Mercurial > pylearn
annotate dataset.py @ 336:0ce6e62ac6e5
Automated merge with ssh://projects@lgcm.iro.umontreal.ca/hg/pylearn
| author | Frederic Bastien <bastienf@iro.umontreal.ca> |
|---|---|
| date | Mon, 16 Jun 2008 17:07:44 -0400 |
| parents | 89d88807e958 7d2f7b8fe213 |
| children | 7d4792fc28ae |
| rev | line source |
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1 |
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2 from lookup_list import LookupList as Example |
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3 from misc import unique_elements_list_intersection |
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4 from string import join |
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5 from sys import maxint |
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6 import numpy, copy |
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| 166 | 8 from exceptions import * |
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9 |
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10 class AttributesHolder(object): |
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11 def __init__(self): pass |
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12 |
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13 def attributeNames(self): |
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14 raise AbstractFunction() |
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15 |
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16 def setAttributes(self,attribute_names,attribute_values,make_copies=False): |
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17 """ |
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18 Allow the attribute_values to not be a list (but a single value) if the attribute_names is of length 1. |
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19 """ |
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20 if len(attribute_names)==1 and not (isinstance(attribute_values,list) or isinstance(attribute_values,tuple) ): |
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21 attribute_values = [attribute_values] |
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22 if make_copies: |
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23 for name,value in zip(attribute_names,attribute_values): |
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24 self.__setattr__(name,copy.deepcopy(value)) |
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25 else: |
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26 for name,value in zip(attribute_names,attribute_values): |
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27 self.__setattr__(name,value) |
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28 |
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29 def getAttributes(self,attribute_names=None, return_copy=False): |
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30 """ |
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31 Return all (if attribute_names=None, in the order of attributeNames()) or a specified subset of attributes. |
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32 """ |
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33 if attribute_names is None: |
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34 attribute_names = self.attributeNames() |
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35 if return_copy: |
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36 return [copy.copy(self.__getattribute__(name)) for name in attribute_names] |
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37 else: |
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38 return [self.__getattribute__(name) for name in attribute_names] |
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39 |
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40 class DataSet(AttributesHolder): |
| 16 | 41 """A virtual base class for datasets. |
| 42 | |
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43 A DataSet can be seen as a generalization of a matrix, meant to be used in conjunction |
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44 with learning algorithms (for training and testing them): rows/records are called examples, and |
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45 columns/attributes are called fields. The field value for a particular example can be an arbitrary |
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46 python object, which depends on the particular dataset. |
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47 |
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48 We call a DataSet a 'stream' when its length is unbounded (in which case its __len__ method |
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49 should return sys.maxint). |
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50 |
| 16 | 51 A DataSet is a generator of iterators; these iterators can run through the |
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52 examples or the fields in a variety of ways. A DataSet need not necessarily have a finite |
| 16 | 53 or known length, so this class can be used to interface to a 'stream' which |
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54 feeds on-line learning (however, as noted below, some operations are not |
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55 feasible or not recommended on streams). |
| 16 | 56 |
| 57 To iterate over examples, there are several possibilities: | |
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58 - for example in dataset: |
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59 - for val1,val2,... in dataset: |
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60 - for example in dataset(field1, field2,field3, ...): |
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61 - for val1,val2,val3 in dataset(field1, field2,field3): |
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62 - for minibatch in dataset.minibatches([field1, field2, ...],minibatch_size=N): |
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63 - for mini1,mini2,mini3 in dataset.minibatches([field1, field2, field3], minibatch_size=N): |
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64 Each of these is documented below. All of these iterators are expected |
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65 to provide, in addition to the usual 'next()' method, a 'next_index()' method |
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66 which returns a non-negative integer pointing to the position of the next |
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67 example that will be returned by 'next()' (or of the first example in the |
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68 next minibatch returned). This is important because these iterators |
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69 can wrap around the dataset in order to do multiple passes through it, |
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70 in possibly unregular ways if the minibatch size is not a divisor of the |
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71 dataset length. |
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72 |
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73 To iterate over fields, one can do |
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74 - for field in dataset.fields(): |
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75 for field_value in field: # iterate over the values associated to that field for all the dataset examples |
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76 - for field in dataset(field1,field2,...).fields() to select a subset of fields |
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77 - for field in dataset.fields(field1,field2,...) to select a subset of fields |
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78 and each of these fields is iterable over the examples: |
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79 - for field_examples in dataset.fields(): |
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80 for example_value in field_examples: |
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81 ... |
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82 but when the dataset is a stream (unbounded length), it is not recommended to do |
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83 such things because the underlying dataset may refuse to access the different fields in |
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84 an unsynchronized ways. Hence the fields() method is illegal for streams, by default. |
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85 The result of fields() is a L{DataSetFields} object, which iterates over fields, |
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86 and whose elements are iterable over examples. A DataSetFields object can |
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87 be turned back into a DataSet with its examples() method:: |
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88 dataset2 = dataset1.fields().examples() |
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89 and dataset2 should behave exactly like dataset1 (in fact by default dataset2==dataset1). |
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90 |
| 16 | 91 Note: Fields are not mutually exclusive, i.e. two fields can overlap in their actual content. |
| 92 | |
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93 Note: The content of a field can be of any type. Field values can also be 'missing' |
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94 (e.g. to handle semi-supervised learning), and in the case of numeric (numpy array) |
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95 fields (i.e. an ArrayFieldsDataSet), NaN plays the role of a missing value. |
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96 What about non-numeric values? None. |
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97 |
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98 Dataset elements can be indexed and sub-datasets (with a subset |
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99 of examples) can be extracted. These operations are not supported |
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100 by default in the case of streams. |
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101 |
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102 - dataset[:n] returns an Example with the n first examples. |
| 16 | 103 |
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104 - dataset[i1:i2:s] returns an Example with the examples i1,i1+s,...i2-s. |
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105 |
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106 - dataset[i] returns an Example. |
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107 |
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108 - dataset[[i1,i2,...in]] returns a. Example with examples i1,i2,...in. |
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109 |
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110 A similar command gives you a DataSet instead of Examples : |
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111 |
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112 - dataset.subset[:n] returns a DataSet with the n first examples. |
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113 |
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114 - dataset.subset[i1:i2:s] returns a DataSet with the examples i1,i1+s,...i2-s. |
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115 |
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116 - dataset.subset[i] returns a DataSet. |
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117 |
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118 - dataset.subset[[i1,i2,...in]] returns a DataSet with examples i1,i2,...in. |
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119 |
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120 |
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121 - dataset.<property> returns the value of a property associated with |
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122 the name <property>. The following properties should be supported: |
| 41 | 123 - 'description': a textual description or name for the dataset |
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124 - 'fieldtypes': a list of types (one per field) |
| 78 | 125 A DataSet may have other attributes that it makes visible to other objects. These are |
| 126 used to store information that is not example-wise but global to the dataset. | |
| 127 The list of names of these attributes is given by the attribute_names() method. | |
| 41 | 128 |
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129 Datasets can be concatenated either vertically (increasing the length) or |
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130 horizontally (augmenting the set of fields), if they are compatible, using |
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131 the following operations (with the same basic semantics as numpy.hstack |
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132 and numpy.vstack): |
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133 |
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134 - dataset1 | dataset2 | dataset3 == dataset.hstack([dataset1,dataset2,dataset3]) |
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135 |
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136 creates a new dataset whose list of fields is the concatenation of the list of |
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137 fields of the argument datasets. This only works if they all have the same length. |
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138 |
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139 - dataset1 & dataset2 & dataset3 == dataset.vstack([dataset1,dataset2,dataset3]) |
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140 |
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141 creates a new dataset that concatenates the examples from the argument datasets |
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142 (and whose length is the sum of the length of the argument datasets). This only |
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143 works if they all have the same fields. |
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144 |
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145 According to the same logic, and viewing a DataSetFields object associated to |
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146 a DataSet as a kind of transpose of it, fields1 & fields2 concatenates fields of |
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147 a DataSetFields fields1 and fields2, and fields1 | fields2 concatenates their |
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148 examples. |
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149 |
| 41 | 150 A dataset can hold arbitrary key-value pairs that may be used to access meta-data |
| 151 or other properties of the dataset or associated with the dataset or the result | |
| 152 of a computation stored in a dataset. These can be accessed through the [key] syntax | |
| 153 when key is a string (or more specifically, neither an integer, a slice, nor a list). | |
| 78 | 154 |
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155 A DataSet sub-class should always redefine the following methods: |
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156 - __len__ if it is not a stream |
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157 - fieldNames |
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158 - minibatches_nowrap (called by DataSet.minibatches()) |
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159 For efficiency of implementation, a sub-class might also want to redefine |
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160 - valuesHStack |
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161 - valuesVStack |
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162 - hasFields |
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163 - __getitem__ may not be feasible with some streams |
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164 - __iter__ |
| 78 | 165 A sub-class should also append attributes to self._attribute_names |
| 166 (the default value returned by attributeNames()). | |
| 167 By convention, attributes not in attributeNames() should have a name | |
| 168 starting with an underscore. | |
| 169 @todo enforce/test that convention! | |
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170 """ |
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171 |
| 83 | 172 numpy_vstack = lambda fieldname,values: numpy.vstack(values) |
| 173 numpy_hstack = lambda fieldnames,values: numpy.hstack(values) | |
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174 |
| 292 | 175 def __init__(self, description=None, fieldnames=None, fieldtypes=None): |
| 176 """ | |
| 177 @type fieldnames: list of strings | |
| 178 @type fieldtypes: list of python types, same length as fieldnames | |
| 179 @type description: string | |
| 180 @param description: description/name for this dataset | |
| 181 """ | |
| 182 def default_desc(): | |
| 183 return type(self).__name__ \ | |
| 184 + " ( " + join([x.__name__ for x in type(self).__bases__]) + " )" | |
| 185 | |
| 186 #self.fieldnames = fieldnames | |
| 187 | |
| 188 self.fieldtypes = fieldtypes if fieldtypes is not None \ | |
| 189 else [None]*1 #len(fieldnames) | |
| 190 | |
| 191 self.description = default_desc() if description is None \ | |
| 192 else description | |
| 78 | 193 self._attribute_names = ["description"] |
| 292 | 194 |
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195 |
| 292 | 196 attributeNames = property(lambda self: copy.copy(self._attribute_names)) |
| 197 | |
| 198 def __contains__(self, fieldname): | |
| 199 return (fieldname in self.fieldNames()) \ | |
| 200 or (fieldname in self.attributeNames()) | |
| 201 | |
| 202 def __iter__(self): | |
| 203 """Supports the syntax "for i in dataset: ..." | |
| 78 | 204 |
| 292 | 205 Using this syntax, "i" will be an Example instance (or equivalent) with |
| 206 all the fields of DataSet self. Every field of "i" will give access to | |
| 207 a field of a single example. Fields should be accessible via | |
| 208 i["fielname"] or i[3] (in the order defined by the elements of the | |
| 209 Example returned by this iterator), but the derived class is free | |
| 210 to accept any type of identifier, and add extra functionality to the iterator. | |
| 211 | |
| 212 The default implementation calls the minibatches iterator and extracts the first example of each field. | |
| 213 """ | |
| 214 return DataSet.MinibatchToSingleExampleIterator(self.minibatches(None, minibatch_size = 1)) | |
| 215 | |
| 216 def __len__(self): | |
| 217 """ | |
| 218 len(dataset) returns the number of examples in the dataset. | |
| 219 By default, a DataSet is a 'stream', i.e. it has an unbounded length (sys.maxint). | |
| 220 Sub-classes which implement finite-length datasets should redefine this method. | |
| 221 Some methods only make sense for finite-length datasets. | |
| 222 """ | |
| 223 return None | |
| 224 | |
| 78 | 225 |
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226 class MinibatchToSingleExampleIterator(object): |
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227 """ |
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228 Converts the result of minibatch iterator with minibatch_size==1 into |
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229 single-example values in the result. Therefore the result of |
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230 iterating on the dataset itself gives a sequence of single examples |
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231 (whereas the result of iterating over minibatches gives in each |
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232 Example field an iterable object over the individual examples in |
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233 the minibatch). |
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234 """ |
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235 def __init__(self, minibatch_iterator): |
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236 self.minibatch_iterator = minibatch_iterator |
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237 self.minibatch = None |
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238 def __iter__(self): #makes for loop work |
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239 return self |
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240 def next(self): |
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241 size1_minibatch = self.minibatch_iterator.next() |
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242 if not self.minibatch: |
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243 names = size1_minibatch.keys() |
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244 # next lines are a hack, but there was problem when we were getting [array(327)] for instance |
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245 try: |
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246 values = [value[0] for value in size1_minibatch.values()] |
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247 except : |
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248 values = [value for value in size1_minibatch.values()] |
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249 self.minibatch = Example(names,values) |
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250 else: |
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251 self.minibatch._values = [value[0] for value in size1_minibatch.values()] |
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252 return self.minibatch |
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253 |
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254 def next_index(self): |
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255 return self.minibatch_iterator.next_index() |
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256 |
|
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257 class MinibatchWrapAroundIterator(object): |
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258 """ |
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259 An iterator for minibatches that handles the case where we need to wrap around the |
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260 dataset because n_batches*minibatch_size > len(dataset). It is constructed from |
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261 a dataset that provides a minibatch iterator that does not need to handle that problem. |
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262 This class is a utility for dataset subclass writers, so that they do not have to handle |
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263 this issue multiple times, nor check that fieldnames are valid, nor handle the |
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264 empty fieldnames (meaning 'use all the fields'). |
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265 """ |
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266 def __init__(self,dataset,fieldnames,minibatch_size,n_batches,offset): |
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267 self.dataset=dataset |
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268 self.fieldnames=fieldnames |
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269 self.minibatch_size=minibatch_size |
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270 self.n_batches=n_batches |
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271 self.n_batches_done=0 |
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272 self.next_row=offset |
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273 self.L=len(dataset) |
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274 self.offset=offset % self.L |
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275 ds_nbatches = (self.L-self.next_row)/self.minibatch_size |
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276 if n_batches is not None: |
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277 ds_nbatches = min(n_batches,ds_nbatches) |
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278 if fieldnames: |
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279 assert dataset.hasFields(*fieldnames) |
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280 else: |
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281 self.fieldnames=dataset.fieldNames() |
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282 self.iterator = self.dataset.minibatches_nowrap(self.fieldnames,self.minibatch_size, ds_nbatches,self.next_row) |
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283 |
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284 def __iter__(self): |
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285 return self |
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286 |
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287 def next_index(self): |
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288 return self.next_row |
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289 |
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290 def next(self): |
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291 if self.n_batches and self.n_batches_done==self.n_batches: |
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292 raise StopIteration |
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293 elif not self.n_batches and self.next_row ==self.L: |
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294 raise StopIteration |
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295 upper = self.next_row+self.minibatch_size |
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296 if upper <=self.L: |
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297 minibatch = self.iterator.next() |
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298 else: |
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299 if not self.n_batches: |
|
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300 upper=min(upper, self.L) |
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301 # if their is not a fixed number of batch, we continue to the end of the dataset. |
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302 # this can create a minibatch that is smaller then the minibatch_size |
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303 assert (self.L-self.next_row)<=self.minibatch_size |
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304 minibatch = self.dataset.minibatches_nowrap(self.fieldnames,self.L-self.next_row,1,self.next_row).next() |
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305 else: |
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306 # we must concatenate (vstack) the bottom and top parts of our minibatch |
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307 # first get the beginning of our minibatch (top of dataset) |
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308 first_part = self.dataset.minibatches_nowrap(self.fieldnames,self.L-self.next_row,1,self.next_row).next() |
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309 second_part = self.dataset.minibatches_nowrap(self.fieldnames,upper-self.L,1,0).next() |
|
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310 minibatch = Example(self.fieldnames, |
|
268
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311 [self.dataset.valuesVStack(name,[first_part[name],second_part[name]]) |
|
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312 for name in self.fieldnames]) |
|
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313 self.next_row=upper |
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314 self.n_batches_done+=1 |
|
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315 if upper >= self.L and self.n_batches: |
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316 self.next_row -= self.L |
|
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317 ds_nbatches = (self.L-self.next_row)/self.minibatch_size |
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318 if self.n_batches is not None: |
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319 ds_nbatches = min(self.n_batches,ds_nbatches) |
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320 self.iterator = self.dataset.minibatches_nowrap(self.fieldnames,self.minibatch_size, |
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321 ds_nbatches,self.next_row) |
|
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322 return DataSetFields(MinibatchDataSet(minibatch,self.dataset.valuesVStack, |
|
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323 self.dataset.valuesHStack), |
|
74
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324 minibatch.keys()) |
|
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325 |
|
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326 |
|
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327 minibatches_fieldnames = None |
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328 minibatches_minibatch_size = 1 |
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329 minibatches_n_batches = None |
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330 def minibatches(self, |
|
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331 fieldnames = minibatches_fieldnames, |
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332 minibatch_size = minibatches_minibatch_size, |
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333 n_batches = minibatches_n_batches, |
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334 offset = 0): |
|
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335 """ |
|
36
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336 Return an iterator that supports three forms of syntax: |
|
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337 |
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338 for i in dataset.minibatches(None,**kwargs): ... |
| 16 | 339 |
|
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340 for i in dataset.minibatches([f1, f2, f3],**kwargs): ... |
| 16 | 341 |
|
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342 for i1, i2, i3 in dataset.minibatches([f1, f2, f3],**kwargs): ... |
| 16 | 343 |
|
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344 Using the first two syntaxes, "i" will be an indexable object, such as a list, |
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345 tuple, or Example instance. In both cases, i[k] is a list-like container |
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346 of a batch of current examples. In the second case, i[0] is |
|
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347 list-like container of the f1 field of a batch current examples, i[1] is |
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348 a list-like container of the f2 field, etc. |
|
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349 |
|
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350 Using the first syntax, all the fields will be returned in "i". |
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351 Using the third syntax, i1, i2, i3 will be list-like containers of the |
|
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352 f1, f2, and f3 fields of a batch of examples on each loop iteration. |
|
11
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Debugged (to the extent of my tests) the new version of dataset
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353 |
|
36
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354 The minibatches iterator is expected to return upon each call to next() |
|
290
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355 a DataSetFields object, which is a Example (indexed by the field names) whose |
| 80 | 356 elements are iterable and indexable over the minibatch examples, and which keeps a pointer to |
|
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357 a sub-dataset that can be used to iterate over the individual examples |
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358 in the minibatch. Hence a minibatch can be converted back to a regular |
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359 dataset or its fields can be looked at individually (and possibly iterated over). |
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360 |
|
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361 PARAMETERS |
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362 - fieldnames (list of any type, default None): |
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363 The loop variables i1, i2, i3 (in the example above) should contain the |
|
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364 f1, f2, and f3 fields of the current batch of examples. If None, the |
|
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365 derived class can choose a default, e.g. all fields. |
| 16 | 366 |
|
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367 - minibatch_size (integer, default 1) |
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368 On every iteration, the variables i1, i2, i3 will have |
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369 exactly minibatch_size elements. e.g. len(i1) == minibatch_size |
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370 |
|
331
52aa031e1fe3
IMPORTANT: minibatches now returns minibatch_nowrap with a minimum of assert before. Should implement the good behavior, e.g. returning only complete batches and let the user figure out what he wants.
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330
diff
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|
371 @DEPRECATED n_batches : not used anywhere |
|
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372 - n_batches (integer, default None) |
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373 The iterator will loop exactly this many times, and then stop. If None, |
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374 the derived class can choose a default. If (-1), then the returned |
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375 iterator should support looping indefinitely. |
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376 |
|
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377 - offset (integer, default 0) |
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378 The iterator will start at example 'offset' in the dataset, rather than the default. |
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379 |
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380 Note: A list-like container is something like a tuple, list, numpy.ndarray or |
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381 any other object that supports integer indexing and slicing. |
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382 |
|
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383 @ATTENTION: now minibatches returns minibatches_nowrap, which is supposed to return complete |
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384 batches only, raise StopIteration |
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385 |
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386 """ |
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387 #return DataSet.MinibatchWrapAroundIterator(self,fieldnames,minibatch_size,n_batches,offset)\ |
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388 assert offset >= 0 |
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389 assert offset < len(self) |
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390 assert offset + minibatch_size -1 < len(self) |
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335
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391 return self.minibatches_nowrap(fieldnames,minibatch_size,n_batches,offset) |
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392 |
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393 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
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394 """ |
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395 This is the minibatches iterator generator that sub-classes must define. |
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396 It does not need to worry about wrapping around multiple times across the dataset, |
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397 as this is handled by MinibatchWrapAroundIterator when DataSet.minibatches() is called. |
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398 The next() method of the returned iterator does not even need to worry about |
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399 the termination condition (as StopIteration will be raised by DataSet.minibatches |
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400 before an improper call to minibatches_nowrap's next() is made). |
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401 That next() method can assert that its next row will always be within [0,len(dataset)). |
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402 The iterator returned by minibatches_nowrap does not need to implement |
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403 a next_index() method either, as this will be provided by MinibatchWrapAroundIterator. |
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404 """ |
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405 raise AbstractFunction() |
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406 |
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48
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407 def is_unbounded(self): |
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408 """ |
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409 Tests whether a dataset is unbounded (e.g. a stream). |
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410 """ |
| 123 | 411 return len(self)==maxint |
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412 |
|
26
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413 def hasFields(self,*fieldnames): |
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414 """ |
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415 Return true if the given field name (or field names, if multiple arguments are |
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416 given) is recognized by the DataSet (i.e. can be used as a field name in one |
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417 of the iterators). |
|
29
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418 |
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419 The default implementation may be inefficient (O(# fields in dataset)), as it calls the fieldNames() |
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420 method. Many datasets may store their field names in a dictionary, which would allow more efficiency. |
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421 """ |
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422 return len(unique_elements_list_intersection(fieldnames,self.fieldNames()))>0 |
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423 |
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424 def fieldNames(self): |
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425 """ |
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426 Return the list of field names that are supported by the iterators, |
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427 and for which hasFields(fieldname) would return True. |
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428 """ |
|
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429 raise AbstractFunction() |
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430 |
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431 def __call__(self,*fieldnames): |
|
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432 """ |
|
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433 Return a dataset that sees only the fields whose name are specified. |
|
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434 """ |
|
42
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435 assert self.hasFields(*fieldnames) |
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436 return self.fields(*fieldnames).examples() |
|
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437 |
|
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438 def fields(self,*fieldnames): |
|
29
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439 """ |
|
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440 Return a DataSetFields object associated with this dataset. |
|
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441 """ |
|
74
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442 return DataSetFields(self,fieldnames) |
|
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443 |
|
269
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444 def getitem_key(self, fieldname): |
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445 """A not-so-well thought-out place to put code that used to be in |
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446 getitem. |
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447 """ |
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448 #removing as per discussion June 4. --JSB |
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449 |
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450 i = fieldname |
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451 # else check for a fieldname |
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452 if self.hasFields(i): |
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453 return self.minibatches(fieldnames=[i],minibatch_size=len(self),n_batches=1,offset=0).next()[0] |
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454 # else we are trying to access a property of the dataset |
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455 assert i in self.__dict__ # else it means we are trying to access a non-existing property |
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456 return self.__dict__[i] |
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457 |
|
2
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Rewrote DataSet interface and created FiniteDataSet interface.
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458 def __getitem__(self,i): |
|
28
541a273bc89f
Removed __array__ method from dataset, whose
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459 """ |
|
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460 @rtype: Example |
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461 @returns: single or multiple examples |
|
1
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462 |
|
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463 @type i: integer or slice or <iterable> of integers |
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464 @param i: |
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465 dataset[i] returns the (i+1)-th example of the dataset. |
|
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466 dataset[i:j] returns a LookupList with examples i,i+1,...,j-1. |
|
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467 dataset[i:j:s] returns a LookupList with examples i,i+2,i+4...,j-2. |
|
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468 dataset[[i1,i2,..,in]] returns a LookupList with examples i1,i2,...,in. |
|
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469 |
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470 @note: |
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471 Some stream datasets may be unable to implement random access, i.e. |
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472 arbitrary slicing/indexing because they can only iterate through |
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473 examples one or a minibatch at a time and do not actually store or keep |
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474 past (or future) examples. |
|
40
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475 |
|
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476 The default implementation of getitem uses the minibatches iterator |
|
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477 to obtain one example, one slice, or a list of examples. It may not |
|
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478 always be the most efficient way to obtain the result, especially if |
|
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479 the data are actually stored in a memory array. |
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480 """ |
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481 |
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482 if type(i) is int: |
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483 assert i >= 0 # TBM: see if someone complains and want negative i |
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484 if i >= len(self) : |
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485 raise IndexError |
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486 i_batch = self.minibatches_nowrap(self.fieldNames(), |
| 293 | 487 minibatch_size=1, n_batches=1, offset=i) |
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488 return DataSet.MinibatchToSingleExampleIterator(i_batch).next() |
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489 |
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490 #if i is a contiguous slice |
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491 if type(i) is slice and (i.step in (None, 1)): |
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492 offset = 0 if i.start is None else i.start |
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493 upper_bound = len(self) if i.stop is None else i.stop |
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494 upper_bound = min(len(self) , upper_bound) |
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495 #return MinibatchDataSet(self.minibatches_nowrap(self.fieldNames(), |
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496 # minibatch_size=upper_bound - offset, |
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497 # n_batches=1, |
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498 # offset=offset).next()) |
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499 # now returns a LookupList |
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500 return self.minibatches_nowrap(self.fieldNames(), |
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501 minibatch_size=upper_bound - offset, |
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502 n_batches=1, |
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503 offset=offset).next() |
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504 |
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505 # if slice has a step param, convert it to list and handle it with the |
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506 # list code |
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507 if type(i) is slice: |
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508 offset = 0 if i.start is None else i.start |
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509 upper_bound = len(self) if i.stop is None else i.stop |
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510 upper_bound = min(len(self) , upper_bound) |
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511 i = list(range(offset, upper_bound, i.step)) |
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512 |
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513 # handle tuples, arrays, lists |
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514 if hasattr(i, '__getitem__'): |
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515 for idx in i: |
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516 #dis-allow nested slices |
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517 if not isinstance(idx, int): |
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518 raise TypeError(idx) |
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519 if idx >= len(self) : |
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520 raise IndexError |
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521 # call back into self.__getitem__ |
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522 examples = [self.minibatches_nowrap(self.fieldNames(), |
| 293 | 523 minibatch_size=1, n_batches=1, offset=ii).next() |
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524 for ii in i] |
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525 # re-index the fields in each example by field instead of by example |
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526 field_values = [[] for blah in self.fieldNames()] |
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527 for e in examples: |
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528 for f,v in zip(field_values, e): |
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529 f.append(v) |
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530 #build them into a LookupList (a.ka. Example) |
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531 zz = zip(self.fieldNames(),field_values) |
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532 vst = [self.valuesVStack(fieldname,field_values) for fieldname,field_values in zz] |
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533 example = Example(self.fieldNames(), vst) |
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534 #return MinibatchDataSet(example, self.valuesVStack, self.valuesHStack) |
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535 # now returns a LookupList |
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536 return example |
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537 |
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538 # what in the world is i? |
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539 raise TypeError(i, type(i)) |
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540 |
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541 |
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542 """ |
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543 Enables the call dataset.subset[a:b:c] that will return a DataSet |
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544 around the examples returned by __getitem__(slice(a,b,c)) |
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545 |
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546 @SEE DataSet.__getsubset(self) |
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547 """ |
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548 subset = property(lambda s : s.__getsubset(),doc="returns a subset as a DataSet") |
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549 |
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550 |
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551 def __getsubset(self) : |
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552 """ |
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553 Enables the call data.subset[a:b:c], returns a DataSet. |
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554 Default implementation is a simple wrap around __getitem__() using MinibatchDataSet. |
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555 |
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556 @RETURN DataSet |
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557 @SEE DataSet.subset = property(lambda s : s.__getsubset()) |
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558 """ |
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559 _self = self |
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560 class GetSliceReturnsDataSet(object) : |
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561 def __getitem__(self,slice) : |
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562 return MinibatchDataSet(_self.__getitem__(slice)) |
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563 return GetSliceReturnsDataSet() |
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564 |
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565 |
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566 |
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567 def valuesHStack(self,fieldnames,fieldvalues): |
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568 """ |
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569 Return a value that corresponds to concatenating (horizontally) several field values. |
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570 This can be useful to merge some fields. The implementation of this operation is likely |
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571 to involve a copy of the original values. When the values are numpy arrays, the |
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572 result should be numpy.hstack(values). If it makes sense, this operation should |
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573 work as well when each value corresponds to multiple examples in a minibatch |
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574 e.g. if each value is a Ni-vector and a minibatch of length L is a LxNi matrix, |
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575 then the result should be a Lx(N1+N2+..) matrix equal to numpy.hstack(values). |
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576 The default is to use numpy.hstack for numpy.ndarray values, and a list |
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577 pointing to the original values for other data types. |
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578 """ |
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579 all_numpy=True |
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580 for value in fieldvalues: |
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581 if not type(value) is numpy.ndarray: |
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582 all_numpy=False |
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583 if all_numpy: |
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584 return numpy.hstack(fieldvalues) |
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585 # the default implementation of horizontal stacking is to put values in a list |
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586 return fieldvalues |
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587 |
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588 def valuesVStack(self,fieldname,values): |
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589 """ |
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590 @param fieldname: the name of the field from which the values were taken |
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591 @type fieldname: any type |
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592 |
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593 @param values: bits near the beginning or end of the dataset |
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594 @type values: list of minibatches (returned by minibatch_nowrap) |
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595 |
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596 @return: the concatenation (stacking) of the values |
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597 @rtype: something suitable as a minibatch field |
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598 """ |
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599 rval = [] |
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600 for v in values: |
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601 rval.extend(v) |
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602 return rval |
|
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603 |
|
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604 def __or__(self,other): |
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605 """ |
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606 dataset1 | dataset2 returns a dataset whose list of fields is the concatenation of the list of |
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607 fields of the argument datasets. This only works if they all have the same length. |
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608 """ |
|
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609 return HStackedDataSet([self,other]) |
|
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610 |
|
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611 def __and__(self,other): |
|
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612 """ |
|
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613 dataset1 & dataset2 is a dataset that concatenates the examples from the argument datasets |
|
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614 (and whose length is the sum of the length of the argument datasets). This only |
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615 works if they all have the same fields. |
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616 """ |
|
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617 return VStackedDataSet([self,other]) |
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618 |
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619 def hstack(datasets): |
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620 """ |
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621 hstack(dataset1,dataset2,...) returns dataset1 | datataset2 | ... |
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622 which is a dataset whose fields list is the concatenation of the fields |
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623 of the individual datasets. |
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624 """ |
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625 assert len(datasets)>0 |
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626 if len(datasets)==1: |
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627 return datasets[0] |
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628 return HStackedDataSet(datasets) |
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629 |
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630 def vstack(datasets): |
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631 """ |
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632 vstack(dataset1,dataset2,...) returns dataset1 & datataset2 & ... |
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633 which is a dataset which iterates first over the examples of dataset1, then |
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634 over those of dataset2, etc. |
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635 """ |
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636 assert len(datasets)>0 |
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637 if len(datasets)==1: |
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638 return datasets[0] |
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639 return VStackedDataSet(datasets) |
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640 |
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641 class FieldsSubsetDataSet(DataSet): |
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642 """ |
| 167 | 643 A sub-class of L{DataSet} that selects a subset of the fields. |
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644 """ |
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645 def __init__(self,src,fieldnames): |
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646 self.src=src |
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647 self.fieldnames=fieldnames |
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648 assert src.hasFields(*fieldnames) |
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649 self.valuesHStack = src.valuesHStack |
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650 self.valuesVStack = src.valuesVStack |
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651 |
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652 def __len__(self): return len(self.src) |
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653 |
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654 def fieldNames(self): |
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655 return self.fieldnames |
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656 |
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657 def __iter__(self): |
|
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658 class FieldsSubsetIterator(object): |
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659 def __init__(self,ds): |
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660 self.ds=ds |
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661 self.src_iter=ds.src.__iter__() |
|
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662 self.example=None |
|
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663 def __iter__(self): return self |
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664 def next(self): |
|
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665 complete_example = self.src_iter.next() |
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666 if self.example: |
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667 self.example._values=[complete_example[field] |
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668 for field in self.ds.fieldnames] |
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669 else: |
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670 self.example=Example(self.ds.fieldnames, |
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671 [complete_example[field] for field in self.ds.fieldnames]) |
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672 return self.example |
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673 return FieldsSubsetIterator(self) |
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674 |
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675 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
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676 assert self.hasFields(*fieldnames) |
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677 return self.src.minibatches_nowrap(fieldnames,minibatch_size,n_batches,offset) |
|
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678 def dontuse__getitem__(self,i): |
|
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679 return FieldsSubsetDataSet(self.src[i],self.fieldnames) |
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680 |
|
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681 class RenamedFieldsDataSet(DataSet): |
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682 """ |
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683 A sub-class of L{DataSet} that selects and renames a subset of the fields. |
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684 """ |
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685 def __init__(self,src,src_fieldnames,new_fieldnames): |
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686 self.src=src |
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687 self.src_fieldnames=src_fieldnames |
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688 self.new_fieldnames=new_fieldnames |
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689 assert src.hasFields(*src_fieldnames) |
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690 assert len(src_fieldnames)==len(new_fieldnames) |
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691 self.valuesHStack = src.valuesHStack |
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692 self.valuesVStack = src.valuesVStack |
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|
693 |
|
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694 def __len__(self): return len(self.src) |
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|
695 |
|
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|
696 def fieldNames(self): |
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697 return self.new_fieldnames |
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698 |
|
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699 def __iter__(self): |
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700 class FieldsSubsetIterator(object): |
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701 def __init__(self,ds): |
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702 self.ds=ds |
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703 self.src_iter=ds.src.__iter__() |
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704 self.example=None |
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705 def __iter__(self): return self |
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706 def next(self): |
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diff
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|
707 complete_example = self.src_iter.next() |
|
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diff
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|
708 if self.example: |
|
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diff
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|
709 self.example._values=[complete_example[field] |
|
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diff
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|
710 for field in self.ds.src_fieldnames] |
|
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|
711 else: |
|
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diff
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|
712 self.example=Example(self.ds.new_fieldnames, |
|
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diff
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|
713 [complete_example[field] |
|
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|
714 for field in self.ds.src_fieldnames]) |
|
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|
715 return self.example |
|
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diff
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|
716 return FieldsSubsetIterator(self) |
|
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|
717 |
|
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|
718 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
|
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|
719 assert self.hasFields(*fieldnames) |
|
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|
720 return self.src.minibatches_nowrap(fieldnames,minibatch_size,n_batches,offset) |
|
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|
721 def __getitem__(self,i): |
|
333
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bugfix in RenamedDataSet
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diff
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|
722 # return FieldsSubsetDataSet(self.src[i],self.new_fieldnames) |
|
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|
723 complete_example = self.src[i] |
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diff
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|
724 return Example(self.new_fieldnames, |
|
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|
725 [complete_example[field] |
|
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|
726 for field in self.src_fieldnames]) |
|
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|
727 |
|
328
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|
728 |
|
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|
729 |
|
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|
730 class DataSetFields(Example): |
|
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|
731 """ |
| 167 | 732 Although a L{DataSet} iterates over examples (like rows of a matrix), an associated |
|
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|
733 DataSetFields iterates over fields (like columns of a matrix), and can be understood |
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|
734 as a transpose of the associated dataset. |
|
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|
735 |
|
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|
736 To iterate over fields, one can do |
|
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|
737 * for fields in dataset.fields() |
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|
738 * for fields in dataset(field1,field2,...).fields() to select a subset of fields |
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|
739 * for fields in dataset.fields(field1,field2,...) to select a subset of fields |
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740 and each of these fields is iterable over the examples: |
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|
741 * for field_examples in dataset.fields(): |
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|
742 for example_value in field_examples: |
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|
743 ... |
|
241
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If I understand properly, the length of an unbounded stream is sys.maxint
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|
744 but when the dataset is a stream (unbounded length), it is not recommended to do |
|
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|
745 such things because the underlying dataset may refuse to access the different fields in |
|
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|
746 an unsynchronized ways. Hence the fields() method is illegal for streams, by default. |
|
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|
747 The result of fields() is a DataSetFields object, which iterates over fields, |
|
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|
748 and whose elements are iterable over examples. A DataSetFields object can |
|
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749 be turned back into a DataSet with its examples() method: |
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|
750 dataset2 = dataset1.fields().examples() |
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751 and dataset2 should behave exactly like dataset1 (in fact by default dataset2==dataset1). |
|
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|
752 |
|
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|
753 DataSetFields can be concatenated vertically or horizontally. To be consistent with |
|
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diff
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|
754 the syntax used for DataSets, the | concatenates the fields and the & concatenates |
|
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|
755 the examples. |
|
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|
756 """ |
|
74
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diff
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|
757 def __init__(self,dataset,fieldnames): |
|
65
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parents:
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diff
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|
758 original_dataset=dataset |
|
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|
759 if not fieldnames: |
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diff
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|
760 fieldnames=dataset.fieldNames() |
|
274
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diff
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|
761 elif not list(fieldnames)==list(dataset.fieldNames()): |
|
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diff
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|
762 #we must cast to list, othersize('x','y')!=['x','y'] |
|
42
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diff
changeset
|
763 dataset = FieldsSubsetDataSet(dataset,fieldnames) |
|
37
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diff
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|
764 assert dataset.hasFields(*fieldnames) |
|
42
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diff
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|
765 self.dataset=dataset |
|
66
dde1fb1b63ba
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|
766 |
|
64
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diff
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|
767 if isinstance(dataset,MinibatchDataSet): |
|
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|
768 Example.__init__(self,fieldnames,list(dataset._fields)) |
|
65
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diff
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|
769 elif isinstance(original_dataset,MinibatchDataSet): |
|
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|
770 Example.__init__(self,fieldnames, |
|
65
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diff
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|
771 [original_dataset._fields[field] |
|
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diff
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|
772 for field in fieldnames]) |
|
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diff
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|
773 else: |
|
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diff
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|
774 minibatch_iterator = dataset.minibatches(fieldnames, |
|
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diff
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|
775 minibatch_size=len(dataset), |
|
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diff
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|
776 n_batches=1) |
|
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diff
changeset
|
777 minibatch=minibatch_iterator.next() |
|
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changeset
|
778 Example.__init__(self,fieldnames,minibatch) |
|
42
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diff
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|
779 |
|
36
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|
780 def examples(self): |
|
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|
781 return self.dataset |
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|
782 |
|
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diff
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|
783 def __or__(self,other): |
|
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diff
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|
784 """ |
|
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|
785 fields1 | fields2 is a DataSetFields that whose list of examples is the concatenation |
|
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|
786 of the list of examples of DataSetFields fields1 and fields2. |
|
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|
787 """ |
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|
788 return (self.examples() + other.examples()).fields() |
|
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diff
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|
789 |
|
40
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diff
changeset
|
790 def __and__(self,other): |
|
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diff
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|
791 """ |
|
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|
792 fields1 + fields2 is a DataSetFields that whose list of fields is the concatenation |
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793 of the fields of DataSetFields fields1 and fields2. |
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|
794 """ |
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|
795 return (self.examples() | other.examples()).fields() |
|
17
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diff
changeset
|
796 |
|
37
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diff
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|
797 |
|
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|
798 class MinibatchDataSet(DataSet): |
|
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799 """ |
|
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800 Turn a L{Example} of same-length (iterable) fields into an example-iterable dataset. |
|
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|
801 Each element of the lookup-list should be an iterable and sliceable, all of the same length. |
|
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|
802 """ |
|
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|
803 def __init__(self,fields_lookuplist,values_vstack=DataSet().valuesVStack, |
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|
804 values_hstack=DataSet().valuesHStack): |
|
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diff
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|
805 """ |
|
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|
806 The user can (and generally should) also provide values_vstack(fieldname,fieldvalues) |
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807 and a values_hstack(fieldnames,fieldvalues) functions behaving with the same |
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|
808 semantics as the DataSet methods of the same name (but without the self argument). |
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809 """ |
|
211
bd728c83faff
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|
810 |
|
61
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bugfix: in MinibatchDataSet renamed the class variable fields to _fields as parent class have a function called field.
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diff
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|
811 self._fields=fields_lookuplist |
|
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812 assert len(fields_lookuplist)>0 |
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813 self.length=len(fields_lookuplist[0]) |
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814 for field in fields_lookuplist[1:]: |
|
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815 if self.length != len(field) : |
|
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|
816 print 'self.length = ',self.length |
|
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817 print 'len(field) = ', len(field) |
|
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changeset
|
818 print 'self._fields.keys() = ', self._fields.keys() |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
819 print 'field=',field |
|
290
9b533cc7874a
trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
274
diff
changeset
|
820 print 'fields_lookuplist=', fields_lookuplist |
|
36
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Rewriting dataset.py completely
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parents:
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diff
changeset
|
821 assert self.length==len(field) |
|
290
9b533cc7874a
trying to get default implemenations to work
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parents:
274
diff
changeset
|
822 self.valuesVStack=values_vstack |
|
9b533cc7874a
trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
274
diff
changeset
|
823 self.valuesHStack=values_hstack |
|
3
378b68d5c4ad
Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents:
2
diff
changeset
|
824 |
|
378b68d5c4ad
Added first (untested) version of ArrayDataSet
bengioy@bengiomac.local
parents:
2
diff
changeset
|
825 def __len__(self): |
|
36
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
826 return self.length |
|
28
541a273bc89f
Removed __array__ method from dataset, whose
bengioy@grenat.iro.umontreal.ca
parents:
26
diff
changeset
|
827 |
|
290
9b533cc7874a
trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
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diff
changeset
|
828 def dontuse__getitem__(self,i): |
| 80 | 829 if type(i) in (slice,list): |
|
48
b6730f9a336d
Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents:
46
diff
changeset
|
830 return DataSetFields(MinibatchDataSet( |
| 80 | 831 Example(self._fields.keys(),[field[i] for field in self._fields])),self.fieldNames()) |
| 832 if type(i) is int: | |
| 85 | 833 return Example(self._fields.keys(),[field[i] for field in self._fields]) |
|
48
b6730f9a336d
Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents:
46
diff
changeset
|
834 if self.hasFields(i): |
|
61
a8b70a9117ad
bugfix: in MinibatchDataSet renamed the class variable fields to _fields as parent class have a function called field.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
60
diff
changeset
|
835 return self._fields[i] |
|
55
66619ce44497
Efficient implementation of getitem for ArrayDataSet
Yoshua Bengio <bengioy@iro.umontreal.ca>
parents:
48
diff
changeset
|
836 assert i in self.__dict__ # else it means we are trying to access a non-existing property |
|
48
b6730f9a336d
Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents:
46
diff
changeset
|
837 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
|
838 |
|
29
46c5c90019c2
Changed apply_function so that it propagates methods of the source.
bengioy@grenat.iro.umontreal.ca
parents:
28
diff
changeset
|
839 def fieldNames(self): |
|
61
a8b70a9117ad
bugfix: in MinibatchDataSet renamed the class variable fields to _fields as parent class have a function called field.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
60
diff
changeset
|
840 return self._fields.keys() |
|
36
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Rewriting dataset.py completely
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parents:
29
diff
changeset
|
841 |
|
37
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
842 def hasFields(self,*fieldnames): |
|
36
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Rewriting dataset.py completely
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parents:
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diff
changeset
|
843 for fieldname in fieldnames: |
|
61
a8b70a9117ad
bugfix: in MinibatchDataSet renamed the class variable fields to _fields as parent class have a function called field.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
60
diff
changeset
|
844 if fieldname not in self._fields.keys(): |
|
36
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Rewriting dataset.py completely
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diff
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|
845 return False |
|
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parents:
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diff
changeset
|
846 return True |
|
20
266c68cb6136
Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents:
19
diff
changeset
|
847 |
|
37
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
848 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
|
223
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
849 #@TODO bug somewhere here, fieldnames doesnt seem to be well handled |
|
36
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Rewriting dataset.py completely
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diff
changeset
|
850 class Iterator(object): |
|
223
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
851 def __init__(self,ds,fieldnames): |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
852 # tbm: added two next lines to handle fieldnames |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
853 if fieldnames is None: fieldnames = ds._fields.keys() |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
854 self.fieldnames = fieldnames |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
855 |
|
36
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Rewriting dataset.py completely
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parents:
29
diff
changeset
|
856 self.ds=ds |
|
37
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
857 self.next_example=offset |
|
290
9b533cc7874a
trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
parents:
274
diff
changeset
|
858 assert minibatch_size >= 0 |
| 41 | 859 if offset+minibatch_size > ds.length: |
|
36
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
860 raise NotImplementedError() |
|
20
266c68cb6136
Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents:
19
diff
changeset
|
861 def __iter__(self): |
|
266c68cb6136
Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents:
19
diff
changeset
|
862 return self |
|
266c68cb6136
Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents:
19
diff
changeset
|
863 def next(self): |
|
61
a8b70a9117ad
bugfix: in MinibatchDataSet renamed the class variable fields to _fields as parent class have a function called field.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
60
diff
changeset
|
864 upper = self.next_example+minibatch_size |
|
37
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
865 assert upper<=self.ds.length |
|
223
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
866 #minibatch = Example(self.ds._fields.keys(), |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
867 # [field[self.next_example:upper] |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
868 # for field in self.ds._fields]) |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
869 # tbm: modif to use fieldnames |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
870 values = [] |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
871 for f in self.fieldnames : |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
872 #print 'we have field',f,'in fieldnames' |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
873 values.append( self.ds._fields[f][self.next_example:upper] ) |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
874 minibatch = Example(self.fieldnames,values) |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
875 #print minibatch |
|
36
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
876 self.next_example+=minibatch_size |
|
73
69f97aad3faf
Coded untested ApplyFunctionDataSet and CacheDataSet
bengioy@bengiomac.local
parents:
72
diff
changeset
|
877 return minibatch |
|
20
266c68cb6136
Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents:
19
diff
changeset
|
878 |
|
223
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
879 # tbm: added fieldnames to handle subset of fieldnames |
|
517364d48ae0
should have solved the problem with minibatches not handling subsets of fieldnames, although maybe not super efficient
Thierry Bertin-Mahieux <bertinmt@iro.umontreal.ca>
parents:
218
diff
changeset
|
880 return Iterator(self,fieldnames) |
|
20
266c68cb6136
Minor editions, plus adding untested ApplyFunctionDataset for GradientLearner in the works.
bengioy@bengiomac.local
parents:
19
diff
changeset
|
881 |
|
36
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
882 class HStackedDataSet(DataSet): |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
883 """ |
| 167 | 884 A L{DataSet} that wraps several datasets and shows a view that includes all their fields, |
|
36
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
885 i.e. whose list of fields is the concatenation of their lists of fields. |
|
438440ba0627
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parents:
29
diff
changeset
|
886 |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
887 If a field name is found in more than one of the datasets, then either an error is |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
888 raised or the fields are renamed (either by prefixing the __name__ attribute |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
889 of the dataset + ".", if it exists, or by suffixing the dataset index in the argument list). |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
890 |
| 167 | 891 @todo: automatically detect a chain of stacked datasets due to A | B | C | D ... |
|
36
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
892 """ |
| 41 | 893 def __init__(self,datasets,accept_nonunique_names=False,description=None,field_types=None): |
| 894 DataSet.__init__(self,description,field_types) | |
|
36
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Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
895 self.datasets=datasets |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
896 self.accept_nonunique_names=accept_nonunique_names |
|
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Rewriting dataset.py completely
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parents:
29
diff
changeset
|
897 self.fieldname2dataset={} |
|
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Rewriting dataset.py completely
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parents:
29
diff
changeset
|
898 |
|
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Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
899 def rename_field(fieldname,dataset,i): |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
900 if hasattr(dataset,"__name__"): |
|
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Rewriting dataset.py completely
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parents:
29
diff
changeset
|
901 return dataset.__name__ + "." + fieldname |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
902 return fieldname+"."+str(i) |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
903 |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
904 # make sure all datasets have the same length and unique field names |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
905 self.length=None |
|
438440ba0627
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parents:
29
diff
changeset
|
906 names_to_change=[] |
|
438440ba0627
Rewriting dataset.py completely
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parents:
29
diff
changeset
|
907 for i in xrange(len(datasets)): |
|
438440ba0627
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29
diff
changeset
|
908 dataset = datasets[i] |
|
438440ba0627
Rewriting dataset.py completely
bengioy@zircon.iro.umontreal.ca
parents:
29
diff
changeset
|
909 length=len(dataset) |
|
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parents:
29
diff
changeset
|
910 if self.length: |
|
438440ba0627
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parents:
29
diff
changeset
|
911 assert self.length==length |
|
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parents:
29
diff
changeset
|
912 else: |
|
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parents:
29
diff
changeset
|
913 self.length=length |
|
438440ba0627
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parents:
29
diff
changeset
|
914 for fieldname in dataset.fieldNames(): |
|
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parents:
29
diff
changeset
|
915 if fieldname in self.fieldname2dataset: # name conflict! |
|
438440ba0627
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parents:
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diff
changeset
|
916 if accept_nonunique_names: |
|
438440ba0627
Rewriting dataset.py completely
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diff
changeset
|
917 fieldname=rename_field(fieldname,dataset,i) |
|
438440ba0627
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parents:
29
diff
changeset
|
918 names2change.append((fieldname,i)) |
|
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Rewriting dataset.py completely
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parents:
29
diff
changeset
|
919 else: |
|
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parents:
29
diff
changeset
|
920 raise ValueError("Incompatible datasets: non-unique field name = "+fieldname) |
|
438440ba0627
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29
diff
changeset
|
921 self.fieldname2dataset[fieldname]=i |
|
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Rewriting dataset.py completely
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parents:
29
diff
changeset
|
922 for fieldname,i in names_to_change: |
|
438440ba0627
Rewriting dataset.py completely
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29
diff
changeset
|
923 del self.fieldname2dataset[fieldname] |
|
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29
diff
changeset
|
924 self.fieldname2dataset[rename_field(fieldname,self.datasets[i],i)]=i |
|
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Rewriting dataset.py completely
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parents:
29
diff
changeset
|
925 |
|
37
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
bengioy@esprit.iro.umontreal.ca
parents:
36
diff
changeset
|
926 def hasFields(self,*fieldnames): |
|
36
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parents:
29
diff
changeset
|
927 for fieldname in fieldnames: |
|
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diff
changeset
|
928 if not fieldname in self.fieldname2dataset: |
|
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29
diff
changeset
|
929 return False |
|
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parents:
29
diff
changeset
|
930 return True |
|
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29
diff
changeset
|
931 |
|
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diff
changeset
|
932 def fieldNames(self): |
|
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diff
changeset
|
933 return self.fieldname2dataset.keys() |
|
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Rewriting dataset.py completely
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29
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|
934 |
| 41 | 935 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
|
36
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Rewriting dataset.py completely
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diff
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|
936 |
|
44
5a85fda9b19b
Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
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diff
changeset
|
937 class HStackedIterator(object): |
|
36
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Rewriting dataset.py completely
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parents:
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diff
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|
938 def __init__(self,hsds,iterators): |
|
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Rewriting dataset.py completely
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parents:
29
diff
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|
939 self.hsds=hsds |
|
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Rewriting dataset.py completely
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parents:
29
diff
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|
940 self.iterators=iterators |
|
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Rewriting dataset.py completely
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parents:
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diff
changeset
|
941 def __iter__(self): |
|
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parents:
29
diff
changeset
|
942 return self |
|
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parents:
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diff
changeset
|
943 def next(self): |
|
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diff
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|
944 # concatenate all the fields of the minibatches |
|
290
9b533cc7874a
trying to get default implemenations to work
James Bergstra <bergstrj@iro.umontreal.ca>
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diff
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|
945 l=Example() |
| 140 | 946 for iter in self.iterators: |
| 947 l.append_lookuplist(iter.next()) | |
| 948 return l | |
|
36
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Rewriting dataset.py completely
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diff
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|
949 |
| 125 | 950 assert self.hasFields(*fieldnames) |
|
36
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parents:
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diff
changeset
|
951 # find out which underlying datasets are necessary to service the required fields |
|
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Rewriting dataset.py completely
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diff
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|
952 # and construct corresponding minibatch iterators |
| 140 | 953 if fieldnames and fieldnames!=self.fieldNames(): |
|
36
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diff
changeset
|
954 datasets=set([]) |
|
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diff
changeset
|
955 fields_in_dataset=dict([(dataset,[]) for dataset in datasets]) |
|
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Rewriting dataset.py completely
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diff
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|
956 for fieldname in fieldnames: |
| 136 | 957 dataset=self.datasets[self.fieldname2dataset[fieldname]] |
|
36
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diff
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|
958 datasets.add(dataset) |
|
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diff
changeset
|
959 fields_in_dataset[dataset].append(fieldname) |
|
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|
960 datasets=list(datasets) |
|
37
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|
961 iterators=[dataset.minibatches(fields_in_dataset[dataset],minibatch_size,n_batches,offset) |
|
36
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diff
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|
962 for dataset in datasets] |
|
438440ba0627
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|
963 else: |
|
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|
964 datasets=self.datasets |
|
37
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|
965 iterators=[dataset.minibatches(None,minibatch_size,n_batches,offset) for dataset in datasets] |
|
44
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Fixed some more iterator bugs
bengioy@grenat.iro.umontreal.ca
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diff
changeset
|
966 return HStackedIterator(self,iterators) |
|
36
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|
967 |
|
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|
968 |
|
290
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diff
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|
969 def untested_valuesVStack(self,fieldname,fieldvalues): |
|
36
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|
970 return self.datasets[self.fieldname2dataset[fieldname]].valuesVStack(fieldname,fieldvalues) |
|
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|
971 |
|
290
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|
972 def untested_valuesHStack(self,fieldnames,fieldvalues): |
|
36
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|
973 """ |
|
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diff
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|
974 We will use the sub-dataset associated with the first fieldname in the fieldnames list |
|
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diff
changeset
|
975 to do the work, hoping that it can cope with the other values (i.e. won't care |
|
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diff
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|
976 about the incompatible fieldnames). Hence this heuristic will always work if |
|
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Rewriting dataset.py completely
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diff
changeset
|
977 all the fieldnames are of the same sub-dataset. |
|
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|
978 """ |
|
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diff
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|
979 return self.datasets[self.fieldname2dataset[fieldnames[0]]].valuesHStack(fieldnames,fieldvalues) |
|
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diff
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|
980 |
|
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diff
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|
981 class VStackedDataSet(DataSet): |
|
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|
982 """ |
| 167 | 983 A L{DataSet} that wraps several datasets and shows a view that includes all their examples, |
|
36
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diff
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|
984 in the order provided. This clearly assumes that they all have the same field names |
|
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parents:
29
diff
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|
985 and all (except possibly the last one) are of finite length. |
|
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|
986 |
| 167 | 987 @todo: automatically detect a chain of stacked datasets due to A + B + C + D ... |
|
36
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|
988 """ |
|
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diff
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|
989 def __init__(self,datasets): |
|
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diff
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|
990 self.datasets=datasets |
|
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|
991 self.length=0 |
|
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|
992 self.index2dataset={} |
|
37
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diff
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|
993 assert len(datasets)>0 |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
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diff
changeset
|
994 fieldnames = datasets[-1].fieldNames() |
|
38
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changeset
|
995 self.datasets_start_row=[] |
|
37
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diff
changeset
|
996 # 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
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diff
changeset
|
997 # to avoid having to search for the appropriate dataset each time and slice is asked for. |
|
36
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diff
changeset
|
998 for dataset,k in enumerate(datasets[0:-1]): |
|
48
b6730f9a336d
Fixing MinibatchDataSet getitem
bengioy@grenat.iro.umontreal.ca
parents:
46
diff
changeset
|
999 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
|
1000 L=len(dataset) |
|
36
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diff
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|
1001 for i in xrange(L): |
|
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diff
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|
1002 self.index2dataset[self.length+i]=k |
|
38
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changeset
|
1003 self.datasets_start_row.append(self.length) |
|
36
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|
1004 self.length+=L |
|
37
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diff
changeset
|
1005 assert dataset.fieldNames()==fieldnames |
|
38
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|
1006 self.datasets_start_row.append(self.length) |
|
36
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|
1007 self.length+=len(datasets[-1]) |
|
37
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diff
changeset
|
1008 # If length is very large, we should use a more memory-efficient mechanism |
|
73c4212ba5b3
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diff
changeset
|
1009 # that does not store all indices |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
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|
1010 if self.length>1000000: |
|
73c4212ba5b3
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diff
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|
1011 # 1 million entries would require about 60 meg for the index2dataset map |
|
73c4212ba5b3
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diff
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|
1012 # TODO |
|
73c4212ba5b3
Factored the minibatch-writing code into an iterator class inside DataSet
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diff
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|
1013 print "A more efficient mechanism for index2dataset should be implemented" |
|
73c4212ba5b3
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|
1014 |
|
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diff
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|
1015 def __len__(self): |
|
73c4212ba5b3
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|
1016 return self.length |
|
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diff
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|
1017 |
|
73c4212ba5b3
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diff
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|
1018 def fieldNames(self): |
|
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|
1019 return self.datasets[0].fieldNames() |
|
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|
1020 |
|
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diff
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|
1021 def hasFields(self,*fieldnames): |
|
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|
1022 return self.datasets[0].hasFields(*fieldnames) |
|
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diff
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|
1023 |
|
38
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diff
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|
1024 def locate_row(self,row): |
|
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changeset
|
1025 """Return (dataset_index, row_within_dataset) for global row number""" |
|
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|
1026 dataset_index = self.index2dataset[row] |
|
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|
1027 row_within_dataset = self.datasets_start_row[dataset_index] |
|
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|
1028 return dataset_index, row_within_dataset |
|
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|
1029 |
| 41 | 1030 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
|
44
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43
diff
changeset
|
1031 |
|
5a85fda9b19b
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43
diff
changeset
|
1032 class VStackedIterator(object): |
|
37
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bengioy@esprit.iro.umontreal.ca
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diff
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|
1033 def __init__(self,vsds): |
|
73c4212ba5b3
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|
1034 self.vsds=vsds |
|
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diff
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|
1035 self.next_row=offset |
|
38
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changeset
|
1036 self.next_dataset_index,self.next_dataset_row=self.vsds.locate_row(offset) |
|
37
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diff
changeset
|
1037 self.current_iterator,self.n_left_at_the_end_of_ds,self.n_left_in_mb= \ |
|
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diff
changeset
|
1038 self.next_iterator(vsds.datasets[0],offset,n_batches) |
|
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diff
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|
1039 |
|
73c4212ba5b3
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diff
changeset
|
1040 def next_iterator(self,dataset,starting_offset,batches_left): |
|
73c4212ba5b3
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|
1041 L=len(dataset) |
|
73c4212ba5b3
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diff
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|
1042 ds_nbatches = (L-starting_offset)/minibatch_size |
|
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diff
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|
1043 if batches_left is not None: |
|
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|
1044 ds_nbatches = max(batches_left,ds_nbatches) |
|
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|
1045 if minibatch_size>L: |
|
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diff
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|
1046 ds_minibatch_size=L |
|
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diff
changeset
|
1047 n_left_in_mb=minibatch_size-L |
|
38
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|
1048 ds_nbatches=1 |
|
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changeset
|
1049 else: |
|
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|
1050 n_left_in_mb=0 |
|
37
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1051 return dataset.minibatches(fieldnames,minibatch_size,ds_nbatches,starting_offset), \ |
|
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diff
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1052 L-(starting_offset+ds_nbatches*minibatch_size), n_left_in_mb |
|
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diff
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|
1053 |
|
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diff
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|
1054 def move_to_next_dataset(self): |
|
38
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diff
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|
1055 if self.n_left_at_the_end_of_ds>0: |
|
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diff
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|
1056 self.current_iterator,self.n_left_at_the_end_of_ds,self.n_left_in_mb= \ |
|
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diff
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|
1057 self.next_iterator(vsds.datasets[self.next_dataset_index], |
|
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diff
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|
1058 self.n_left_at_the_end_of_ds,1) |
|
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diff
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|
1059 else: |
|
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Finished first untested version of VStackedDataset
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diff
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|
1060 self.next_dataset_index +=1 |
|
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diff
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|
1061 if self.next_dataset_index==len(self.vsds.datasets): |
|
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diff
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|
1062 self.next_dataset_index = 0 |
|
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diff
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|
1063 self.current_iterator,self.n_left_at_the_end_of_ds,self.n_left_in_mb= \ |
|
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diff
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1064 self.next_iterator(vsds.datasets[self.next_dataset_index],starting_offset,n_batches) |
|
37
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|
1065 |
|
73c4212ba5b3
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|
1066 def __iter__(self): |
|
73c4212ba5b3
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1067 return self |
|
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|
1068 |
|
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1069 def next(self): |
|
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1070 dataset=self.vsds.datasets[self.next_dataset_index] |
|
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|
1071 mb = self.next_iterator.next() |
|
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1072 if self.n_left_in_mb: |
|
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1073 extra_mb = [] |
|
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1074 while self.n_left_in_mb>0: |
|
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1075 self.move_to_next_dataset() |
|
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|
1076 extra_mb.append(self.next_iterator.next()) |
|
73
69f97aad3faf
Coded untested ApplyFunctionDataSet and CacheDataSet
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1077 mb = Example(fieldnames, |
|
40
88fd1cce08b9
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diff
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1078 [dataset.valuesVStack(name, |
|
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diff
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|
1079 [mb[name]]+[b[name] for b in extra_mb]) |
|
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1080 for name in fieldnames]) |
|
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|
1081 |
|
37
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|
1082 self.next_row+=minibatch_size |
|
38
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1083 self.next_dataset_row+=minibatch_size |
|
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diff
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1084 if self.next_row+minibatch_size>len(dataset): |
|
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diff
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|
1085 self.move_to_next_dataset() |
|
44
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diff
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|
1086 return examples |
|
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diff
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|
1087 return VStackedIterator(self) |
|
37
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|
1088 |
| 41 | 1089 class ArrayFieldsDataSet(DataSet): |
| 1090 """ | |
| 1091 Virtual super-class of datasets whose field values are numpy array, | |
| 1092 thus defining valuesHStack and valuesVStack for sub-classes. | |
| 1093 """ | |
|
268
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1094 def __init__(self,description=None,field_types=None): |
|
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|
1095 DataSet.__init__(self,description,field_types) |
|
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|
1096 def untested_valuesHStack(self,fieldnames,fieldvalues): |
| 41 | 1097 """Concatenate field values horizontally, e.g. two vectors |
| 1098 become a longer vector, two matrices become a wider matrix, etc.""" | |
| 1099 return numpy.hstack(fieldvalues) | |
|
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|
1100 def untested_valuesVStack(self,fieldname,values): |
| 41 | 1101 """Concatenate field values vertically, e.g. two vectors |
| 1102 become a two-row matrix, two matrices become a longer matrix, etc.""" | |
| 1103 return numpy.vstack(values) | |
| 1104 | |
|
316
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1105 |
|
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1106 |
|
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1107 class NArraysDataSet(ArrayFieldsDataSet) : |
|
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|
1108 """ |
|
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|
1109 An NArraysDataSet stores fields that are numpy tensor, whose first axis |
|
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|
1110 iterates over examples. It's a generalization of ArrayDataSet. |
|
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|
1111 """ |
|
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|
1112 #@TODO not completely implemented yet |
|
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|
1113 def __init__(self, data_arrays, fieldnames, **kwargs) : |
|
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|
1114 """ |
|
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|
1115 Construct an NArraysDataSet from a list of numpy tensor (data_arrays) and a list |
|
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|
1116 of fieldnames. The number of arrays must be the same as the number of |
|
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|
1117 fieldnames. Each set of numpy tensor must have the same first dimension (first |
|
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|
1118 axis) corresponding to the number of examples. |
|
5fe6d0c93109
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|
1119 |
|
321
f03ae06fadc8
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|
1120 Every tensor is treated as a numpy array (using numpy.asarray) |
|
316
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|
1121 """ |
|
318
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|
1122 ArrayFieldsDataSet.__init__(self,**kwargs) |
|
316
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|
1123 assert len(data_arrays) == len(fieldnames) |
|
5fe6d0c93109
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|
1124 assert len(fieldnames) > 0 |
|
322
ad8be93b3c55
small bugs fixed with NArrayDataSet
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diff
changeset
|
1125 ndarrays = [numpy.asarray(a) for a in data_arrays] |
|
321
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|
1126 lens = [a.shape[0] for a in ndarrays] |
|
f03ae06fadc8
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|
1127 num_examples = lens[0] #they must all be equal anyway |
|
316
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|
1128 self._fieldnames = fieldnames |
|
322
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|
1129 for k in ndarrays : |
|
321
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changeset
|
1130 assert k.shape[0] == num_examples |
|
f03ae06fadc8
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changeset
|
1131 self._datas = ndarrays |
|
f03ae06fadc8
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|
1132 # create dict |
|
f03ae06fadc8
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|
1133 self.map_field_idx = dict() |
|
f03ae06fadc8
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|
1134 for k in range(len(fieldnames)): |
|
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changeset
|
1135 self.map_field_idx[fieldnames[k]] = k |
|
316
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|
1136 |
|
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1137 |
|
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|
1138 def __len__(self) : |
|
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|
1139 """ |
|
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|
1140 Length of the dataset is based on the first array = data_arrays[0], using its shape |
|
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|
1141 """ |
|
318
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|
1142 return self._datas[0].shape[0] |
|
316
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|
1143 |
|
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|
1144 def fieldNames(self) : |
|
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1145 """ |
|
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|
1146 Returns the fieldnames as set in self.__init__ |
|
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|
1147 """ |
|
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1148 return self._fieldnames |
|
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|
1149 |
|
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1150 def field_pos(self,fieldname) : |
|
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1151 """ |
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1152 Returns the index of a given fieldname. Fieldname must exists! see fieldNames(). |
|
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1153 """ |
|
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1154 return self.map_field_idx[fieldname] |
|
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1155 |
|
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|
1156 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
|
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|
1157 cursor = Example(fieldnames,[0]*len(fieldnames)) |
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|
1158 fieldnames = self.fieldNames() if fieldnames is None else fieldnames |
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|
1159 for n in xrange(n_batches): |
|
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|
1160 if offset == len(self): |
|
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|
1161 break |
|
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|
1162 for f in range(len(cursor._names)) : |
|
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|
1163 idx = self.field_pos(cursor._names[f]) |
|
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|
1164 sub_data = self._datas[idx][offset : offset+minibatch_size] |
|
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|
1165 cursor._values[f] = sub_data |
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|
1166 offset += len(sub_data) #can be less than minibatch_size at end |
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|
1167 yield cursor |
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1168 |
|
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|
1169 #return ArrayDataSetIterator(self,fieldnames,minibatch_size,n_batches,offset) |
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1170 |
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1171 |
|
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1172 |
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1173 |
| 41 | 1174 class ArrayDataSet(ArrayFieldsDataSet): |
| 1175 """ | |
| 1176 An ArrayDataSet stores the fields as groups of columns in a numpy tensor, | |
| 1177 whose first axis iterates over examples, second axis determines fields. | |
| 1178 If the underlying array is N-dimensional (has N axes), then the field | |
| 1179 values are (N-2)-dimensional objects (i.e. ordinary numbers if N=2). | |
| 1180 """ | |
| 1181 | |
|
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|
1182 def __init__(self, data_array, fields_columns, **kwargs): |
|
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|
1183 """ |
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|
1184 Construct an ArrayDataSet from the underlying numpy array (data) and |
|
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|
1185 a map (fields_columns) from fieldnames to field columns. The columns of a field are specified |
|
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|
1186 using the standard arguments for indexing/slicing: integer for a column index, |
|
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|
1187 slice for an interval of columns (with possible stride), or iterable of column indices. |
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|
1188 """ |
|
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|
1189 ArrayFieldsDataSet.__init__(self, **kwargs) |
| 41 | 1190 self.data=data_array |
|
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diff
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|
1191 self.fields_columns=fields_columns |
| 41 | 1192 |
| 1193 # check consistency and complete slices definitions | |
|
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diff
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|
1194 for fieldname, fieldcolumns in self.fields_columns.items(): |
| 41 | 1195 if type(fieldcolumns) is int: |
| 1196 assert fieldcolumns>=0 and fieldcolumns<data_array.shape[1] | |
|
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|
1197 if 1: |
|
227
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|
1198 #I changed this because it didn't make sense to me, |
|
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|
1199 # and it made it more difficult to write my learner. |
|
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|
1200 # If it breaks stuff, let's talk about it. |
|
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|
1201 # - James 22/05/2008 |
|
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|
1202 self.fields_columns[fieldname]=[fieldcolumns] |
|
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|
1203 else: |
|
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|
1204 self.fields_columns[fieldname]=fieldcolumns |
| 41 | 1205 elif type(fieldcolumns) is slice: |
| 1206 start,step=None,None | |
| 1207 if not fieldcolumns.start: | |
| 1208 start=0 | |
| 1209 if not fieldcolumns.step: | |
| 1210 step=1 | |
| 1211 if start or step: | |
|
42
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Testing basic functionality and removing obvious bugs
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parents:
41
diff
changeset
|
1212 self.fields_columns[fieldname]=slice(start,fieldcolumns.stop,step) |
| 41 | 1213 elif hasattr(fieldcolumns,"__iter__"): # something like a list |
| 1214 for i in fieldcolumns: | |
| 1215 assert i>=0 and i<data_array.shape[1] | |
| 1216 | |
|
42
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Testing basic functionality and removing obvious bugs
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diff
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|
1217 def fieldNames(self): |
|
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Testing basic functionality and removing obvious bugs
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diff
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|
1218 return self.fields_columns.keys() |
| 41 | 1219 |
|
42
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diff
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|
1220 def __len__(self): |
|
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diff
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|
1221 return len(self.data) |
| 41 | 1222 |
|
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|
1223 def __getitem__(self,key): |
|
55
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|
1224 """More efficient implementation than the default __getitem__""" |
|
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diff
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|
1225 fieldnames=self.fields_columns.keys() |
|
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|
1226 values=self.fields_columns.values() |
| 80 | 1227 if type(key) is int: |
|
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diff
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|
1228 return Example(fieldnames, |
|
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|
1229 [self.data[key,col] for col in values]) |
| 80 | 1230 if type(key) is slice: |
|
316
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|
1231 return Example(fieldnames,[self.data[key,col] for col in values]) |
| 80 | 1232 if type(key) is list: |
| 1233 for i in range(len(key)): | |
| 1234 if self.hasFields(key[i]): | |
| 1235 key[i]=self.fields_columns[key[i]] | |
|
316
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|
1236 return Example(fieldnames, |
|
5fe6d0c93109
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314
diff
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|
1237 #we must separate differently for list as numpy |
|
5fe6d0c93109
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314
diff
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|
1238 # doesn't support self.data[[i1,...],[i2,...]] |
|
5fe6d0c93109
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|
1239 # when their is more then two i1 and i2 |
|
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314
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|
1240 [self.data[key,:][:,col] |
|
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|
1241 if isinstance(col,list) else |
|
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|
1242 self.data[key,col] for col in values]) |
| 80 | 1243 |
|
55
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diff
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|
1244 # else check for a fieldname |
| 80 | 1245 if self.hasFields(key): |
|
105
8c0a1b11b007
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Frederic Bastien <bastienf@iro.umontreal.ca>
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101
diff
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|
1246 return self.data[:,self.fields_columns[key]] |
|
55
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diff
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|
1247 # else we are trying to access a property of the dataset |
| 80 | 1248 assert key in self.__dict__ # else it means we are trying to access a non-existing property |
| 1249 return self.__dict__[key] | |
|
55
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|
1250 |
|
290
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|
1251 def dontuse__iter__(self): |
|
270
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|
1252 class ArrayDataSetIteratorIter(object): |
|
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|
1253 def __init__(self,dataset,fieldnames): |
|
228
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|
1254 if fieldnames is None: fieldnames = dataset.fieldNames() |
|
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|
1255 # store the resulting minibatch in a lookup-list of values |
|
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|
1256 self.minibatch = Example(fieldnames,[0]*len(fieldnames)) |
|
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|
1257 self.dataset=dataset |
|
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|
1258 self.current=0 |
|
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|
1259 self.columns = [self.dataset.fields_columns[f] |
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|
1260 for f in self.minibatch._names] |
|
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|
1261 self.l = self.dataset.data.shape[0] |
|
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|
1262 def __iter__(self): |
|
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|
1263 return self |
|
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|
1264 def next(self): |
|
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|
1265 #@todo: we suppose that we need to stop only when minibatch_size == 1. |
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|
1266 # Otherwise, MinibatchWrapAroundIterator do it. |
|
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|
1267 if self.current>=self.l: |
|
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|
1268 raise StopIteration |
|
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|
1269 sub_data = self.dataset.data[self.current] |
|
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|
1270 self.minibatch._values = [sub_data[c] for c in self.columns] |
|
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|
1271 |
|
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|
1272 self.current+=1 |
|
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|
1273 return self.minibatch |
|
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|
1274 |
|
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|
1275 return ArrayDataSetIteratorIter(self,self.fieldNames()) |
|
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|
1276 |
|
42
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|
1277 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
|
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|
1278 cursor = Example(fieldnames,[0]*len(fieldnames)) |
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|
1279 fieldnames = self.fieldNames() if fieldnames is None else fieldnames |
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|
1280 for n in xrange(n_batches): |
|
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|
1281 if offset == len(self): |
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|
1282 break |
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|
1283 sub_data = self.data[offset : offset+minibatch_size] |
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|
1284 offset += len(sub_data) #can be less than minibatch_size at end |
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|
1285 cursor._values = [sub_data[:,self.fields_columns[f]] for f in cursor._names] |
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|
1286 yield cursor |
|
42
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diff
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|
1287 |
|
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|
1288 #return ArrayDataSetIterator(self,fieldnames,minibatch_size,n_batches,offset) |
|
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diff
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|
1289 |
|
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diff
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|
1290 |
|
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diff
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|
1291 class CachedDataSet(DataSet): |
|
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diff
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|
1292 """ |
| 167 | 1293 Wrap a L{DataSet} whose values are computationally expensive to obtain |
|
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diff
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|
1294 (e.g. because they involve some computation, or disk access), |
|
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diff
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|
1295 so that repeated accesses to the same example are done cheaply, |
|
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diff
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|
1296 by caching every example value that has been accessed at least once. |
|
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diff
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|
1297 |
|
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diff
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|
1298 Optionally, for finite-length dataset, all the values can be computed |
|
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diff
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|
1299 (and cached) upon construction of the CachedDataSet, rather at the |
|
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diff
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|
1300 first access. |
|
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|
1301 |
| 167 | 1302 @todo: when cache_all_upon_construction create mini-batches that are as |
|
77
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|
1303 large as possible but not so large as to fill up memory. |
|
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1304 |
| 167 | 1305 @todo: add disk-buffering capability, so that when the cache becomes too |
|
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diff
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|
1306 big for memory, we cache things on disk, trying to keep in memory only |
|
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|
1307 the record most likely to be accessed next. |
|
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|
1308 """ |
|
73
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|
1309 def __init__(self,source_dataset,cache_all_upon_construction=False): |
|
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|
1310 self.source_dataset=source_dataset |
|
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|
1311 self.cache_all_upon_construction=cache_all_upon_construction |
|
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diff
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|
1312 self.cached_examples = [] |
|
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|
1313 if cache_all_upon_construction: |
|
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|
1314 # this potentially brings all the source examples |
|
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|
1315 # into memory at once, which may be too much |
|
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|
1316 # the work could possibly be done by minibatches |
|
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|
1317 # that are as large as possible but no more than what memory allows. |
|
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diff
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|
1318 fields_values = source_dataset.minibatches(minibatch_size=len(source_dataset)).__iter__().next() |
|
152
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diff
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|
1319 assert all([len(self)==len(field_values) for field_values in fields_values]) |
|
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diff
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|
1320 for example in fields_values.examples(): |
|
171
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diff
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|
1321 self.cached_examples.append(copy.copy(example)) |
|
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diff
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|
1322 |
|
73
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|
1323 self.fieldNames = source_dataset.fieldNames |
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|
1324 self.hasFields = source_dataset.hasFields |
|
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|
1325 self.valuesHStack = source_dataset.valuesHStack |
|
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|
1326 self.valuesVStack = source_dataset.valuesVStack |
|
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diff
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|
1327 |
|
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|
1328 def __len__(self): |
|
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|
1329 return len(self.source_dataset) |
|
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diff
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|
1330 |
|
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diff
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|
1331 def minibatches_nowrap(self,fieldnames,minibatch_size,n_batches,offset): |
|
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diff
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|
1332 class CacheIterator(object): |
|
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diff
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|
1333 def __init__(self,dataset): |
|
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|
1334 self.dataset=dataset |
|
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|
1335 self.current=offset |
|
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|
1336 self.all_fields = self.dataset.fieldNames()==fieldnames |
|
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|
1337 def __iter__(self): return self |
|
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|
1338 def next(self): |
|
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|
1339 upper = self.current+minibatch_size |
|
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diff
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|
1340 cache_len = len(self.dataset.cached_examples) |
|
135
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diff
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|
1341 if upper>cache_len: # whole minibatch is not already in cache |
|
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|
1342 # cache everything from current length to upper |
|
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|
1343 for example in self.dataset.source_dataset[cache_len:upper]: |
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|
1344 self.dataset.cached_examples.append(example) |
|
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diff
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|
1345 all_fields_minibatch = Example(self.dataset.fieldNames(), |
|
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diff
changeset
|
1346 zip(*self.dataset.cached_examples[self.current:self.current+minibatch_size])) |
|
163
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bugfix, we should advence by the minibatch size.
Frederic Bastien <bastienf@iro.umontreal.ca>
parents:
159
diff
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|
1347 self.current+=minibatch_size |
|
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|
1348 if self.all_fields: |
|
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diff
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|
1349 return all_fields_minibatch |
|
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diff
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|
1350 return Example(fieldnames,[all_fields_minibatch[name] for name in fieldnames]) |
|
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diff
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|
1351 return CacheIterator(self) |
|
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diff
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|
1352 |
|
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diff
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|
1353 def dontuse__getitem__(self,i): |
| 153 | 1354 if type(i)==int and len(self.cached_examples)>i: |
| 1355 return self.cached_examples[i] | |
| 1356 else: | |
|
251
7e6edee187e3
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243
diff
changeset
|
1357 return self.source_dataset[i] |
|
252
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diff
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|
1358 |
|
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|
1359 def __iter__(self): |
|
856d14dc4468
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diff
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|
1360 class CacheIteratorIter(object): |
|
856d14dc4468
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diff
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|
1361 def __init__(self,dataset): |
|
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|
1362 self.dataset=dataset |
|
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|
1363 self.l = len(dataset) |
|
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|
1364 self.current = 0 |
|
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|
1365 self.fieldnames = self.dataset.fieldNames() |
|
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|
1366 self.example = Example(self.fieldnames,[0]*len(self.fieldnames)) |
|
252
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|
1367 def __iter__(self): return self |
|
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|
1368 def next(self): |
|
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|
1369 if self.current>=self.l: |
|
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|
1370 raise StopIteration |
|
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|
1371 cache_len = len(self.dataset.cached_examples) |
|
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|
1372 if self.current>=cache_len: # whole minibatch is not already in cache |
|
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diff
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|
1373 # cache everything from current length to upper |
|
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|
1374 self.dataset.cached_examples.append( |
|
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|
1375 self.dataset.source_dataset[self.current]) |
|
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|
1376 self.example._values = self.dataset.cached_examples[self.current] |
|
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|
1377 self.current+=1 |
|
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diff
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|
1378 return self.example |
|
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diff
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|
1379 |
|
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diff
changeset
|
1380 return CacheIteratorIter(self) |
|
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|
1381 |
|
57
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diff
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|
1382 class ApplyFunctionDataSet(DataSet): |
|
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|
1383 """ |
|
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|
1384 A L{DataSet} that contains as fields the results of applying a |
|
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|
1385 given function example-wise or minibatch-wise to all the fields of |
|
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|
1386 an input dataset. The output of the function should be an iterable |
|
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1387 (e.g. a list or a LookupList) over the resulting values. |
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1388 |
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1389 The function take as input the fields of the dataset, not the examples. |
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1390 |
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1391 In minibatch mode, the function is expected to work on minibatches |
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1392 (takes a minibatch in input and returns a minibatch in output). More |
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1393 precisely, it means that each element of the input or output list |
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1394 should be iterable and indexable over the individual example values |
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1395 (typically these elements will be numpy arrays). All of the elements |
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1396 in the input and output lists should have the same length, which is |
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1397 the length of the minibatch. |
|
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1398 |
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1399 The function is applied each time an example or a minibatch is accessed. |
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1400 To avoid re-doing computation, wrap this dataset inside a CachedDataSet. |
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1401 |
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1402 If the values_{h,v}stack functions are not provided, then |
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1403 the input_dataset.values{H,V}Stack functions are used by default. |
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1404 |
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1405 """ |
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1406 |
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1407 def __init__(self,input_dataset,function,output_names,minibatch_mode=True, |
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1408 values_hstack=None,values_vstack=None, |
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1409 description=None,fieldtypes=None): |
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1410 """ |
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1411 Constructor takes an input dataset that has as many fields as the function |
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1412 expects as inputs. The resulting dataset has as many fields as the function |
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1413 produces as outputs, and that should correspond to the number of output names |
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1414 (provided in a list). |
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1415 |
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1416 Note that the expected semantics of the function differs in minibatch mode |
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1417 (it takes minibatches of inputs and produces minibatches of outputs, as |
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1418 documented in the class comment). |
|
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1419 |
|
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1420 TBM: are filedtypes the old field types (from input_dataset) or the new ones |
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1421 (for the new dataset created)? |
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1422 """ |
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1423 self.input_dataset=input_dataset |
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1424 self.function=function |
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1425 self.output_names=output_names |
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1426 self.minibatch_mode=minibatch_mode |
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1427 DataSet.__init__(self,description,fieldtypes) |
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1428 self.valuesHStack = values_hstack if values_hstack else input_dataset.valuesHStack |
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1429 self.valuesVStack = values_vstack if values_vstack else input_dataset.valuesVStack |
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1430 |
|
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1431 def __len__(self): |
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1432 return len(self.input_dataset) |
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1433 |
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1434 def fieldNames(self): |
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1435 return self.output_names |
|
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1436 |
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1437 def minibatches_nowrap(self, fieldnames, *args, **kwargs): |
|
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1438 all_input_fieldNames = self.input_dataset.fieldNames() |
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1439 mbnw = self.input_dataset.minibatches_nowrap |
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1440 |
|
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|
1441 for input_fields in mbnw(all_input_fieldNames, *args, **kwargs): |
|
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|
1442 if self.minibatch_mode: |
|
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1443 all_output_fields = self.function(*input_fields) |
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1444 else: |
|
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1445 input_examples = zip(*input_fields) #makes so that [i] means example i |
|
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1446 output_examples = [self.function(*input_example) |
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1447 for input_example in input_examples] |
|
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1448 all_output_fields = zip(*output_examples) |
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|
1449 |
|
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|
1450 all_outputs = Example(self.output_names, all_output_fields) |
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|
1451 #print 'input_fields', input_fields |
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|
1452 #print 'all_outputs', all_outputs |
|
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1453 if fieldnames==self.output_names: |
| 293 | 1454 rval = all_outputs |
|
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|
1455 else: |
| 293 | 1456 rval = Example(fieldnames,[all_outputs[name] for name in fieldnames]) |
|
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|
1457 #print 'rval', rval |
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|
1458 #print '--------' |
| 293 | 1459 yield rval |
|
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|
1460 |
|
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|
1461 def untested__iter__(self): # only implemented for increased efficiency |
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1462 class ApplyFunctionSingleExampleIterator(object): |
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1463 def __init__(self,output_dataset): |
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|
1464 self.current=0 |
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1465 self.output_dataset=output_dataset |
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1466 self.input_iterator=output_dataset.input_dataset.__iter__() |
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1467 def __iter__(self): return self |
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1468 def next(self): |
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1469 if self.output_dataset.minibatch_mode: |
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1470 function_inputs = [[input] for input in self.input_iterator.next()] |
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1471 outputs = self.output_dataset.function(*function_inputs) |
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1472 assert all([hasattr(output,'__iter__') for output in outputs]) |
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1473 function_outputs = [output[0] for output in outputs] |
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1474 else: |
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1475 function_inputs = self.input_iterator.next() |
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1476 function_outputs = self.output_dataset.function(*function_inputs) |
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1477 return Example(self.output_dataset.output_names,function_outputs) |
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1478 return ApplyFunctionSingleExampleIterator(self) |
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|
1479 |
|
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|
1480 def supervised_learning_dataset(src_dataset,input_fields,target_fields,weight_field=None): |
|
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|
1481 """ |
| 167 | 1482 Wraps an arbitrary L{DataSet} into one for supervised learning tasks |
| 1483 by forcing the user to define a set of fields as the 'input' field | |
| 1484 and a set of fields as the 'target' field. Optionally, a single | |
| 1485 weight_field can also be defined. | |
|
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|
1486 """ |
|
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|
1487 args = ((input_fields,'input'),(output_fields,'target')) |
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1488 if weight_field: args+=(([weight_field],'weight')) |
|
36
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|
1489 return src_dataset.merge_fields(*args) |
|
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|
1490 |
|
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|
1491 |
|
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|
1492 |
|
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1493 |