Mercurial > pylearn

annotate dataset.py @ 12:ff4e551490f1

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Added LookupList type in lookup_list.py and used it to keep order of field names in Example in ArrayDataSet. Example is now just = LookupList.
author bengioy@esprit.iro.umontreal.ca
date Wed, 26 Mar 2008 18:21:57 -0400
parents be128b9127c8
children 759d17112b23
rev   line source
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1
12
ff4e551490f1 Added LookupList type in lookup_list.py and used it to keep order
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2 from lookup_list import LookupList
ff4e551490f1 Added LookupList type in lookup_list.py and used it to keep order
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3 Example = LookupList
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4
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5 class DataSet(object):
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6 """
3fddb1c8f955 Rewrote DataSet interface and created FiniteDataSet interface.
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7 This is a virtual base class or interface for datasets.
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8 A dataset is basically an iterator over Examples (or anything that
be128b9127c8 Debugged (to the extent of my tests) the new version of dataset
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9 behaves like an Example). It does not necessarily
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10 have a fixed length (this is useful for 'streams' which feed on-line learning).
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11 Datasets with fixed and known length are instances of FiniteDataSet, a subclass
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12 which supports indexing (dataset[i]) and slicing (dataset[1000:2000]).
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13 To iterate over a subset of the fields, one should use the dataset.zip(field1, field2,field3, ...)
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14 method which returns an iterator over only the desired fields.
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15 Fields are not mutually exclusive, i.e. two fields can overlap in their actual content.
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16 The content of a field can be of any type, but often will be a numpy array.
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17 If one iterates through minibatches of examples (with the minibatches() method
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18 or with the minibatch_size argument of the zip() method), then the fields
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19 returned by the iterator's next method should be iterators over the
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20 individual values within the minibatch (typically these will be arrays
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21 with minibatch_size rows).
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22 """
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23
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24 def __init__(self):
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25 pass
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27 def __iter__(self):
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28 """
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29 Return an iterator, whose next() method returns the next example or the next
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30 minibatch in the dataset. A minibatch (of length > 1) is also an example, but
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31 whose fields should be something one can iterate on again in order to obtain
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32 the individual examples.
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33 """
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34 raise NotImplementedError
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35
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36 def zip(self,*fieldnames):
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37 """
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38 Return an iterator which sees only the specified fields (each fieldname is a
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39 field key, typically a string). The value returned at each iteration
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40 is a tuple with one element per field. Hence it can be used like this:
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41 for f1, f2, f3 in dataset.zip('field1','field2','field3'):
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42 ... use f1, f2, and f3
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43 """
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44 raise NotImplementedError
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45
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46 def minibatches(self,minibatch_size,*fieldnames):
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47 """
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48 Similar to zip but iterate over minibatches.
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49 Return a minibatch iterator, whose next() method returns an 'example'
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50 whose fields are iteratable objects (which can iterate over the individual
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51 values of that field in the minibatch).
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52 """
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53 raise NotImplementedError
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54
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55 def fieldNames(self):
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56 """Return the list of field names in the examples of this dataset."""
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57 raise NotImplementedError
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58
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59 def rename(*new_field_specifications):
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60 """
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61 Return a new dataset that maps old fields (of self) to new fields (of the returned
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62 dataset). The minimal syntax that should be supported is the following:
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63 new_field_specifications = [new_field_spec1, new_field_spec2, ...]
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64 new_field_spec = ([old_field1, old_field2, ...], new_field)
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65 In general both old_field and new_field should be strings, but some datasets may also
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66 support additional indexing schemes within each field (e.g. column slice
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67 of a matrix-like field).
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68 """
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69 raise NotImplementedError
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70
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71 class FiniteDataSet(DataSet):
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72 """
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73 Virtual interface, a subclass of DataSet for datasets which have a finite, known length.
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74 Examples are indexed by an integer between 0 and self.length()-1,
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75 and a subdataset can be obtained by slicing. This may not be appropriate in general
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76 but only for datasets which can be thought of like ones that access rows AND fields
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77 in an efficient random access way. Users are encouraged to expect only the generic dataset
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78 interface in general. A FiniteDataSet is mainly useful when one has to obtain
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79 a subset of examples (e.g. for splitting a dataset into training and test sets).
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80 """
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81
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82 def __init__(self):
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83 pass
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84
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85 def __iter__(self):
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86 return FiniteDataSetIterator(self)
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87
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88 def zip(self,*fieldnames):
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89 return FiniteDataSetIterator(self,1,fieldnames)
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90
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91 def minibatches(self,minibatch_size,*fieldnames):
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92 return FiniteDataSetIterator(self,minibatch_size,fieldnames)
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93
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94 def __getattr__(self,fieldname):
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95 """Return an that can iterate over the values of the field in this dataset."""
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96 return self(fieldname)
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97
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98 def __call__(self,*fieldnames):
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99 """Return a sub-dataset containing only the given fieldnames as fields."""
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100 raise NotImplementedError
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101
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102 def __len__(self):
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103 """len(dataset) returns the number of examples in the dataset."""
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104 raise NotImplementedError
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105
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106 def __getitem__(self,i):
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107 """dataset[i] returns the (i+1)-th example of the dataset."""
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108 raise NotImplementedError
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109
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110 def __getslice__(self,*slice_args):
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111 """dataset[i:j] returns the subdataset with examples i,i+1,...,j-1."""
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112 raise NotImplementedError
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113
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114 class FiniteDataSetIterator(object):
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115 """
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116 If the fieldnames list is empty, it means that we want to see ALL the fields.
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117 """
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118 def __init__(self,dataset,minibatch_size=1,fieldnames=[]):
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119 self.dataset=dataset
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120 self.minibatch_size=minibatch_size
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121 assert minibatch_size>=1 and minibatch_size<=len(dataset)
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122 self.current = -self.minibatch_size
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123 self.fieldnames = fieldnames
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124
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125 def __iter__(self):
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126 return self
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127
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128 def next(self):
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129 self.current+=self.minibatch_size
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130 if self.current>=len(self.dataset):
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131 self.current=-self.minibatch_size
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132 raise StopIteration
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133 if self.minibatch_size==1:
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134 complete_example=self.dataset[self.current]
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135 else:
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136 complete_example=self.dataset[self.current:self.current+self.minibatch_size]
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137 if self.fieldnames:
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138 return Example(self.fieldnames,list(complete_example))
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139 else:
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140 return complete_example
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141
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142
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143 # we may want ArrayDataSet defined in another python file
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144
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145 import numpy
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146
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147 class ArrayDataSet(FiniteDataSet):
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148 """
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149 An ArrayDataSet behaves like a numpy array but adds the notion of named fields
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150 from DataSet (and the ability to view multiple field values as an 'Example').
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151 It is a fixed-length and fixed-width dataset
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152 in which each element is a numpy array or a number, hence the whole
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153 dataset corresponds to a numpy array. Fields
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154 must correspond to a slice of array columns. If the dataset has fields,
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155 each 'example' is just a one-row ArrayDataSet, otherwise it is a numpy array.
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156 Any dataset can also be converted to a numpy array (losing the notion of fields
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157 by the numpy.array(dataset) call.
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158 """
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159
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160 def __init__(self,dataset=None,data=None,fields=None):
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161 """
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162 There are two ways to construct an ArrayDataSet: (1) from an
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163 existing dataset (which may result in a copy of the data in a numpy array),
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164 or (2) from a numpy.array (the data argument), along with an optional description
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165 of the fields (a LookupList of column slices indexed by field names).
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166 """
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167 if dataset!=None:
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168 assert data==None and fields==None
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169 # Make ONE big minibatch with all the examples, to separate the fields.
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170 n_examples=len(dataset)
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171 batch = dataset.minibatches(n_examples).next()
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172 # Each field of the underlying dataset must be convertible to a numpy array of the same type
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173 # currently just double, but should use the smallest compatible dtype
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174 n_fields = len(batch)
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175 fieldnames = batch.fields.keys()
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176 total_width = 0
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177 type = None
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178 fields = LookupList()
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179 for i in xrange(n_fields):
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180 field = array(batch[i])
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181 assert field.shape[0]==n_examples
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182 width = field.shape[1]
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183 start=total_width
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184 total_width += width
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185 fields[fieldnames[i]]=slice(start,total_width,1)
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186 # many complicated things remain to be done:
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187 # - find common dtype
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188 # - decide what to do with extra dimensions if not the same in all fields
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189 # - try to see if we can avoid the copy?
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190 raise NotImplementedError
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191 if data!=None:
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192 assert dataset==None
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193 self.data=data
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194 self.fields=fields
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195 self.width = data.shape[1]
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196 if fields:
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197 for fieldname,fieldslice in fields.items():
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198 # make sure fieldslice.start and fieldslice.step are defined
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199 start=fieldslice.start
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200 step=fieldslice.step
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201 if not start:
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202 start=0
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203 if not step:
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204 step=1
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205 if not fieldslice.start or not fieldslice.step:
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206 fields[fieldname] = fieldslice = slice(start,fieldslice.stop,step)
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207 # and coherent with the data array
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208 assert fieldslice.start>=0 and fieldslice.stop<=self.width
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209
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210 def __getattr__(self,fieldname):
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211 """
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212 Return a numpy array with the content associated with the given field name.
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213 If this is a one-example dataset, then a row, i.e., numpy array (of one less dimension
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214 than the dataset itself) is returned.
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215 """
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216 if len(self.data)==1:
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217 return self.data[0,self.fields[fieldname]]
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218 return self.data[:,self.fields[fieldname]]
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219
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220 def __call__(self,*fieldnames):
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221 """Return a sub-dataset containing only the given fieldnames as fields."""
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222 min_col=self.data.shape[1]
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223 max_col=0
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224 for field_slice in self.fields.values():
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225 min_col=min(min_col,field_slice.start)
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226 max_col=max(max_col,field_slice.stop)
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227 new_fields=LookupList()
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228 for fieldname,fieldslice in self.fields.items():
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229 new_fields[fieldname]=slice(fieldslice.start-min_col,fieldslice.stop-min_col,fieldslice.step)
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230 return ArrayDataSet(data=self.data[:,min_col:max_col],fields=new_fields)
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231
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232 def fieldNames(self):
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233 """Return the list of field names that are supported by getattr and getFields."""
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234 return self.fields.keys()
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235
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236 def __len__(self):
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237 """len(dataset) returns the number of examples in the dataset."""
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238 return len(self.data)
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239
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240 def __getitem__(self,i):
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241 """
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242 dataset[i] returns the (i+1)-th Example of the dataset. If there are no fields
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243 the result is just a numpy array (for the i-th row of the dataset data matrix).
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244 """
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245 if self.fields:
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246 fieldnames,fieldslices=zip(*self.fields.items())
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247 return Example(self.fields.keys(),[self.data[i,fieldslice] for fieldslice in self.fields.values()])
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248 else:
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249 return self.data[i]
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250
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251 def __getslice__(self,*slice_args):
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252 """dataset[i:j] returns the subdataset with examples i,i+1,...,j-1."""
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253 return ArrayDataSet(data=self.data[apply(slice,slice_args)],fields=self.fields)
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254
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255 def __array__(self):
7
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
256 if not self.fields:
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
257 return self.data
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
258 # else, select subsets of columns mapped by the fields
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
259 columns_used = numpy.zeros((self.data.shape[1]),dtype=bool)
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
260 for field_slice in self.fields.values():
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
261 for c in xrange(field_slice.start,field_slice.stop,field_slice.step):
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
262 columns_used[c]=True
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
263 # try to figure out if we can map all the slices into one slice:
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
264 mappable_to_one_slice = True
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
265 start=0
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
266 while start<len(columns_used) and not columns_used[start]:
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
267 start+=1
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
268 stop=len(columns_used)
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
269 while stop>0 and not columns_used[stop-1]:
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
270 stop-=1
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
271 step=0
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
272 i=start
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
273 while i<stop:
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
274 j=i+1
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
275 while j<stop and not columns_used[j]:
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
276 j+=1
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
277 if step:
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
278 if step!=j-i:
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
279 mappable_to_one_slice = False
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
280 break
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
281 else:
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
282 step = j-i
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
283 i=j
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
284 if mappable_to_one_slice:
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
285 return self.data[:,slice(start,stop,step)]
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
286 # else make contiguous copy
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
287 n_columns = sum(columns_used)
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
288 result = zeros((len(self.data),n_columns)+self.data.shape[2:],self.data.dtype)
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
289 print result.shape
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
290 c=0
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
291 for field_slice in self.fields.values():
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
292 slice_width=field_slice.stop-field_slice.start/field_slice.step
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
293 # copy the field here
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
294 result[:,slice(c,slice_width)]=self.data[:,field_slice]
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
295 c+=slice_width
6f8f338686db Moved iterating counter into a FiniteDataSetIterator to allow embedded iterations and multiple threads iterating at the same time on a dataset.
bengioy@bengiomac.local
parents: 6
diff changeset
296 return result
11
be128b9127c8 Debugged (to the extent of my tests) the new version of dataset
bengioy@esprit.iro.umontreal.ca
parents: 9
diff changeset
297
be128b9127c8 Debugged (to the extent of my tests) the new version of dataset
bengioy@esprit.iro.umontreal.ca
parents: 9
diff changeset
298