator(object): |
|
37
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|
970 def __init__(self,vsds): |
|
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|
971 self.vsds=vsds |
|
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|
972 self.next_row=offset |
|
38
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|
973 self.next_dataset_index,self.next_dataset_row=self.vsds.locate_row(offset) |
|
37
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|
974 self.current_iterator,self.n_left_at_the_end_of_ds,self.n_left_in_mb= \ |
|
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975 self.next_iterator(vsds.datasets[0],offset,n_batches) |
|
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|
976 |
|
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|
977 def next_iterator(self,dataset,starting_offset,batches_left): |
|
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|
978 L=len(dataset) |
|
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|
979 ds_nbatches = (L-starting_offset)/minibatch_size |
|
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|
980 if batches_left is not None: |
|
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|
981 ds_nbatches = max(batches_left,ds_nbatches) |
|
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|
982 if minibatch_size>L: |
|
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|
983 ds_minibatch_size=L |
|
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984 n_left_in_mb=minibatch_size-L |
|
38
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|
985 ds_nbatches=1 |
|
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986 else: |
|
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|
987 n_left_in_mb=0 |
|
37
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|
988 return dataset.minibatches(fieldnames,minibatch_size,ds_nbatches,starting_offset), \ |
|
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|
989 L-(starting_offset+ds_nbatches*minibatch_size), n_left_in_mb |
|
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|
990 |
|
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|
991 def move_to_next_dataset(self): |
|
38
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992 if self.n_left_at_the_end_of_ds>0: |
|
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|
993 self.current_iterator,self.n_left_at_the_end_of_ds,self.n_left_in_mb= \ |
|
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|
994 self.next_iterator(vsds.datasets[self.next_dataset_index], |
|
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changeset
|
995 self.n_left_at_the_end_of_ds,1) |
|
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|
996 else: |
|
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|
997 self.next_dataset_index +=1 |
|
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|
998 if self.next_dataset_index==len(self.vsds.datasets): |
|
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|
999 self.next_dataset_index = 0 |
|
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|
1000 self.current_iterator,self.n_left_at_the_end_of_ds,self.n_left_in_mb= \ |
|
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|
1001 self.next_iterator(vsds.datasets[self.next_dataset_index],starting_offset,n_batches) |
|
37
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|
1002 |
|
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|
1003 def __iter__(self): |
|
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|
1004 return self |
|
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|
1005 |
|
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|
1006 def next(self): |
|
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|
1007 dataset=self.vsds.datasets[self.next_dataset_index] |
|
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|
1008 mb = self.next_iterator.next() |
|
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|
1009 if self.n_left_in_mb: |
|
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|
1010 extra_mb = [] |
|
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|
1011 while self.n_left_in_mb>0: |
|
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|
1012 self.move_to_next_dataset() |
|
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diff
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|
1013 extra_mb.append(self.next_iterator.next()) |
|
73
69f97aad3faf
Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents:
72
diff
changeset
|
1014 mb = Example(fieldnames, |
|
40
88fd1cce08b9
replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
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parents:
39
diff
changeset
|
1015 [dataset.valuesVStack(name, |
|
88fd1cce08b9
replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
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diff
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|
1016 [mb[name]]+[b[name] for b in extra_mb]) |
|
88fd1cce08b9
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diff
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|
1017 for name in fieldnames]) |
|
88fd1cce08b9
replaced infinity for length by raise UnboundedDataSet and use & instead of + to concatenate datasets
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diff
changeset
|
1018 |
|
37
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Factored the minibatch-writing code into an iterator class inside DataSet
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diff
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|
1019 self.next_row+=minibatch_size |
|
38
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diff
changeset
|
1020 self.next_dataset_row+=minibatch_size |
|
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diff
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|
1021 if self.next_row+minibatch_size>len(dataset): |
|
d637ad8f7352
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diff
changeset
|
1022 self.move_to_next_dataset() |
|
44
5a85fda9b19b
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diff
changeset
|
1023 return examples |
|
5a85fda9b19b
Fixed some more iterator bugs
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diff
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|
1024 return VStackedIterator(self) |
|
37
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diff
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|
1025 |
| 41 | 1026 class ArrayFieldsDataSet(DataSet): |
| 1027 """ | |
| 1028 Virtual super-class of datasets whose field values are numpy array, | |
| 1029 thus defining valuesHStack and valuesVStack for sub-classes. | |
| 1030 """ | |
|
268
3f1cd8897fda
reverting dataset
James Bergstra <bergstrj@iro.umontreal.ca>
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266
diff
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|
1031 def __init__(self,description=None,field_types=None): |
|
3f1cd8897fda
reverting dataset
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266
diff
changeset
|
1032 DataSet.__init__(self,description,field_types) |
|
290
9b533cc7874a
trying to get default implemenations to work
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diff
changeset
|
1033 def untested_valuesHStack(self,fieldnames,fieldvalues): |
| 41 | 1034 """Concatenate field values horizontally, e.g. two vectors |
| 1035 become a longer vector, two matrices become a wider matrix, etc.""" | |
| 1036 return numpy.hstack(fieldvalues) | |
|
290
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diff
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|
1037 def untested_valuesVStack(self,fieldname,values): |
| 41 | 1038 """Concatenate field values vertically, e.g. two vectors |
| 1039 become a two-row matrix, two matrices become a longer matrix, etc.""" | |
| 1040 return numpy.vstack(values) | |
| 1041 | |
|
316
5fe6d0c93109
getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
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|
1042 |
|
5fe6d0c93109
getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
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|
1043 |
|
5fe6d0c93109
getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
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|
1044 class NArraysDataSet(ArrayFieldsDataSet) : |
|
5fe6d0c93109
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|
1045 """ |
|
5fe6d0c93109
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|
1046 An NArraysDataSet stores fields that are numpy tensor, whose first axis |
|
5fe6d0c93109
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|
1047 iterates over examples. It's a generalization of ArrayDataSet. |
|
5fe6d0c93109
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|
1048 """ |
|
5fe6d0c93109
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changeset
|
1049 #@TODO not completely implemented yet |
|
5fe6d0c93109
getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
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|
1050 def __init__(self, data_arrays, fieldnames, **kwargs) : |
|
5fe6d0c93109
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|
1051 """ |
|
5fe6d0c93109
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parents:
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changeset
|
1052 Construct an NArraysDataSet from a list of numpy tensor (data_arrays) and a list |
|
5fe6d0c93109
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parents:
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changeset
|
1053 of fieldnames. The number of arrays must be the same as the number of |
|
5fe6d0c93109
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parents:
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diff
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|
1054 fieldnames. Each set of numpy tensor must have the same first dimension (first |
|
5fe6d0c93109
getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
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parents:
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diff
changeset
|
1055 axis) corresponding to the number of examples. |
|
5fe6d0c93109
getitem in ArrayDataSet is set up again, supposed to be faster than default one, has been tested agains the default behaviour. In particular, now always return a LookupList
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|
1056 |
|
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1057 Every tensor is treated as a numpy matrix (using numpy.asmatrix) |
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1058 """ |
|
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1059 ArrayFieldsDataSet.__init__(self,**kwargs) |
|
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1060 assert len(data_arrays) == len(fieldnames) |
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1061 assert len(fieldnames) > 0 |
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1062 num_examples = numpy.asmatrix(data_arrays[0]).shape[0] |
|
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1063 for k in range(len(data_arrays)) : |
|
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1064 assert numpy.asmatrix(data_arrays[k]).shape[0] == num_examples |
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1065 self._fieldnames = fieldnames |
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1066 self._datas = [] |
|
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1067 for k in range(len(data_arrays)) : |
|
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1068 self._datas.append( numpy.asmatrix(data_arrays[k]) ) |
|
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1069 #raise NotImplemented |
|
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1070 |
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1071 |
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1072 def __len__(self) : |
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1073 """ |
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1074 Length of the dataset is based on the first array = data_arrays[0], using its shape |
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1075 """ |
|
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1076 return self._datas[0].shape[0] |
|
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1077 |
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1078 def fieldNames(self) : |
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1079 """ |
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1080 Returns the fieldnames as set in self.__init__ |
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1081 """ |
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1082 return self._fieldnames |
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1083 |
|
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1084 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
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1085 cursor = Example(fieldnames,[0]*len(fieldnames)) |
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1086 fieldnames = self.fieldNames() if fieldnames is None else fieldnames |
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1087 for n in xrange(n_batches): |
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1088 if offset == len(self): |
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1089 break |
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1090 for f in range(len(cursor._names)) : |
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1091 idx = self._fieldnames.index(cursor._names[f]) |
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1092 assert idx >= 0 |
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1093 sub_data = self._datas[f][offset : offset+minibatch_size] |
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1094 cursor._values[f] = sub_data |
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1095 offset += len(sub_data) #can be less than minibatch_size at end |
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1096 yield cursor |
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1097 |
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1098 #return ArrayDataSetIterator(self,fieldnames,minibatch_size,n_batches,offset) |
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1099 |
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1100 |
|
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1101 |
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1102 |
| 41 | 1103 class ArrayDataSet(ArrayFieldsDataSet): |
| 1104 """ | |
| 1105 An ArrayDataSet stores the fields as groups of columns in a numpy tensor, | |
| 1106 whose first axis iterates over examples, second axis determines fields. | |
| 1107 If the underlying array is N-dimensional (has N axes), then the field | |
| 1108 values are (N-2)-dimensional objects (i.e. ordinary numbers if N=2). | |
| 1109 """ | |
| 1110 | |
|
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1111 def __init__(self, data_array, fields_columns, **kwargs): |
|
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1112 """ |
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|
1113 Construct an ArrayDataSet from the underlying numpy array (data) and |
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1114 a map (fields_columns) from fieldnames to field columns. The columns of a field are specified |
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1115 using the standard arguments for indexing/slicing: integer for a column index, |
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1116 slice for an interval of columns (with possible stride), or iterable of column indices. |
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1117 """ |
|
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1118 ArrayFieldsDataSet.__init__(self, **kwargs) |
| 41 | 1119 self.data=data_array |
|
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1120 self.fields_columns=fields_columns |
| 41 | 1121 |
| 1122 # check consistency and complete slices definitions | |
|
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|
1123 for fieldname, fieldcolumns in self.fields_columns.items(): |
| 41 | 1124 if type(fieldcolumns) is int: |
| 1125 assert fieldcolumns>=0 and fieldcolumns<data_array.shape[1] | |
|
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1126 if 1: |
|
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1127 #I changed this because it didn't make sense to me, |
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1128 # and it made it more difficult to write my learner. |
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1129 # If it breaks stuff, let's talk about it. |
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1130 # - James 22/05/2008 |
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1131 self.fields_columns[fieldname]=[fieldcolumns] |
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1132 else: |
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1133 self.fields_columns[fieldname]=fieldcolumns |
| 41 | 1134 elif type(fieldcolumns) is slice: |
| 1135 start,step=None,None | |
| 1136 if not fieldcolumns.start: | |
| 1137 start=0 | |
| 1138 if not fieldcolumns.step: | |
| 1139 step=1 | |
| 1140 if start or step: | |
|
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|
1141 self.fields_columns[fieldname]=slice(start,fieldcolumns.stop,step) |
| 41 | 1142 elif hasattr(fieldcolumns,"__iter__"): # something like a list |
| 1143 for i in fieldcolumns: | |
| 1144 assert i>=0 and i<data_array.shape[1] | |
| 1145 | |
|
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1146 def fieldNames(self): |
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1147 return self.fields_columns.keys() |
| 41 | 1148 |
|
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1149 def __len__(self): |
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1150 return len(self.data) |
| 41 | 1151 |
|
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1152 def __getitem__(self,key): |
|
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1153 """More efficient implementation than the default __getitem__""" |
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1154 fieldnames=self.fields_columns.keys() |
|
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1155 values=self.fields_columns.values() |
| 80 | 1156 if type(key) is int: |
|
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1157 return Example(fieldnames, |
|
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1158 [self.data[key,col] for col in values]) |
| 80 | 1159 if type(key) is slice: |
|
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1160 return Example(fieldnames,[self.data[key,col] for col in values]) |
| 80 | 1161 if type(key) is list: |
| 1162 for i in range(len(key)): | |
| 1163 if self.hasFields(key[i]): | |
| 1164 key[i]=self.fields_columns[key[i]] | |
|
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1165 return Example(fieldnames, |
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1166 #we must separate differently for list as numpy |
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1167 # doesn't support self.data[[i1,...],[i2,...]] |
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1168 # when their is more then two i1 and i2 |
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1169 [self.data[key,:][:,col] |
|
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diff
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|
1170 if isinstance(col,list) else |
|
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diff
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|
1171 self.data[key,col] for col in values]) |
| 80 | 1172 |
|
55
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Efficient implementation of getitem for ArrayDataSet
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diff
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|
1173 # else check for a fieldname |
| 80 | 1174 if self.hasFields(key): |
|
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bugfix, we keep all the line, but only a some columns
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diff
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|
1175 return self.data[:,self.fields_columns[key]] |
|
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parents:
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diff
changeset
|
1176 # else we are trying to access a property of the dataset |
| 80 | 1177 assert key in self.__dict__ # else it means we are trying to access a non-existing property |
| 1178 return self.__dict__[key] | |
|
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diff
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|
1179 |
|
290
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diff
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|
1180 def dontuse__iter__(self): |
|
270
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code cleanup and small optimisation
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diff
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|
1181 class ArrayDataSetIteratorIter(object): |
|
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diff
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|
1182 def __init__(self,dataset,fieldnames): |
|
228
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|
1183 if fieldnames is None: fieldnames = dataset.fieldNames() |
|
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parents:
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diff
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|
1184 # store the resulting minibatch in a lookup-list of values |
|
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diff
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|
1185 self.minibatch = Example(fieldnames,[0]*len(fieldnames)) |
|
228
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parents:
203
diff
changeset
|
1186 self.dataset=dataset |
|
270
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diff
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|
1187 self.current=0 |
|
238
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diff
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|
1188 self.columns = [self.dataset.fields_columns[f] |
|
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diff
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|
1189 for f in self.minibatch._names] |
|
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diff
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|
1190 self.l = self.dataset.data.shape[0] |
|
228
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|
1191 def __iter__(self): |
|
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|
1192 return self |
|
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diff
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|
1193 def next(self): |
|
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203
diff
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|
1194 #@todo: we suppose that we need to stop only when minibatch_size == 1. |
|
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optimisation of ArrayDataSet
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diff
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|
1195 # Otherwise, MinibatchWrapAroundIterator do it. |
|
270
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code cleanup and small optimisation
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diff
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|
1196 if self.current>=self.l: |
|
228
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diff
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|
1197 raise StopIteration |
|
6f55e301c687
optimisation of ArrayDataSet
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diff
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|
1198 sub_data = self.dataset.data[self.current] |
|
238
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Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
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diff
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|
1199 self.minibatch._values = [sub_data[c] for c in self.columns] |
|
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diff
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|
1200 |
|
270
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diff
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|
1201 self.current+=1 |
|
228
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parents:
203
diff
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|
1202 return self.minibatch |
|
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parents:
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diff
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|
1203 |
|
270
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diff
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|
1204 return ArrayDataSetIteratorIter(self,self.fieldNames()) |
|
228
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Frederic Bastien <bastienf@iro.umontreal.ca>
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diff
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|
1205 |
|
42
9b68774fcc6b
Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
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41
diff
changeset
|
1206 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
|
290
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diff
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|
1207 cursor = Example(fieldnames,[0]*len(fieldnames)) |
|
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diff
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|
1208 fieldnames = self.fieldNames() if fieldnames is None else fieldnames |
|
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parents:
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diff
changeset
|
1209 for n in xrange(n_batches): |
|
9b533cc7874a
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parents:
274
diff
changeset
|
1210 if offset == len(self): |
|
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parents:
274
diff
changeset
|
1211 break |
|
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274
diff
changeset
|
1212 sub_data = self.data[offset : offset+minibatch_size] |
|
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parents:
274
diff
changeset
|
1213 offset += len(sub_data) #can be less than minibatch_size at end |
|
9b533cc7874a
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274
diff
changeset
|
1214 cursor._values = [sub_data[:,self.fields_columns[f]] for f in cursor._names] |
|
9b533cc7874a
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parents:
274
diff
changeset
|
1215 yield cursor |
|
42
9b68774fcc6b
Testing basic functionality and removing obvious bugs
bengioy@grenat.iro.umontreal.ca
parents:
41
diff
changeset
|
1216 |
|
290
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diff
changeset
|
1217 #return ArrayDataSetIterator(self,fieldnames,minibatch_size,n_batches,offset) |
|
57
1aabd2e2bb5f
Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
56
diff
changeset
|
1218 |
|
1aabd2e2bb5f
Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
56
diff
changeset
|
1219 |
|
1aabd2e2bb5f
Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
56
diff
changeset
|
1220 class CachedDataSet(DataSet): |
|
1aabd2e2bb5f
Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
56
diff
changeset
|
1221 """ |
| 167 | 1222 Wrap a L{DataSet} whose values are computationally expensive to obtain |
|
57
1aabd2e2bb5f
Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
56
diff
changeset
|
1223 (e.g. because they involve some computation, or disk access), |
|
1aabd2e2bb5f
Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
56
diff
changeset
|
1224 so that repeated accesses to the same example are done cheaply, |
|
1aabd2e2bb5f
Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
56
diff
changeset
|
1225 by caching every example value that has been accessed at least once. |
|
1aabd2e2bb5f
Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
56
diff
changeset
|
1226 |
|
1aabd2e2bb5f
Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
56
diff
changeset
|
1227 Optionally, for finite-length dataset, all the values can be computed |
|
1aabd2e2bb5f
Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
56
diff
changeset
|
1228 (and cached) upon construction of the CachedDataSet, rather at the |
|
1aabd2e2bb5f
Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
56
diff
changeset
|
1229 first access. |
|
73
69f97aad3faf
Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents:
72
diff
changeset
|
1230 |
| 167 | 1231 @todo: when cache_all_upon_construction create mini-batches that are as |
|
77
1e2bb5bad636
toying with different ways to implement learners
bengioy@bengiomac.local
parents:
74
diff
changeset
|
1232 large as possible but not so large as to fill up memory. |
|
1e2bb5bad636
toying with different ways to implement learners
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74
diff
changeset
|
1233 |
| 167 | 1234 @todo: add disk-buffering capability, so that when the cache becomes too |
|
73
69f97aad3faf
Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents:
72
diff
changeset
|
1235 big for memory, we cache things on disk, trying to keep in memory only |
|
69f97aad3faf
Coded untested ApplyFunctionDataSet and CacheDataSet
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parents:
72
diff
changeset
|
1236 the record most likely to be accessed next. |
|
57
1aabd2e2bb5f
Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
56
diff
changeset
|
1237 """ |
|
73
69f97aad3faf
Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents:
72
diff
changeset
|
1238 def __init__(self,source_dataset,cache_all_upon_construction=False): |
|
69f97aad3faf
Coded untested ApplyFunctionDataSet and CacheDataSet
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parents:
72
diff
changeset
|
1239 self.source_dataset=source_dataset |
|
69f97aad3faf
Coded untested ApplyFunctionDataSet and CacheDataSet
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72
diff
changeset
|
1240 self.cache_all_upon_construction=cache_all_upon_construction |
|
152
3f627e844cba
Fixes in CacheDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
151
diff
changeset
|
1241 self.cached_examples = [] |
|
73
69f97aad3faf
Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents:
72
diff
changeset
|
1242 if cache_all_upon_construction: |
|
77
1e2bb5bad636
toying with different ways to implement learners
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diff
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|
1243 # this potentially brings all the source examples |
|
1e2bb5bad636
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parents:
74
diff
changeset
|
1244 # into memory at once, which may be too much |
|
1e2bb5bad636
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parents:
74
diff
changeset
|
1245 # the work could possibly be done by minibatches |
|
1e2bb5bad636
toying with different ways to implement learners
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74
diff
changeset
|
1246 # that are as large as possible but no more than what memory allows. |
|
146
8173e196e291
Trying to make CacheDataSet work
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
144
diff
changeset
|
1247 fields_values = source_dataset.minibatches(minibatch_size=len(source_dataset)).__iter__().next() |
|
152
3f627e844cba
Fixes in CacheDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
151
diff
changeset
|
1248 assert all([len(self)==len(field_values) for field_values in fields_values]) |
|
3f627e844cba
Fixes in CacheDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
151
diff
changeset
|
1249 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
|
1250 self.cached_examples.append(copy.copy(example)) |
|
57
1aabd2e2bb5f
Added empty classes with doc: CachedDataSet and ApplyFunctionDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
56
diff
changeset
|
1251 |
|
73
69f97aad3faf
Coded untested ApplyFunctionDataSet and CacheDataSet
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72
diff
changeset
|
1252 self.fieldNames = source_dataset.fieldNames |
|
69f97aad3faf
Coded untested ApplyFunctionDataSet and CacheDataSet
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72
diff
changeset
|
1253 self.hasFields = source_dataset.hasFields |
|
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Coded untested ApplyFunctionDataSet and CacheDataSet
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diff
changeset
|
1254 self.valuesHStack = source_dataset.valuesHStack |
|
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Coded untested ApplyFunctionDataSet and CacheDataSet
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72
diff
changeset
|
1255 self.valuesVStack = source_dataset.valuesVStack |
|
69f97aad3faf
Coded untested ApplyFunctionDataSet and CacheDataSet
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72
diff
changeset
|
1256 |
|
69f97aad3faf
Coded untested ApplyFunctionDataSet and CacheDataSet
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72
diff
changeset
|
1257 def __len__(self): |
|
69f97aad3faf
Coded untested ApplyFunctionDataSet and CacheDataSet
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diff
changeset
|
1258 return len(self.source_dataset) |
|
69f97aad3faf
Coded untested ApplyFunctionDataSet and CacheDataSet
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72
diff
changeset
|
1259 |
|
69f97aad3faf
Coded untested ApplyFunctionDataSet and CacheDataSet
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72
diff
changeset
|
1260 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
|
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Coded untested ApplyFunctionDataSet and CacheDataSet
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72
diff
changeset
|
1261 class CacheIterator(object): |
|
69f97aad3faf
Coded untested ApplyFunctionDataSet and CacheDataSet
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diff
changeset
|
1262 def __init__(self,dataset): |
|
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Coded untested ApplyFunctionDataSet and CacheDataSet
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diff
changeset
|
1263 self.dataset=dataset |
|
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Coded untested ApplyFunctionDataSet and CacheDataSet
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diff
changeset
|
1264 self.current=offset |
|
254
8ec867d12428
optimication in CachedDataSet.minibatches_nowrap
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diff
changeset
|
1265 self.all_fields = self.dataset.fieldNames()==fieldnames |
|
73
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diff
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|
1266 def __iter__(self): return self |
|
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diff
changeset
|
1267 def next(self): |
|
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Coded untested ApplyFunctionDataSet and CacheDataSet
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diff
changeset
|
1268 upper = self.current+minibatch_size |
|
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diff
changeset
|
1269 cache_len = len(self.dataset.cached_examples) |
|
135
0d8e721cc63c
Fixed bugs in dataset to make test_mlp.py work
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parents:
134
diff
changeset
|
1270 if upper>cache_len: # whole minibatch is not already in cache |
|
73
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diff
changeset
|
1271 # cache everything from current length to upper |
|
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diff
changeset
|
1272 for example in self.dataset.source_dataset[cache_len:upper]: |
|
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diff
changeset
|
1273 self.dataset.cached_examples.append(example) |
|
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diff
changeset
|
1274 all_fields_minibatch = Example(self.dataset.fieldNames(), |
|
152
3f627e844cba
Fixes in CacheDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
151
diff
changeset
|
1275 zip(*self.dataset.cached_examples[self.current:self.current+minibatch_size])) |
|
163
d7d67651d67c
bugfix, we should advence by the minibatch size.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
159
diff
changeset
|
1276 self.current+=minibatch_size |
|
254
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optimication in CachedDataSet.minibatches_nowrap
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diff
changeset
|
1277 if self.all_fields: |
|
73
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diff
changeset
|
1278 return all_fields_minibatch |
|
69f97aad3faf
Coded untested ApplyFunctionDataSet and CacheDataSet
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diff
changeset
|
1279 return Example(fieldnames,[all_fields_minibatch[name] for name in fieldnames]) |
|
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Coded untested ApplyFunctionDataSet and CacheDataSet
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diff
changeset
|
1280 return CacheIterator(self) |
|
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1281 |
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1282 def dontuse__getitem__(self,i): |
| 153 | 1283 if type(i)==int and len(self.cached_examples)>i: |
| 1284 return self.cached_examples[i] | |
| 1285 else: | |
|
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1286 return self.source_dataset[i] |
|
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1287 |
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1288 def __iter__(self): |
|
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1289 class CacheIteratorIter(object): |
|
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1290 def __init__(self,dataset): |
|
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1291 self.dataset=dataset |
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1292 self.l = len(dataset) |
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1293 self.current = 0 |
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1294 self.fieldnames = self.dataset.fieldNames() |
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1295 self.example = Example(self.fieldnames,[0]*len(self.fieldnames)) |
|
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1296 def __iter__(self): return self |
|
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1297 def next(self): |
|
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1298 if self.current>=self.l: |
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1299 raise StopIteration |
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1300 cache_len = len(self.dataset.cached_examples) |
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1301 if self.current>=cache_len: # whole minibatch is not already in cache |
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1302 # cache everything from current length to upper |
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1303 self.dataset.cached_examples.append( |
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1304 self.dataset.source_dataset[self.current]) |
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1305 self.example._values = self.dataset.cached_examples[self.current] |
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1306 self.current+=1 |
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1307 return self.example |
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1308 |
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1309 return CacheIteratorIter(self) |
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1310 |
|
57
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1311 class ApplyFunctionDataSet(DataSet): |
|
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1312 """ |
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1313 A L{DataSet} that contains as fields the results of applying a |
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1314 given function example-wise or minibatch-wise to all the fields of |
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1315 an input dataset. The output of the function should be an iterable |
|
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1316 (e.g. a list or a LookupList) over the resulting values. |
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1317 |
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1318 The function take as input the fields of the dataset, not the examples. |
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1319 |
|
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1320 In minibatch mode, the function is expected to work on minibatches |
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1321 (takes a minibatch in input and returns a minibatch in output). More |
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1322 precisely, it means that each element of the input or output list |
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1323 should be iterable and indexable over the individual example values |
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1324 (typically these elements will be numpy arrays). All of the elements |
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1325 in the input and output lists should have the same length, which is |
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1326 the length of the minibatch. |
|
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1327 |
|
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1328 The function is applied each time an example or a minibatch is accessed. |
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1329 To avoid re-doing computation, wrap this dataset inside a CachedDataSet. |
|
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1330 |
|
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1331 If the values_{h,v}stack functions are not provided, then |
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1332 the input_dataset.values{H,V}Stack functions are used by default. |
|
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1333 |
|
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1334 """ |
|
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1335 |
|
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1336 def __init__(self,input_dataset,function,output_names,minibatch_mode=True, |
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1337 values_hstack=None,values_vstack=None, |
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1338 description=None,fieldtypes=None): |
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1339 """ |
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1340 Constructor takes an input dataset that has as many fields as the function |
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1341 expects as inputs. The resulting dataset has as many fields as the function |
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1342 produces as outputs, and that should correspond to the number of output names |
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1343 (provided in a list). |
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1344 |
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1345 Note that the expected semantics of the function differs in minibatch mode |
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1346 (it takes minibatches of inputs and produces minibatches of outputs, as |
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1347 documented in the class comment). |
|
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1348 |
|
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1349 TBM: are filedtypes the old field types (from input_dataset) or the new ones |
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1350 (for the new dataset created)? |
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1351 """ |
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1352 self.input_dataset=input_dataset |
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1353 self.function=function |
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1354 self.output_names=output_names |
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1355 self.minibatch_mode=minibatch_mode |
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1356 DataSet.__init__(self,description,fieldtypes) |
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1357 self.valuesHStack = values_hstack if values_hstack else input_dataset.valuesHStack |
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1358 self.valuesVStack = values_vstack if values_vstack else input_dataset.valuesVStack |
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1359 |
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1360 def __len__(self): |
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1361 return len(self.input_dataset) |
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1362 |
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1363 def fieldNames(self): |
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1364 return self.output_names |
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1365 |
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1366 def minibatches_nowrap(self, fieldnames, *args, **kwargs): |
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1367 all_input_fieldNames = self.input_dataset.fieldNames() |
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1368 mbnw = self.input_dataset.minibatches_nowrap |
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1369 |
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1370 for input_fields in mbnw(all_input_fieldNames, *args, **kwargs): |
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1371 if self.minibatch_mode: |
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1372 all_output_fields = self.function(*input_fields) |
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1373 else: |
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1374 input_examples = zip(*input_fields) #makes so that [i] means example i |
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1375 output_examples = [self.function(*input_example) |
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1376 for input_example in input_examples] |
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1377 all_output_fields = zip(*output_examples) |
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1378 |
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1379 all_outputs = Example(self.output_names, all_output_fields) |
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1380 #print 'input_fields', input_fields |
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1381 #print 'all_outputs', all_outputs |
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1382 if fieldnames==self.output_names: |
| 293 | 1383 rval = all_outputs |
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1384 else: |
| 293 | 1385 rval = Example(fieldnames,[all_outputs[name] for name in fieldnames]) |
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|
1386 #print 'rval', rval |
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1387 #print '--------' |
| 293 | 1388 yield rval |
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1389 |
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1390 def untested__iter__(self): # only implemented for increased efficiency |
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1391 class ApplyFunctionSingleExampleIterator(object): |
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1392 def __init__(self,output_dataset): |
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1393 self.current=0 |
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1394 self.output_dataset=output_dataset |
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1395 self.input_iterator=output_dataset.input_dataset.__iter__() |
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1396 def __iter__(self): return self |
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1397 def next(self): |
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1398 if self.output_dataset.minibatch_mode: |
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1399 function_inputs = [[input] for input in self.input_iterator.next()] |
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1400 outputs = self.output_dataset.function(*function_inputs) |
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1401 assert all([hasattr(output,'__iter__') for output in outputs]) |
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1402 function_outputs = [output[0] for output in outputs] |
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1403 else: |
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1404 function_inputs = self.input_iterator.next() |
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1405 function_outputs = self.output_dataset.function(*function_inputs) |
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1406 return Example(self.output_dataset.output_names,function_outputs) |
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1407 return ApplyFunctionSingleExampleIterator(self) |
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1408 |
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1409 def supervised_learning_dataset(src_dataset,input_fields,target_fields,weight_field=None): |
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1410 """ |
| 167 | 1411 Wraps an arbitrary L{DataSet} into one for supervised learning tasks |
| 1412 by forcing the user to define a set of fields as the 'input' field | |
| 1413 and a set of fields as the 'target' field. Optionally, a single | |
| 1414 weight_field can also be defined. | |
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1415 """ |
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1416 args = ((input_fields,'input'),(output_fields,'target')) |
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1417 if weight_field: args+=(([weight_field],'weight')) |
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1418 return src_dataset.merge_fields(*args) |
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1419 |
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1420 |
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1421 |
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1422 |